Copyright: ¸ 1990-2000 MDL Information Systems


What Is New in Searching In ISIS/Base?

*	New features in searching in ISIS/Base 2.3

*	New features in searching in ISIS/Base 2.2.1

*	New features in searching in ISIS/Base 2.2

*	New features in searching in ISIS/Base 2.1

*	New features in searching in ISIS/Base 2.0.2

*	New features in searching in ISIS/Base 2.0


New Features in Searching in ISIS/Base 2.0

ISIS/Base 2.0 has new features in the following categories:

Setting the Search Domain

Searching

Viewing Search Results

Storing Binary Data in a Database

Manipulating Lists

Calculated Fields

Sorting Search Results

Printing search results

Changing Hview and Connectivity Information

Database Objects

Settings

Menu Changes

Form Changes


New Features in Searching in ISIS/Base 2.0.2

*	Your ISIS Administrator can provide a private remote access file in which you can store your own forms, lists, queries, and other objects. For more information on remote-access files, see your ISIS Administrator.


New Features in Searching in ISIS/Base 2.1

*	New command: Polymer in the Search menu searches the database for molecules that match the current polymer query in ways that you specify.

*	The following searches now use a search mechanism that allows ISIS to recognize attached data, polymers, and other chemically-significant brackets: MEXACT, ISOMER. (This search mechanism is the same as the search mechanism for PARENT, TAUTOMER, and FLEX searches).

Note: The original search mechanism (searching by SEMA name) is still available through the = and ISOMER search operators in the Query Builder. For more information on the Query Builder (QB) search, click here.


New Features in Searching in ISIS/Base 2.2

ISIS/Base 2.2 is Year 2000-compliant:

*	In Query mode, you enter dates in the form MM/DD/YY. ISIS interprets 2-digit years as follows:

Before January 1, 2000, ISIS/Base interprets 1/1/00 as 1/1/1900 (January 1, 1900).

On or after January 1, 2000, ISIS/Base interprets 1/1/00 as 1/1/2000 (January 1, 2000).

*	In Update mode, you must enter years in 4-digit format (such as 12/15/1999) to register records.


New Features in Searching in ISIS/Base 2.2.1

There are no new features in Searching in ISIS/Base 2.2.1.


New Features in Searching in ISIS/Base 2.3

There are no new features in Searching in ISIS/Base 2.3.


What is New in Forms in ISIS/Base?

*	New features in forms in ISIS/Base 2.2.1

*	New features in forms in ISIS/Base 2.2

*	New features in forms in ISIS/Base 2.1

*	New features in forms in ISIS/Base 2.0.2

*	New features in forms in ISIS/Base 2.0


New Features in Forms in ISIS/Base 2.0

ISIS/Base 2.0 has new features in the following categories:

*	Use the [image] tool to create table outlines.

*	Add, reorder, replace, and delete columns in a table.

*	Change the style of multiple box labels and column headings.

*	Set a fill color or pattern in boxes or columns.

*	Set individual display options for each structure that appears in a form.

*	Paste graphics from other applications directly onto your form.

*	Edit the properties of a box, column, or table from one dialog box.

*	Create uncoupled tables for viewing data.

*	Set defaults that apply to the forms that you create. Choose Options > Settings > Form Defaults.

*	Save printing options (such as margins and headers/footers) with a form.

*	The Layout mode is now called Forms.

*	The Style menu commands are now located on the Object menu.

*	The Database > Change Form command was removed. You now choose File > Open Form.

*	The [image] tool has a new appearance, [image].


New Features in Forms in ISIS/Base 2.0.2

*	Windows 3.1/ 95/NT Users only: Select objects, then press the right mouse button to use a pop-up menu with commands that apply to the selected objects.


New Features in Forms in ISIS/Base 2.1

There are no new features in Forms in ISIS/Base 2.1.


New Features in Forms in ISIS/Base 2.2

There are no new features in Forms in ISIS/Base 2.2.


New Features in Forms in ISIS/Base 2.2.1

There are no new features in Forms in ISIS/Base 2.2.1.


Editing Box, Column, or Table Properties

Double-click on a box, table, or column to open the properties dialog box. Then, click these six tabs to edit the properties of a box, column, or table:

Field Names: Connect or change a field connected to a box, column, or table. Add or edit a label for a box or column.

Data/Label: Edit a label and set the label alignment, color, and font, and/or set the data alignment, color, and font.

Border/Pattern: Style box or table borders and set a fill pattern or color for a box or column.

Chem Display: Set the chemical display for structures, reactions, 3D-models, and sequences for a particular box.

Floating Boxes: Set reaction conditions to display above or below a reactant, arrow, or product in a reaction.

Function: Create a calculation to display as the result of a search, display default data, add a PL function, make a box invisible, or change the sequence ID of a box or table.


Setting the Search Domain

*	The List > Set Domain and List > Clear Domain commands are removed. You now choose Search > Set Search Domain To.

*	When you open a list of search results, you can choose whether to set the search domain to the list or to the entire database.


Searching

General

*	Undo any cut, paste, or clear process that involves an ISIS/Base form.

*	Obtain a partial list of search results when you interrupt an SSS or RSS search.

*	Switch to another application during a search (PC only).

Search By Form (SBF) and ID Search (ID)

*	In SBF and ID searches, enter as many as 25 text/numeric queries into a single table.

*	For a single SBF search with multiple queries, the results of a search no longer depend on whether the queries are in boxes or tables. For queries in boxes, or in the same line of a table, ISIS now retrieves only records for which all conditions match within the same subrecord. The deepest common parent field defines the subrecords within which all conditions must match. To obtain the same search results as earlier versions of ISIS, change the general ISIS/Base setting to [image] Search By Form logic level at deepest common parent. For information on how to change settings, click here.

3D Searching

*	Use new general settings to specify fixed-atom tolerances for exact model and submodel searching. For information on how to change these settings, click here.

*	In CFS searching, optionally extend the definition of a rotatable bond to include bonds between unsaturated centers (for example, biphenyls).

*	In CFS searching, optionally rotate bonds in other parts of the molecule (global relaxation) during conformational fitting. Global relaxation increases the number of hits during bump checking, and produces fitted structures that are more realistic.

Biopolymer Searching

*	Retrieve stored biopolymers from your database with one of the following searches: SSS/Biopoly, SSS3D, or CFS/Biopoly.


Viewing Search Results

*	Use [image] and [image] to go to first and last records, respectively, within a list or table.

*	Change the appearance of structural data in a box or column. Structural data includes molecules, reactions, 3D models, residues, and sequences. New features include:

*	Highlight reaction or molecule queries on the hit.

*	(Reactions only) Show/hide atom-atom maps, show/hide reacting centers, show/hide inversion/retention marks.

*	(Reactions only) Display reaction conditions

*	Scaling structures and reactions to fit within a form box or table applies solely to the display in ISIS/Base, and is not retained in ISIS/Draw. Structures and reactions that you transfer to ISIS/Draw or copy to the Clipboard are scaled either As Drawn or Defaults (formerly Standard Bond).

*	Structures and reactions that you copy to the Clipboard and paste into other applications are scaled exactly as they appear in ISIS/Base.


Manipulating Lists

*	Delete the currently displayed item from the list.

*	Move an item from the current list to another list.

*	Copy an item from the current list to another list.

*	List logic: Merge, intersect, or subtract any two lists in the database, not just the current list.

*	Automatically create a temporary list each time you perform a search.


Calculated Fields

In remote databases, you can create calculated fields that allow you to perform calculations on a set of data. For example:

*	Calculate the average or median of several activity measurements of a compound.

*	Count the number of bottles of each compound.

*	Calculate the sum of the yields of all the products of a reaction.

*	Determine the maximum or minimum value in a series, such as the maximum of several activity measurements or the earliest date of synthesis.

You can display these values on your form or use them to sort your search results. For information on creating calculated fields, click here.

To create calculated fields, you need to understand the database structure. We strongly recommend that you study Calculated Fields: Concepts/Examples before you attempt to create calculated fields.

Note: Do not confuse calculated fields with form calculations. A form calculation uses data from different database fields.


Sorting Search Results

*	For remote databases, sort search results by data in fields at any level of the database. For example, sort reaction records by reaction yield.

*	Sort search results automatically after a search.

*	Create sorting instructions that you can edit, save in the database, or export to disk.

*	Sort results of similarity searches in reaction databases (RSim and MSim) and similarity searches in molecule databases (MSim) searches by similarity value.

*	Use derived data fields to sort CFS search results by torsional degrees of freedom (TDF) (CFS_TDF field), van der Waals energy difference (CFS_VDW field), and RMS deviation (CFS_RMS field).


Printing Search Results

*	Print headers and footers on each page. You can automatically print date, time, and database name in headers and footers.

*	Preview how forms will appear on the printed page.

*	Switch to another application during printing (PC only).


Changing Hview and Connectivity Information

You can now use the Configure Database command in the File menu to change both the Hview and connectivity information of a remote-access file. For more information, see the ISIS/Base Database Maintenance 2.0 manual.


Database Objects

You can now save any of the following as objects within a local database or the remote-access file of a remote database:

*	Procedural Language (PL) programs

*	Sorting instructions

*	Lists of search results

*	ISIS/Base forms

*	Queries

*	Molecules and reactions


Menu Changes

There are many changes to ISIS/Base menus.

File menu

*	Open Form replaces Change Form in Database menu.

*	New command: Page Layout changes the layout of forms on the printed page.

Options menu

*	Settings replaces Preferences.

*	Setting in the Search tab of general ISIS/Base settings replaces 3D Sprout/Orient.

Object and Style menus (merged into Object menu)

*	Font, Pen Width, Pen Color, and Line in Style menu have moved to Object menu.

*	Box/Column/Table Properties in Object menu replace Table, Set Field, and Reaction Floating Boxes in Object menu and Box, Column, and Sides in Style menu.

Database menu

*	Definition renamed to View Definition.

*	Manager renamed to Object Manager.

*	Calculated Field replaces Edit Definition for remote databases only.

*	Change Form moved to File menu and renamed Open Form.

Search menu

*	Set Search Domain To replaces Set Domain and Clear Domain in List menu.

List menu

*	Save renamed to Save List.

*	Restore renamed to Open List.

*	New commands: Discard Item, Move Item To, Copy Item To, Repeat Move or Copy To, Sort On Search, and Delete Temporary Lists.

*	Set Domain and Clear Domain combined into Set Search Domain To and moved to Search menu.


Differences Between ISIS and Other MDL Products: Searching

The differences in searching, query features, sorting, and printing between ISIS and other MDL products are in Differences Between ISIS and Other MDL Products: Searching.

This is a 5-page document written in a new, compact style. We designed it to be printed.

Read Differences Between ISIS and Other MDL Products to learn what you need to know to search effectively in ISIS.

To see Differences Between ISIS and Other MDL Products, click here.


Differences Between ISIS and Other MDL Products: Searching

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Architecture/Organization	2.1

*	Differences in Search Types and Query Features	2.2

*	Differences in Features of the MACCS-II Substance Module	2.3

*	Differences in Sorting and Printing	2.4

*	Task Order in ISIS	2.5

*	Help	2.6

We recommend that you print this 5-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

2.1 Architecture/Organization

Some of the ISIS terminology might be different.

For example, instead of opening a database, you open a search domain. You can always choose Help > Index (Draw + Base only) to find out how the terminology that you use is defined in ISIS.

Objects (such as molecules, queries, lists, databases, and forms) are stored in different places instead of in your login directory.

For example, in a remote search, objects are typically stored in the remote-access file (RAF) with your search domain. You can export an object to your login directory or to any other RAF.

ISIS/Draw and ISIS/Base are two separate programs.

Use ISIS/Draw to create structures for reports or as graphical queries that search your databases. Use ISIS/Base to search your databases with text/numeric and/or graphical queries. You can easily transfer a graphical query between programs.

You can customize your forms.

For example, you can change the font size, type, or color of the label on the box that contains molecular weight values. (A form is the set of boxes and tables that hold your query and display your results after a search.)

2.2 Differences in Search Types and Query Features

ISIS contains:

*	Searches and query features that might differ functionally from those of the same name in other MDL products.

*	New searches that you might want to do.

For information on specific searches and queries, choose Help > ISIS/Base Search Types. You see the Searching Examples screen. Click The ISIS/Base Chemical Searches - and How to Do Them, and then click the search of your choice. You will see a brief definition of the search and how to do it. You can then click Searching Concepts/Examples to see the full definition of the search, complete with searching examples.

2.2.1 Search Types and Queries

The differences between ISIS 2.3 and other MDL products (or previous versions of ISIS) with the same search type and query are as follows:

Tautomer queries might retrieve fewer records.

ISIS 2.3 uses an improved algorithm with a more restricted definition of a tautomer. Consequently, tautomer queries might retrieve fewer records in ISIS 2.3 than in MACCS-II 2.3.

Rgroup queries with aromatic rings might retrieve more accurate records.

ISIS 2.3 uses an improved algorithm for Rgroup queries with aromatic rings. Consequently, Rgroup queries with aromatic rings might retrieve more accurate records in ISIS 2.3 than in MACCS-II 2.3.

Large and complex structures can be retrieved in ISIS.

ISIS 2.3 contains no limitations on the size of large and complex molecules that are retrieved from the database. Consequently, queries that specify the retrieval of large and complex structures might retrieve more records in ISIS 2.3 than in MACCS-II 2.3 and REACCS 8.2/8.2.1.

MACCS-II 2.3 and REACCS 8.2/8.2.1 can solely retrieval structures with a maximum number of 255 atoms, 255 bonds, 255 fragments, 271 bonds and fragments, 255 3D features, 255 fixed-atom constraints, 128 hydrogens and lone pairs, 999 link nodes, and 8 crossing bonds to abbreviated structures. The retrieval of structures in ISIS 2.3 has none of these limits (essentially no limits).

Complex ring systems can be retrieved in ISIS.

ISIS 2.3 uses an improved algorithm for ring perception. Consequently, queries that specify the retrieval of complex ring systems might retrieve more records in ISIS 2.3 than in MACCS-II 2.3.

Multiple fragment queries might retrieve different printed formulas.

ISIS 2.3 contains no limitations on the number of fragments in a single query, and the fragments are now sorted in ascending alphabetical order. Consequently, you might see differences between ISIS 2.3 and MACCS-II 2.3 or REACCS 8.2/8.2.1 in the printed formula for some structures.

2.3 Differences in Features of the MACCS-II Substance Module

Head-to-Tail and Either/Unknown Polymers Display Differently

In ISIS, the head-to-tail repeat pattern is the default for polymer brackets, and is not displayed explicitly. In MACCS-II, the either/unknown polymer repeat pattern is the default, and head-to-tail repeat pattern is displayed explicitly. The following example shows how ISIS and MACCS-II display a copolymer that contains brackets with both head-to-tail and either/unknown repeat patterns:

SRU Labels and Curved Brackets Can Be Registered

ISIS allows you to register structures to your database that contain SRU labels and/or curved brackets. For example:

where the subscripts p, q, and r on the structural repeating unit (SRU) brackets are SRU labels. Brackets can have one of two styles: square or curved. SRU labels and bracket style are stored in molfiles that you export from ISIS. MACCS-II, however, displays these structures with the default SRU label (n) and the default bracket style (square).

No Display States for Attached Data (Sgroup Data)

ISIS no longer restricts where you can display attached data (called Sgroup data in MACCS-II) on a structure. Consequently, ISIS does not require you to specify display states for attached data.

2.4 Differences in Sorting and Printing

Information in a database is stored either in a single level (called a flat database) or in multiple levels (called a hierarchical database). Data storage in a hierarchical database is more efficient in that you can store several sets of data with each record. However, you sort and print your results differently than you would with a flat database.

MACCS-II and ChemBase databases are flat, and REACCS databases are hierarchical. ISIS allows you to use any of these databases, and, in addition, allows you to use hierarchical molecule and relational databases.

2.4.1 Sorting

You can specify a set of sorting instructions for a single sorting process.

Specify a single sorting instruction for each field that you want to sort. Enter the most important sorting instructions first.

You can sort automatically after a search.

Specify before your search that you want your data to be sorted automatically after the search. (Alternatively, you can sort your data manually.)

You can sort many fields at any level in the database.

You can sort the data from one to three child fields (fields with data) that share the same parent field (a field that points to a set of related child fields). Specify as many parent fields as you want. For example, you can sort variations within a reaction record so that the variation subrecords with the highest yields appear first.

You can sort calculated fields that you define yourself (for remote databases only).

If you define a calculated field, you can also sort combined data from a lower-level field. For example, the parent field LETHAL points to several LD50 values in the child field LD50_RESULT. Define and sort the calculated field AVG_LD50_RESULT that contains the average of all the LD50 values in LD50_RESULT.

You can reuse your sorting instructions.

ISIS does not preserve the order of sorted subrecords that you save. Therefore, we recommend that you save your sorting instructions, and then restore them when you need them. (You can also export your sorting instructions to a text file.)

You can sort records by their similarity values.

When you conduct either a Molecule Similarity (MSim) or a Reaction Similarity (RSim) search, you can specify that your results are sorted by their similarity values. In an MSim search, you can sort by structural (molecular) similarity values. In an RSim search, you can sort by structural similarity values and/or by transformational (reacting center) similarity values.

2.4.2 Printing

You can print large amounts of data.

A hierarchical database might have several sets of data associated with each record. You can print all the data or all the specific data that is associated with a single record.

You can specify headers and footers on each page of a printed form.

Headers and footers are part of your form. You can specify the font and color of the text in the headers and footers, and you can specify the automatic addition of the following: Current page number, database name, time of day, the date, and the starting and ending contexts for what is printed. You can then save the form. Your header and footer specifications are also saved.

You can change the appearance of a page while you review it prior to printing.

Information on page layout and number of forms per page is part of your form. You can change the appearance of a page (in the Page Layout dialog) before you print it. When you save the form, your specifications for the page layout and number of forms per page are also saved.

2.5 Task Order in ISIS

Always perform the tasks in the order shown.

If an order is not given and you are not sure what to do next, choose The ISIS/Base Chemical Searches - and How to Do Them from the SEARCHING with ISIS/Base screen, and then click the search of your choice. You will see the full definition of the search and how to do it. (Alternatively, for a general overview of ISIS, you can choose Help > MDL Help Files: Overview, and then click ISIS Overview & Documentation.)

2.6 Help

The ISIS Help System can show you:

*	How to choose a suitable search, and then how to do it.

Choose Help > Index (Draw + Base only). In the Search dialog, enter searches, choosing the most appropriate (ISIS/Base). Click Show Topics, and then click Go To. You see the ISIS/Base SearchSelector screen.

*	How to perform any search that you choose.

Choose The ISIS/Base Chemical Searches - and How to Do Them from the SEARCHING with ISIS/Base screen, and then click the search of your choice. You will see the full definition of the search and how to do it.

*	Specific reference information.

Choose Index (Draw + Base only) from the ISIS/Base or ISIS/Draw help menu, or click the Search button in the help system. Enter a word that describes the information you want to find. The search engine locates specific reference information.

Be careful! The information that you find when you search the Index is often very specific, and might not include the step-by-step instructions that allow you to complete a task.

*	Specific searching concepts and examples.

Choose Index (Draw + Base only) from the ISIS/Base help menu. In the Search dialog, enter searching examples (ISIS/Base). Click Show Topics, and then click Go To. You see the Searching Examples screen. Click The ISIS/Base Chemical Searches - and How to Do Them, and then click the search of your choice. You will see a brief definition of the search and how to do it. You can then click Searching Concepts/Examples to see the full definition of the search, complete with searching examples. This information is presented in a Request-A-Document format, much like an actual paper document. We recommend that you print it and then browse through it.


ISIS/Base Menus

Database menu

Edit menu

File menu

List menu

Object menu

Options menu

Search menu


File Menu

Close Database

Configure Database...

Exit/Quit

Export

Import

New Database...

New Form

Open Database...

Open Form...

Page Layout...

Print...

Print/Page Setup...

Save Form

Save Form As...


Close Database
Close Database (File menu)

Closes the database in the active window.

For more information, see:

To close a database


New Form
New Form (File menu)

Removes the current form and opens a new, empty, and untitled ISIS/Base form. This command is available when a database is open in the active window.

This command is available solely in Forms mode.

For more information, see:

Create a new form


Save Form
Save Form (File menu)

Saves the current form in the database. You must provide a form name if this is the first time the file is being saved. If the form has been saved before, the existing form name (and description, if present) are used. This command is available when a database is open in the active window.

Caution: Save overwrites the existing form with the changes that were made. If you want to preserve the original form, use the Save As command and give the form a different name.

This command is available solely in Forms mode.

For more information, see:

Save a form

Export a form to a file


New Database...
New Database... (File menu)

Displays the New Database dialog, allowing you to create a new local database or set up access to a remote database.

For more information, see:

Create Database (for local databases)

New Remote Database (for remote databases)


Open Database...
Open Database... (File menu)

Displays a dialog box allowing you to open a local or remote database.

Note: To open a database created with a version of ISIS/Base earlier than 2.0 on the Macintosh, you need to run a separate upgrade utility. For more information, see your ISIS Administrator.

For more information, see:

To open a local database

To open a remote database


Configure Database...(File menu)

Displays a dialog allowing you to configure a local or remote database:

*	For local databases, displays the Configure Local Database dialog, where you specify whether to record changes to the local database in a log (journal) file.

*	For remote databases, displays the Configure Remote Database dialog, where you can change the network connectivity information and Hview for the remote-access file.

Note: You cannot configure an open database.

For more information, see the dialog-box help:

Configure Local Database

Configure Remote Database


PL
PL (File menu)

Allows you to execute commands in the Procedural Language. This menu item is available only if you have PL installed.

Execute PL Program

Displays a dialog box allowing you to specify .EPL files that contain Procedural Language command sequences to execute.

Debug PL Program

Displays a dialog box allowing you to specify .EPL files that contain Procedural Language command sequences to debug.

For more information, see the documentation for the ISIS/Application Development Kit.


Open Form...
Open Form... (File menu)

Displays the Open Form dialog box, allowing you to open an existing form. The form you select becomes the current form.

File > Open Form is available solely when a database is open in the active window.

For more information, see:

To open a form

To import a form


Save Form As...
Save Form As... (File menu)

Displays a dialog box allowing you to save the current form in the database as a database object.

File > Save Form As is available solely when you:

*	Have a database open in the active window.

*	Are in Forms mode

For more information, see:

To save the form


Import
Import (File menu)

Allows you to import the contents of a selected file into ISIS/Base. Choose File > Import and choose a file type from the cascading menu. You see a dialog box where you specify the drive, directory or folder, and name of the file that you want to import.

Macintosh users: To import a file that was created on the PC, press the Option key when you pull down the File menu and choose an import type.

Form...

List...

MolFile...

RDfile...

RxnFile...

SDfile...

Sorting Instructions...


MolFile...

Displays a dialog box allowing you to import a molfile and display the structure in the selected form box or column.

Import > Molfile is available solely when you:

*	Are in Query or Update mode

*	Select a box or table cell that is connected to either a 2D-structure database field (MOLSTRUCTURE) or a 3D-structure database field (MODELSTRUCTURE).

Macintosh users: To import a molfile that was created on the PC, press the Option key when you pull down the File menu and choose Import > Molfile.

For more information, see:

To import a molfile


RxnFile...

Displays a dialog box allowing you to import a rxnfile and display the reaction in the selected form box or column.

Import > Rxnfile is available solely when you:

*	Are in Query or Update mode

*	Select a box or table cell that is connected to a reaction (RXNSTRUCTURE) field. On the PC, rxnfiles have the default extension .RXN.

Macintosh users: To import a rxnfile that was created on the PC, press the Option key when you pull down the File menu and choose Import > Rxnfile.

For more information, see:

To import a rxnfile


RDfile...

Displays a dialog box allowing you to import the data in an RDfile and register it into the current database. The Import RDfile dialog allows you to specify how ISIS/Base registers a record that has the same ID or structure as a record that is already in the database.

Import > RDfile is available solely in Update mode.

Macintosh users: To import an RDfile that was created on the PC, press the Option key when you pull down the File menu and choose Import > RDfile.

For more information, see the:

Import RDFile dialog box help

ISIS/Base Database Maintenance Manual

ISIS Administrator at your site


SDfile...

Displays a dialog box allowing you to register the data in an SDfile to the database. The Import SDfile dialog allows you to specify how ISIS/Base registers a record that has the same ID or structure as a record that is already in the database.

Import > SDfile is available solely in Update mode.

Macintosh users: To import an SDfile that was created on the PC, press the Option key when you pull down the File menu and choose Import > SDfile.

For more information, see the:

Import SDFile dialog box help

ISIS/Base Database Maintenance Manual

ISIS Administrator at your site


Form...

Displays a dialog box allowing you to import a form file into the database and makes it the current form. If necessary, ISIS/Base clears the current form from the active window before importing the new form.

Import > Form is available in all modes.

Macintosh users: To import a form file that was created on the PC, press the Option key when you pull down the File menu and choose Import > Form.

For more information, see:

To import a form


List...

Displays a dialog box allowing you to import a list of search results file into the database, make it the current list, and set the search domain to the imported list. The list file contains record ID numbers of search results in either binary or ASCII format.

*	For remote databases, displays the Host File Name dialog, where you specify the name of the list file. Use the file-naming conventions of the operating system on your host computer.

*	For local databases, displays the Open File dialog, where you specify the name of the list file. On the PC, list files have the default file extension .LST.

Import > List is available solely in Query and Browse modes.

Macintosh users: To import a list file that was created on the PC, press the Option key when you pull down the File menu and choose Import > List.

For more information, see:

To import a list of search results (for local databases)

To import a list of search results (for remote databases)


Sorting Instructions...

Imports a sorting instruction file into the database. The imported sorting instructions become the current sorting instructions. Choose the sorting instruction file that you want from the Open File dialog box.

A sorting instruction file contains a set of ISIS/Base database sorting instructions in ASCII format.

Import > Sort is available solely in Query and Browse modes.

Macintosh users: To import a sorting instructions file that was created on the PC, press the Option key when you pull down the File menu and choose Import > Sorting Instructions.

For more information, see:

To import sorting instructions


Export
Export (File menu)

Allows you to export structures, reactions, data, and database objects in a format that can be read by ISIS and other MDL Programs.

Macintosh users: To export a file for use on the PC, press the Option key when you pull down the File menu and choose an export type.

CFS SDfile...

CPSS RxnFile...

Form...

List...

Local Database...

MolFile...

RDfile...

REACCS RxnFile...

SDfile...

Sorting Instructions...

Table...


MolFile...

Displays a dialog box allowing you to save the structure in the selected box or column as a molfile.

Export > MolFile is available solely when you:

*	Are in Query, Browse, or Update mode.

*	Have a query in a 2D structure (MOLSTRUCTURE) or 3D structure (MODELSTRUCTURE) box or table cell on the form.

*	Select the box or table cell that contains the query.

PC users: Use the default .MOL extension in the file name.

Macintosh users: To export a molfile for use on the PC, press the Option key when you pull down the File menu and choose Export > Molfile.

For more information, see:

To export a 2D or 3D structure to a molfile


CPSS RxnFile...

Displays a dialog box allowing you to save a reaction in the selected box or column as a rxnfile that can be read by CPSS.

Export > CPSS RxnFile is available solely when you:

*	Are in Query, Browse, or Update mode

*	Have a query in a reaction (RXNSTRUCTURE) box or table cell on the form.

*	Select the box or table cell that contains the reaction

PC users: Use the default .RXN extension in the file name.

Macintosh users: To export a CPSS RxnFile for use on the PC, press the Option key when you pull down the File menu and choose Export > CPSS RxnFile.

For more information, see:

To export a reaction to a rxnfile


REACCS RxnFile...

Displays a dialog box allowing you to save a reaction in the selected box or column as a rxnfile that can be read by REACCS.

Export > REACCS RxnFile is available solely when you:

*	Are in Query, Browse, or Update mode

*	Have a query in a reaction (RXNSTRUCTURE) box or table cell on the form.

*	Select the box or table cell that contains the reaction

PC users: Use the default .RXN extension in the file name.

Macintosh users: To export a REACCS RxnFile for use on the PC, press the Option key when you pull down the File menu and choose Export > REACCS RxnFile.

For more information, see:

To export a reaction to a rxnfile


RDfile...

Displays the Export Fields dialog, allowing you to save data from the records in the current list to an RDfile. You must specify the database fields that you want to export.

An RDfile contains structures, data, and (optionally) reactions in ASCII format. You can export multiple records to an RDfile to transfer between databases. RDfiles have a hierarchical file-structure allowing you to export data from fields in lower-levels of the database hierarchy.

Export > RDFile is available solely in Browse mode.

PC users: Use the default .RDF extension in the file name.

Macintosh users: To export an RDfile for use on the PC, press the Option key when you pull down the File menu and choose Export > RDfile.

For more information, see the:

Export RDFile dialog-box help

ISIS/Base Database Maintenance Manual

ISIS Administrator at your site


SDfile...

Displays the Export Fields dialog, allowing you to save data from the records in the current list to an SDfile. You must specify the database fields that you want to export.

An SDfile contains structures and data (ASCII format). You can export multiple records to an SDfile to transfer between databases. SDfiles have a flat file-structure allowing you to export data from fields in the root (top) level of the database hierarchy.

Remote databases only: ISIS/Base allows lower-level fields to be exported to an SDfile because of the way in which ISIS views flexible fields as a hierarchy. However, the hierarchy is collapsed so that these fields are written to the SDfile as top-level fields.

Export > SDFile is available solely in Browse mode.

PC users: Use the default .SDF extension in the file name.

Macintosh users: To export an SDfile for use on the PC, press the Option key when you pull down the File menu and choose Export > SDfile.

For more information, see the:

Export SDFile dialog-box help

ISIS/Base Database Maintenance Manual

ISIS Administrator at your site


Form...

Displays the Save As dialog, allowing you to save the current form as a file in ASCII format (form file).

Export > Form is available in all modes.

PC users: Use the default .FRM extension in the file name.

Macintosh users: To export a form file for use on the PC, press the Option key when you pull down the File menu and choose Export > Form.

For more information, see:

To export a form as an ISIS form file


List...

Displays a dialog box allowing you to save the current list of search results as a file in ASCII format (list file):

*	For remote databases, displays the Host File Name dialog, where you specify the name of the list file. Use the file-naming conventions of the operating system on your host computer.

*	For local databases, displays the Save As dialog, where you specify the name of the list file.

Export > List is available solely when you:

*	Are in Query, Browse, or Update mode

*	Have a current list of search results

PC users: Use the default .LST extension in the file name.

Macintosh users: To export a list file for use on the PC, press the Option key when you pull down the File menu and choose Export > List.

For more information, see:

Exporting Search Results (for remote databases)

Exporting Search Results (for local databases)


Table...

Displays a dialog box allowing you to save text and numeric data from records in the selected table as a file in ASCII format.

Export > Table is available solely when you:

*	Are in Query, Browse, or Update mode

*	Select a table on the form

PC users: Use the default .TBL extension in the file name.

Macintosh users: To export a table file for use on the PC, press the Option key when you pull down the File menu and choose Export > Table.

For more information, see:

ISIS/Base Database Maintenance Manual


Local Database...

Creates a new local database from the records in the current list of search results. Displays the Export Fields dialog, allowing you to specify the fields that you want to include in the new database. In addition, copies of the database objects in the current database are exported into the new database.

Export > Local Database is available solely in Browse mode.

PC users: Use the default .DB extension in the file name.

For more information, see:

Export Fields dialog-box help

ISIS/Base Database Maintenance Manual


CFS SDfile...

Displays a dialog box allowing you to save fitted 3D structures and data from a Conformationally Flexible Substructure (CFS) search as a CFS SDfile in ASCII format.

Export > CFS SDfile is available solely when you:

*	Have a remote 3D molecule database in the active window

*	Are in Browse mode

PC and Macintosh users: To save the CFS SDfile on the host computer, begin the file name with the following: HOST::

Macintosh users: To export a CFS SDfile for use on the PC, press the Option key when you pull down the File menu and choose Export > CFS SDfile.

For more information, see:

To export search results to a CFS SDfile,


Sorting Instructions...

Saves the current sorting instructions as a file in ASCII format. Displays the Save As dialog, where you specify the name of the file.

PC users: Use the default .SRT extension in the filename.

Macintosh users: To export sorting instructions for use on the PC, press the Option key when you pull down the File menu and choose Export > Sort.

For more information, see:

To export sorting instructions


Page Layout...
Page Layout... (File menu)

Displays the Page Layout dialog, allowing you to change the appearance of the printed page. The dialog display how the pages will appear when you print the contents of the active window.

File > Page Layout is available solely when a database is open in the active window.

For more information, see:

Previewing and changing page layout


Print/Page Setup... (File menu)

Displays a dialog box allowing you to specify the paper size and page orientation required for printing, and other printing options. Consult your system documentation for information on printing.

Print Setup is the PC command, Page Setup is the Macintosh equivalent.

File > Print Setup and File > Page Setup are available solely when a database is open in the active window.

Note: OSF/Motif users, see your System Administrator for further information on how to print.


Print...
Print... (File menu)

Displays the Print dialog box, allowing you to:

*	Specify which records to print

*	Change the appearance of the printed page

*	Create and edit headers and footers.

File > Print is available solely when a database is open in the active window.

For more information, see:

To print search results

To print a query

To print the form with database fields


Exit/Quit (File menu)

Closes the active window and exits the current ISIS/Base session. If you have an open window that contains work that you have not saved, a dialog asks if you want to save or abandon the changes, or cancel the command.

Exit is the PC command, Quit is the Macintosh equivalent.


Edit Menu

These commands are available solely when a database is open in the active window.

Clear

Clear Data

Copy

Copy Form To Clipboard

Cut

Delete Record

Duplicate

New Record

Paste

Select All

Transfer to ISIS/Draw

Undo


Undo
Undo (Edit menu)

Reverses the last command that you performed. Edit > Undo only works for some commands and is available solely in Forms mode.


Cut
Cut (Edit menu)

Removes one or more selected objects from the active window and places them on the Clipboard. This overwrites the previous contents of the Clipboard (if any). The objects remains on the Clipboard until you perform another Cut or Copy operation.

Edit > Cut is available solely in Forms, Query, and Update modes.

In Query and Update mode, Cut removes the data from the selected box or column.

In Forms mode, Cut removes the selected form objects, such as boxes and columns.

Note: To recover cut objects, choose Edit > Undo.


Copy
Copy (Edit menu)

Copies one or more selected objects from the active window to the Clipboard. This overwrites the previous contents of the Clipboard (if any). The original objects stay on the screen. The objects remains on the Clipboard until you perform another Cut or Copy operation.

In Query, Browse, and Update modes, Copy copies the data in the selected box or column to the Clipboard.

In Forms mode, Copy copies the selected form objects (such as boxes and columns) to the Clipboard.


Paste
Paste (Edit menu)

Takes the last objects placed in the Clipboard (by Cut or Copy) and places them in the active window. If placed in a new window, the objects are placed in approximately the same position as they were in their original location. You can paste objects an unlimited number of times.

Paste is available solely in Forms, Query, and Update modes.

In Forms mode, Paste inserts the contents of the clipboard onto the form as a form object.

In Query and Update modes, Paste inserts the contents of the clipboard into the box or column as data.

PC only: You can paste an object from the Clipboard as an embedded object. This works only if the application from which the object was copied supports object embedding.


Clear
Clear (Edit menu)

Deletes one or more selected objects from the active window without placing them on the Clipboard.

Clear is available solely in Forms, Query, and Update modes.

In Query and Update modes, Clear deletes the data in the box or column.

In Forms mode, Clear deletes the selected form objects, such as boxes and columns.

Note: To recover cleared objects, choose Edit > Undo.


Copy Form To Clipboard
Copy Form To Clipboard (Edit menu)

Copies the current form (with displayed data, if present) from the active window to the Clipboard. This overwrites the previous contents of the Clipboard (if any). The original form stays on the screen, and remains on the Clipboard until you perform another Cut, Copy, or Clear operation.


Select All
Select All (Edit menu)

Selects every form box and table in the active window and gives them all selection handles.

Select All is available solely in Forms mode.


Duplicate
Duplicate (Edit menu)

Makes an exact copy of one or more selected form boxes or tables, slightly offset from the originals.

Duplicate is available solely in Forms mode.


Transfer To ISIS/Draw
Transfer To ISIS/Draw (Edit menu)

Copies the structure or reaction in the selected box or column to ISIS/Draw. If ISIS/Draw is not running, starts ISIS/Draw and copies the structure or reaction to ISIS/Draw.

Transfer To ISIS/Draw is available solely when you:

*	Are in Query, Browse, or Update mode

*	Select a box or table cell that contains a structure or reaction.


New Record
New Record (Edit menu)

Creates a new record in the database in the active window. For a hierarchical database, creates a new record or subrecord (subordinate record).

New Record is available solely in Update mode.

Note: When you complete data entry of a new record, choose Database > End Update if you do not have additional records to enter or Edit > New Record if there are additional records to enter. The current new record is registered. (To cancel the registration of the new record, choose Database > Abort Update.)

For more information, see:

The ISIS/Base Database Maintenance Manual


Delete Record
Delete Record (Edit menu)

Deletes the displayed record from the database. For a hierarchical database, deletes a record or subrecord (subordinate record).

Delete Record is available solely in Update mode.

For more information, see:

The ISIS/Base Database Maintenance Manual


Clear Data
Clear Data (Edit menu)

These commands can be useful for clearing part or all of a query that is no longer suitable.

These commands are available solely in Query mode.

Form

Clears the contents of the form.

Box

Clears the contents of the box that you select.

All Boxes

Clears the contents of all boxes that you select.

Cell

Clears the contents of an individual cell in a table.

Row

Clears the horizontal row in a table.

Table

Clears the contents of the table columns that you select.


Options Menu

These commands are available solely when a database is open in the active window.

CFS Options...

CFS View

Ruler Settings...

Settings

Show Ruler

Snap to Ruler

Zoom


Zoom
Zoom (Options menu)

Allows you to choose a smaller or larger size in which to display the form and data.

100% Size

Shows the objects in the active window at their original size.

25%, 50%, 75%, 133% 200%

Shows the objects in the active window at one quarter, one half, three quarter, original plus 33%, or double size.


Ruler Settings
Ruler Settings... (Options menu)

Displays the Ruler Settings dialog, allowing you to you set the units (inches or centimeters), number of increments, and other information about the ruler.

Ruler Settings is available solely in Forms mode.

For more information, see:

To use the ruler for precise measurement


Settings (Options menu)

Allows you to specify the settings that apply to default form properties and to defaults for the current ISIS/Base session.

Session...

Displays the Settings dialog, allowing you to set all of ISIS/Base's default settings for the current session. These settings apply to all databases that you open during the current session. By default, these settings are saved in the file ISISBASE.CFG.

Form Defaults...

Displays the Form Defaults dialog, where you set defaults for ISIS/Base forms. These defaults apply solely when you create new form objects. By default, these settings are saved in the file BASEFORM.CFG.

Form Defaults is available solely in Forms mode.

For more information, see:

Settings


Show Ruler
Show Ruler (Options menu)

Shows (or hides) the current ruler at the top and left sides of the work area. Markers show the current position of the pointer.

To change the ruler divisions, choose Options > Ruler Settings.

Show Ruler is available solely in Forms mode.

For more information, see:

To use the ruler for precise measurements


Snap To Ruler
Snap To Ruler (Options menu)

When checked, any object that you subsequently draw is sized using the increments marked on the current ruler. For example, if you specified Centimeters and 5, an object such as a box can only be drawn in 0.2 centimeter (2 millimeter) increments.

To specify how the ruler is displayed (centimeters or inches) and how many division marks to display, choose Options > Ruler Settings.

Snap to Ruler is available solely in Forms mode.

For more information, see:

To use the ruler for precise measurements


CFS Options... (Options menu)

Displays the CFS Options dialog box, where you change the options for Conformationally Flexible Substructure (CFS) searching and viewing.

CFS Options is available solely when you have a remote 3D molecule database in the active window.

For more information, see the dialog-box help:

CFS Options


CFS View (Options menu)

When checked, fits 3D structures in the current list to the current query using the current set of CFS options. Use this command before you view a list of CFS search results that you have previously saved or exported.

CFS View is available solely when you have a remote 3D molecule database in the active window.

Note: This command is automatically activated after you conduct a CFS search.

For more information, see:

CFS     CFS/Biopoly


Object Menu

These commands are available solely when a database is open in the active window.

Align...

Box/Column/Table Properties...

Bring to Front

Font...

Group

Line

Multiply Box...

Partition Box...

Pen Color

Pen Width

Send to Back

Ungroup


Box/Column/Table Properties... (Object menu)

Displays a dialog box that allows you to edit the properties of the selected form objects. The text of this command varies based on whether you select a box, table column, or an entire table. For example, if you select a column within a table, the command is Object > Column Properties.

Box Properties, Column Properties, and Table Properties are available solely when you select one or more form objects of the single type (box, column, or table). In addition, Object > Column Properties is available solely in Forms mode.

For more information, see:

Editing Boxes

Editing Columns and Tables


Font... (Object menu)

Displays the Font Manager dialog, allowing you to choose fonts, font sizes, and text styles.

Font is available solely in Forms mode.

For more information, see:

To change the font, size, or style of text

To change the font of box labels and column headings

To change the font, size, or style of data


Partition Box... (Object menu)

Displays the Partition Box dialog, allowing you to specify the number of horizontal and vertical partitions in the box that you selected.

Partition Box is available solely when you:

*	Are in Forms Mode

*	Select one or more boxes

For more information, see:

To divide a box into multiple boxes


Multiply Box... (Object menu)

Displays the Multiply Box dialog, allowing you to specify the number of horizontal and vertical repetitions of the box that you selected.

Multiply Box is available solely when you:

*	Are in Forms Mode

*	Select one box

For more information, see:

To create multiple copies of a box


Align... (Object menu)

Displays the Alignment Options dialog, allowing you to align selected objects horizontally, vertically, or both horizontally and vertically.

Align is available solely when you have selected two or more objects in Forms mode.

For more information, see:

To align boxes, tables, lines, or text


Pen Color (Object menu)

Allows you to change the color of selected boxes, tables, lines, and text in a form. Displays a cascading menu that contains eight pen colors. A check mark shows the current pen color.

Pen Color is available solely in Forms mode.

Other

Displays the Color dialog, where you can choose additional colors that are not on the list of eight pen colors.

For more information, see:

To change the color of box labels and column headings

To change the color of data display in a form

To change the color of the entire form

To change the width, color, or line style of a line


Pen Width (Object menu)

Allows you to change the pen width of selected box and/or table borders, and lines in a form. Displays a cascading menu that contains ten pen widths. A check mark shows the current pen width.

Pen Width is available solely in Forms mode.

For more information, see:

To change the width, color, or line style of a line

To change the width of lines and borders


Line (Object menu)

Allows you to change the line style of selected box and/or table borders and lines in a form. Displays a cascading menu that contains four line styles. A check mark shows the current line style.

Line is available solely in Forms mode.

For more information, see:

To change the width, color, or line style of a line

To change the style of lines and borders


Bring To Front (Object menu)

When objects overlap, brings a selected object (or group) from behind and places it on top of the other objects. You need to select only the object that you want to place on top, not the other objects.

Note: You cannot bring an object to the front when the object is completely covered and its handles are not visible; instead you must send the covering object to the back with Object > Send to Back.

Bring To Front is available solely in Forms mode.


Send To Back (Object menu)

When objects overlap, sends the top selected object (or group) to the back. You need to select only the object that you want to send to the back, not the other objects.

Send to Back also uncovers objects and groups previously hidden by other objects or groups.

Send to Back is available solely in Forms mode.


Group (Object menu)

Combines selected objects into a single unit so that a command applied to the group affects the whole group.

Group is available solely when you:

*	Are in Forms mode.

*	Select one or more objects

For more information, see:

To group objects


Ungroup (Object menu)

Reverses the Group command. Ungroup dissolves a group of objects and gives each object its own individual selection handles.

This command is available solely in Forms mode.

For more information, see:

To ungroup objects


Database Menu

These commands are available solely when a database is open in the active window.

Abort Update

Calculated Fields...

Edit Definition...

End Update

Go To Record

Object Manager...

Restore Molecule...

Restore Reaction...

Save Molecule...

Save Reaction...

View Definition...


Edit Definition... (Database menu)

Displays the Edit Database Definition dialog, allowing you to view and edit the database definition.

Edit Definition is available solely when you:

*	Have a local database in the active window

*	Are in Query, Browse, or Update mode

For more information, see the:

Edit Database Definition dialog-box help

ISIS/Base Database Maintenance Manual


Calculated Fields... (Database menu)

For remote searching only: Displays the Calculated Fields dialog, which allows you to create or delete calculated fields in the remote-access file of your database. To create a calculated field, you need to understand the database structure and know all the calculations that you can perform on the data.

Calculated Fields is available only when you:

*	Have a remote database in the active window

*	Are in Query, Browse, or Update mode

For more information, see the dialog-box help:

Calculated Fields


View Definition... (Database menu)

Displays the View Database Definition dialog, allowing you to view each database field name and field type.

View Definition is available in all modes.

For more information, see the dialog-box help:

View Database Definition


Object Manager... (Database menu)

Displays the Object Manager dialog, allowing you to manage database objects that are saved in the database file.

Object Manager is available in all modes.

For more information, see the dialog-box help:

Object Manager


Save Molecule... (Database menu)

Displays the Object Name dialog, allowing you to save the selected 2D or 3D structure as an object in the database.

Save Molecule is available solely when you:

*	Are in Query, Browse, or Update mode.

*	Have a structure in a 2D structure (MOLSTRUCTURE) or 3D structure (MODELSTRUCTURE) box or table cell on the form.

*	Select the box or table cell that contains the 2D or 3D structure

For more information, see:

To save a 2D or 3D structure as a database object


Restore Molecule.. (Database menu)

Displays the Select Object dialog, allowing you to restore a 2D or 3D structure that was previously saved with Save Molecule. The restored molecule displays in the box or table cell that you selected.

Restore Molecule is available when you:

*	Are in Query or Update mode.

*	Have a 2D or 3D structure on the form.

*	Select the box or table cell that contains the 2D or 3D structure.

For more information, see:

To restore a 2D or 3D structure from the database


Save Reaction... (Database menu)

Displays the Object Name dialog, allowing you to save the selected reaction as an object in the database.

Save Reaction is available solely when you:

*	Are in Query, Browse, or Update mode

*	Have a reaction in a RXNSTRUCTURE box or table cell on the form.

*	Select the box or table cell that contains the reaction.

For more information, see:

To save a reaction as a database object


Restore Reaction... (Database menu)

Displays the Select Object dialog, allowing you to restore a reaction that was previously saved with Save Reaction. The restored reaction displays in the box or table cell that you selected.

Restore Reaction is available solely when you.

*	Are in Query or Update mode

*	Have a reaction in a box or table cell on the form

*	Select the box or table cell that contains the reaction

For more information, see:

To restore a reaction from the database


Go To Record (Database menu)

Allows you to specify the number of the record that you want to view. The record must be on the current list.

Go To Record is available solely in Browse and Update modes.


End Update (Database menu)

Registers the new record or changes to an existing record.

Relational databases: The new records or changes to existing records are committed from the holding buffer into the database for registration.

End Update is available solely when you:

*	Are in Update mode

*	Have entered or changed data in any box or table cell on the form that is connected to a database field

For more information, see:

The ISIS/Base Database Maintenance Manual


Abort Update (Database menu)

Cancels the new record or changes to an existing record without updating the database.

Relational databases: The new records or changes to existing records are rolled back from the holding buffer and are not committed into the database.

Abort Update is available solely when you:

*	Are in Update mode

*	Have changed data in any box or table cell on the form that is connected to a database field

Note: Records are not registered into the database until you choose End Update.

For more information, see:

The ISIS/Base Database Maintenance Manual


Search Menu

These commands are available solely when a database is open in the active window, and solely in Query mode.

AutoMap RXN

By Form

CFS...

Current Mol

Current Rxn

Formula...

Polymer...

Query Builder...

Restore Query...

Retrieve All

RSS

Save Query...

Set Search Domain To

Similarity...

SSS

Subset RXN

View Last Query


AutoMap RXN (Search menu)

For remote searching only: Allows you to atom-to-atom map the atoms of the reactants and products in a transformation automatically.

AutoMap RXN is available only when you:

*	Have an entire reaction in ISIS/Base. An entire reaction contains at least one reactant and at least one product.

For more information, see:

Specifying an Atom-Atom Map on a Reaction

Searches that Require Atom-Atom Maps: RSS/Rxn or SBF in a Reaction Database


By Form (Search menu)

Searches the database for records that contain your text/numeric query exactly as you specify it or your structural query (molecule or reaction) both exactly as you specify it and as a substructure wholly within a larger structure.

In addition, you can combine text/numeric and structural queries. For example, you can specify the text/numeric query > 350 molecular weight AND the substructure query benzene.

By Form is available only when you:

*	Are in Query mode.

*	Have a text/numeric and/or a structural query on the form. (Your text/numeric query must use the correct syntax.)

For more information, see:

Molecule records: SBF in a remote database or SBF in a local database

Reaction records: SBF in a remote database or SBF in a local database

3D Structure records: SBF in a remote database or SBF in a local database


Current RXN (Search menu)

Searches the database for reactions that contain your query exactly as you specify it.

Current RXN is available only when you:

*	Are in Query mode.

*	Have a reaction query or reaction component query (with a reaction arrow) in the RXNSTRUCTURE box or table cell on the form.

*	Select the box or table cell that contains the query.

For more information, see:

Reaction records: REXACT/Comp or REXACT/Rxn in a remote database; or REXACT/Rxn in a local database


Formula... (Search menu)

Searches the database for records that contain the formula that you specify in your query. Your formula query can be:

*	An exact formula and no other atoms, such as C17H19NO3, or

*	A subformula and any additional atoms, such as C5H10, or

*	A subformula and any additional atoms except a specific atom, such as C5H10N0, where N0 represents zero nitrogens.

Formula is available only when you:

*	Are in Query mode.

*	Select the box or table cell on the form that is connected to the formula field (*fmla_MOLSTRUCTURE for a local database, MOLFORMULA for a remote database).

For more information, see:

Molecule records: FMLA in a remote database or FMLA in a local database

Reaction records: FMLA in a remote database or FMLA in a local database


Query Builder... (Search menu)

Searches the database for records that match your search query in the Query Builder dialog. You can create any of the other searches in ISIS in the Query Builder. However, you must use an all-text search query.

Thus, we recommend that you use another search where possible!

This search does have one unique feature: You can combine AND, OR and NOT boolean operators in a search query.

Query Builder is available only when you:

*	Are in Query mode.

For more information, see:

Molecule records: QB in a remote database or QB in a local database

Reaction records: QB in a remote database or QB in a local database

3D Structure records: QB in a remote database or QB in a local database


RSS (Search menu)

Searches the database for records that contain your query either as a reaction substructure or as a reaction component substructure (with a reaction arrow) embedded wholly within a larger reaction.

RSS (Reaction Substructure Search) is available only when you:

*	Are in Query mode.

*	Have a reaction query or a reaction-component query (with a reaction arrow) in the RXNSTRUCTURE box or table cell on the form.

*	Select the box or table cell that contains the query.

For more information, see:

Reaction records: RSS/Comp or RSS/Rxn in a remote database; or
RSS/Comp RSS/Rxn in a local database


Similarity... (Search menu)

For remote searching only: Searches the database for records that are structurally similar to your query (in a molecule database) or for reactions that are structurally and/or transformationally similar to your query (in a reaction database). You specify the degree of similarity in both cases to be an arbitrary value between 0 and 100 (these are not actual units). The higher the value, the more similarity.

3D Database Users: An MSim search uses solely the 2D information on a molecule, such as atom types, bond types, and connectivity.

Similarity is available only when you:

*	Are in Query mode.

*	Have a structure query on the form in the MOLSTRUCTURE box or table cell or a reaction query on the form in the RXNSTRUCTURE box or table cell.

*	Select the box or table cell that contains the query.

For more information, see:

Molecule records: MSim in a remote database

Reaction records: MSim in a remote database or RSim in a remote database


Subset RXN (Search menu)

For remote searching only: Searches the database for reaction records that contain the exact reactant or product that you specify in your query. The reactants and products in the query must be complete molecules with no substructure query features.

Note: Your query is either a reactant with a reaction arrow or a product with a reaction arrow. In previous versions of ISIS, this was a Subset Reaction search. This version of the help system refers to a Subset Reaction search as an REXACT search (in which you use the Subset RXN command).

Subset RXN is available only when you:

*	Are in Query mode.

*	Have a reaction-component query (with a reaction arrow) in the RXNSTRUCTURE box or table cell on the form.

*	Select the box or table cell that contains the query.

For more information, see:

Reaction records: REXACT/Comp in a remote database


Retrieve All (Search menu)

Retrieves all records in the current search domain.

Retrieve All is available solely in Query mode.

For more information, see:

Molecule records: ALL in a remote database or ALL in a local database

Reaction records: ALL in a remote database or ALL in a local database

3D Structure records: ALL in a remote database or ALL in a local database


Step-by-Step Instructions

Click one of the following:

Molecule records: remote (ALL) database or local (ALL) database

Reaction records: remote database (ALL) or local database (ALL)

3D Structure records: remote database (ALL) or local database (ALL)


SSS (Search menu)

Searches the database for records that contain your query as a substructure embedded wholly within a larger structure.

SSS (Substructure Search) is available solely when you:

*	Are in Query mode.

*	Have a query in a 2D structure (MOLSTRUCTURE) or 3D structure (MODELSTRUCTURE) box or table cell on the form.

*	Select the box or table cell that contains the query.

For more information, see:

Molecule records: SSS in a remote database or SSS in a local database

Reaction records: SSS in a remote database or SSS in a local database

3D Structure records: SSS3D in a remote database


Step-by-Step Instructions

Click one of the following:

Molecule records: remote (SSS) database or local (SSS) database

Reaction records: remote database (SSS) or local database (SSS)

3D Structure records: remote database (SSS3D


Searching Concepts/Examples

Click one of the following:

Molecule records: remote (MEXACT) database or local (MEXACT) database

Reaction records: remote database (MEXACT) or local database (MEXACT)

3D Structure records: remote database (MEXACT)


CFS... (Search menu)

For remote searching only: Searches the database for 3D structures that fit the query, or that can be made to fit the query by rotating single bonds. For example:

Displays the CFS Options dialog, where you specify search options.

CFS is available solely when you:

*	Are in Query mode.

*	Have a query in a 3D structure (MODELSTRUCTURE) box or table cell on the form.

*	Select the box or table cell that contains the query.

For more information, see the dialog-box help:

CFS Options


Current Mol... (Search menu)

For remote databases, searches the database for an exact match or related form (isomer, tautomer, parent molecule, or alternative representation) of the current molecule query. Displays the Search Current dialog, where you specify the type of match that you want.

For local databases, searches the database for an exact match of the current molecule query.

Current Mol is available solely when you:

*	Are in Query mode.

*	Have a query in a 2D structure (MOLSTRUCTURE) or 3D structure (MODELSTRUCTURE) box or table cell on the form.

*	Select the box or table cell that contains the query.

For more information, see:

Molecule records: MEXACT, ISOMER, TAUT, PARENT, or FLEX in a remote database; or MEXACT in a local database

Reaction records: MEXACT, ISOMER, TAUT, PARENT, or FLEX in a remote database; or MEXACT in a local database

3D Structure records: 3DEXACT in a remote database or 3DEXACT in a local database


Polymer... (Search menu)

For remote databases, searches the database for molecules that match the current polymer query in ways that you specify. Displays the Polymer dialog, where you specify the type of match that you want.

Polymer is available solely when you:

*	Are in Query mode.

*	Have a polymer query in a 2D structure (MOLSTRUCTURE) box or table cell on the form.

*	Select the box or table cell that contains the query.

For more information, see:

Molecule records: POLY/Exact, POLY/Both, POLY/Co, POLY/Sub


View Last Query (Search menu)

Allows you to view the last executed search query. Does not affect the current list of records.

View Last Query is available solely in Query mode.


Save Query... (Search menu)

Displays the Save Query dialog, allowing you to save the current query as a database object in the database.

Save Query is available solely in Query mode.

For more information, see the dialog-box help:

Save Query


Restore Query... (Search menu)

Displays the Select Object dialog, allowing you to restore a query that was previously saved with Save Query.

Restore Query is available solely when:

*	You are in Query mode.

*	The database contains one or more queries that have been previously saved.

For more information, see the dialog-box help:

Select Object


Set Search Domain To (Search menu)

Sets the current search domain to a list of search results that you specify.

Current List

Sets the search domain to the current list.

Other List...

Displays the Select Object dialog, allowing you to set the search domain to a list that is stored in the database. Search > Set Search Domain To > Other List is available solely when the database contains one or more lists that have been previously saved.

Entire Database

Sets the search domain to the complete database (all records).

Set Search Domain To is available solely in Query mode.


List Menu

These commands are available solely when a database is open in the active window.

Copy Item To

Delete Temporary Lists

Discard Item

Logic...

Move Item To

Open List...

Repeat Move Or Copy To <listname>

Save List...

Sort...

Sort On Search


Save List... (List menu)

Displays the Save List dialog, allowing you to save the current list of search results as a database object.

Save List is available solely in Query, Browse, and Update modes, and solely when a current list exists.

For more information, see the dialog-box help:

Save List


Open List... (List menu)

Displays the Open List dialog, allowing you to restore a list of search results that was previously saved in the database with the Save List command.

Open List is available solely in Query, Browse, and Update modes.

For more information, see the dialog-box help:

Open List


Discard Item (List menu)

Deletes the displayed record from the current list of search results and stores it in a temporary list called Discard.

Discard Item is available solely in Browse mode, and solely when a current list exists.

Note: Discard Item affects only the list. It does not delete records from the database.

For more information, see:

To delete records from a list of search results


Move Item To (List menu)

Moves the displayed record from the current list of search results to another list, called the target list. When you move a record to the target list, ISIS deletes that record from the current list.

List...

Displays the Move Item dialog, allowing you to specify a list in the database as the target list.

New List...

Displays the Move Item To a New List dialog, allowing you to create a new list to move the record into.

Move Item To is available solely in Browse mode, and solely when a current list exists.

For more information, see the dialog-box help:

Move Item

Move Item To New List


Copy Item To (List menu)

Copies the displayed record from the current lists of search results to another list, called the target list.

List...

Displays the Copy Item dialog, allowing you to specify a list in the database as the target list.

New List...

Displays the Copy Item To a New List dialog, allowing you to create a new list to copy the record into.

Copy Item To is available solely in Browse mode, and solely when a current list exists.

For more information, see the dialog-box help:

Copy Item

Copy Item to New List


Repeat Move Or Copy To <listname> (List menu)

Moves or copies the displayed record to the named list of search results. To specify the list to move or copy the record to, choose List > Move Item To or List > Copy Item To.

Repeat Move To and Repeat Copy To are available solely in Browse mode, and solely when you have already defined a target list with the Move Item To command or the Copy Item To command.

For more information, see:

Manipulating Search Results


Logic... (List menu)

Displays the List Logic dialog, allowing you to perform logical operations on lists of search results.

Logic is available solely in Query, Browse, and Update modes, and solely when a current list exists.

For more information, see the dialog-box help:

List Logic


Sort... (List menu)

Sorts the records in the current list according to the current sorting instructions. Displays the Sort Dialog, where you create or edit sorting instructions.

Sort is available solely in Query, Browse, and Update modes.

For more information, see the dialog-box help:

Sort


Sort On Search (List menu)

When checked, uses the current sorting instructions to sort search results automatically, immediately after a search.

Sort On Search is available solely in Query, Browse, and Update modes.

For more information, see:

The ISIS/Base Chemical Searches-- and How to Do Them


Delete Temporary Lists (List menu)

Deletes all temporary lists that ISIS created automatically. Does not delete temporary lists that you saved manually.

Delete Temporary List is available solely in Query, Browse, and Update modes.


ISIS/Base Tools

To view information about a tool, click the tool.


ISIS/Draw Transfer Icon

Copies the structure or reaction in the selected box or column in your form to ISIS/Draw. If ISIS/Draw is not running, starts ISIS/Draw and copies the structure or reaction to ISIS/Draw.

This tool is available solely when the selected box or column contains a structure or reaction.


Display Up Tool

In Query mode, moves the record indicator to the previous line in a table cell.

In Browse and Update modes, displays the previous record or subrecord in the list, depending on which box or column in the form is highlighted.

This tool is available solely in Query, Browse, and Update modes.

The keyboard equivalent of this tool is the Up arrow key.


Display Down Tool

In Query mode, moves the record indicator to the next line in a table cell.

In Browse and Update modes, displays the next record or subrecord in the list, depending on which box or column in the form is highlighted.

This tool is available solely in Query, Browse, and Update modes.

The keyboard equivalent of this tool is the Down arrow key.


First Record Tool

In Browse and Update modes, displays the first record or subrecord in the list, depending on which box or column in the form is highlighted.

This tool is available solely in Browse and Update modes.

The keyboard equivalent of this tool is the Home key.


Last Record Tool

In Browse and Update modes, displays the last record or subrecord in the list, depending on which box or column in the form is highlighted.

This tool is available solely in Browse and Update modes.

The keyboard equivalent of this tool is the End key.


Record Number Tool

In Browse and Update modes, displays the record or subrecord number that you specify, depending on which box or column in the form is highlighted. For example, type 2 to see the second record in the list.

This tool is available solely in Browse and Update modes.

The keyboard equivalent of this tool is the # key.


Select Tool

Use this tool to select one or more boxes or columns in your form. You typically select a form box or table column, and then choose an action to apply to it. Double-click a box or table column to connect it to a field in the database.

This tool is available solely in Forms mode.


Box Tool

Click here for step-by-step instructions

Draws a box outline in your form. Use a form box to enter or display a structure, a reaction, or data.

This tool is available solely in Forms mode.


Line Tool

Click here for step-by-step instructions

Draws an unattached line. Use unattached lines to enhance the appearance of a form.

This tool is available solely in Forms mode.


Text Tool

Click here for step-by-step instructions

Writes unattached text that enhances the appearance of a form. Also labels a box or column with a name that indicates the data that it contains.

This tool is available solely in Forms mode.


Table Outline Tool

Click here for step-by-step instructions

Draws a table outline.

This tool is available solely in Forms mode.


Settings

Set all of the ISIS/Base default settings with the Settings dialog box. You can specify settings that:

*	Apply only when you create new objects within a form, or new forms (saved in the file BASEFORM.CFG)

*	Apply to the way ISIS/Base works in general (saved in the file ISISBASE.CFG)

BASEFORM.CFG and ISISBASE.CFG are updated whenever you modify settings and then save the modifications.

You can also save different sets of settings to multiple settings files.

To modify ISIS/Base settings

To create your own settings files

To read a settings file into ISIS/Base


To modify ISIS/Base settings

1.	Do one of the following:

*	To set general ISIS/Base settings, choose Options > Settings > Session.

*	To specify settings for any new objects within a form, or for new forms that you create: Choose Options > Settings > Form Defaults.

2.	Click a tab to see settings that affect a specific area of ISIS/Base.

3.	Modify one or more settings.

4.	(Optional) To save your modifications to the currently-open ISIS/Base settings file, click Save. If you don't do this, the modifications to settings will not be saved the next time you run ISIS/Base.

5.	Click OK.

Note: Changes that you make in the Forms Default dialog take effect only when you create a new object in an existing form, or a new form. They do not affect existing forms.


To create your own settings files

Use this procedure to save the current settings to a new settings file.

1.	Do one of the following:

*	Choose Options > Settings > Form Defaults

*	Choose Options > Settings > Session

2.	Click a tab to see settings that affect a specific area of ISIS/Base.

3.	Modify one or more settings.

4.	(Optional) Click another tab and modify more settings.

5.	Click Save As.

6.	Enter a name for the settings file.

PC users: The file name must end with the .CFG extension.

7.	Click OK.

8.	Click OK.


To read a settings file into ISIS/Base

1.	Do one of the following:

*	Choose Options > Settings > Form Defaults

*	Choose Options > Settings > Session

2.	Click Read.

3.	Select a settings file.

4.	Click OK.

Note: Changes that you make in the Forms Default dialog by reading in a settings file take effect only when you create a new object in an existing form, or a new form. They do not affect existing forms.


Reactions: Sorting Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This request-a-document contains:

*	Basic Concepts	100.1

*	Sorting Examples	100.2

We recommend that you print this 11-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on sorting search results, see the step-by-step instructions for the search of your choice.

100.1 Basic Concepts

100.1.1 Flat and Hierarchical Databases

ISIS databases can be either flat or hierarchical. In the following example, the database organization is flat, because the database contains only one level of data:

In this example, MOL is a parent field. Parent fields do not store data, but point to one or more child fields that contain the actual data. In this example, the child fields are STRUCTURE, CAS_NUMBER, MOLECULE_NAME, BOILING_POINT, and DATE. Each record has only one set of data associated with it.

However, your database might have more than one set of data that is associated with a molecule or reaction. Each set of data becomes a branch in a hierarchical database. The following is a portion of a hierarchical reaction database:

In this example, one reaction has several variations associated with it. Each variation, in turn, has several associated literature references and reaction conditions. The result is a hierarchy of three levels. The highest level in the database hierarchy has data associated with a specific reaction: the reaction (RXNSTRUCTURE) and its ID number (RXNREGNO). The middle level in the hierarchy provides data that is associated with a specific variation of the original reaction, such as the variation number (VARIATION_NO). The lowest level in the hierarchy provides the text of a specific literature reference for a given variation (LITTEXT_DATA), and data on reaction conditions (TIME, TEMP, PRESSURE).

Each level of the database has a parent field that points to one or more child fields that store data. In this example, RXN, VARIATION, CONDITIONS, and LITTEXT are parent fields at each level of the hierarchy.

100.1.2 Subrecords

A hierarchical database contains subrecords (subordinate records) that contain separate sets of data within the main record. For example:

*	In a reaction database, each reaction might have several variations associated with it. For example, the yield of a product might vary according to reaction conditions such as reaction temperature, catalyst, and solvent. This information is stored in the variation subrecords within each reaction.

*	In a molecule database, you might have several bottles of each compound. Each batch has its own set of associated test results. Information on each bottle is stored in the bottle subrecords within each molecule record.

Subrecords are defined by parent fields at lower levels of the database. For example, variation subrecords in a reaction database are defined by the VARIATION parent field. Each set of literature references (LITTEXT parent field) or reaction conditions (CONDITIONS parent field) is a subrecord within a variation subrecord:

You can sort subrecords. For example, you might want to sort bottle subrecords within each molecule record so that bottles with the highest amounts are displayed first:

100.1.3 Sorting in Hierarchical Databases

In remote databases only, you can sort records or subrecords by any child field below it in the hierarchy. For example, you can sort reaction records (RXN parent field) by reaction temperature (RXN>VARIATION>CONDITIONS>TEMP).

In local databases, you can sort record or subrecords solely by child fields that are directly attached to the corresponding parent field. For example, you can sort reaction records (RXN parent field) by RXNREGNO, or variation subrecords (VARIATION parent field) by VARIATION_NO.

You can sort records and subrecords by a maximum of three child fields.

You can sort records and subrecords by any of the following types of data: date, integer, real, fixed text, variable text, and range. You cannot sort by the following types of data: structure, reaction, or sketch.

100.1.4 Order of Sorting

The order of sorting can be either of the following:

*	Low to high places the smallest values first (ascending order). Fixed- and variable-text data is sorted in ascending alphanumeric order.

*	High to low places the largest values first (descending order). Fixed- and variable-text data is sorted in descending alphanumeric order.

100.1.5 Sorting Instructions

To specify how to sort your search results, you must create sorting instructions. Each sorting instruction has the following syntax:

Sort each parent-field by child-field from order

Parent-field specifies the records or subrecords to sort, child-field is the field that contains the data by which to sort, and order is either high to low or low to high.

For example, the following sorting instruction sorts reaction records (RXN parent field) so that those with the lowest reaction temperatures appear first:

Sort each RXN by >VARIATION>CONDITIONS>TEMP from low to high

The following sorting instruction sorts variation subrecords (VARIATION parent field) so that variations with the lowest reaction temperatures appear first:

Sort each RXN>VARIATION by >CONDITIONS>TEMP from low to high

The order in which you specify sorting instructions affects sorting. ISIS sorts your records as follows:

1.	ISIS applies the first sorting instruction to all records.

2.	If several records have the same value for the field specified in the first sorting instruction, ISIS uses the second sorting instruction to decide the order.

3.	If several records have the same value for the fields specified in the first two sorting instructions, ISIS uses the third sorting instruction to decide the order.

Consequently, you generally want to place the sorting instruction with the most important data first, so that ISIS sorts all records by that data.

For example, you might want to sort variation subrecords so that variations with the least extreme reaction conditions (lowest reaction temperatures and shortest reaction times) appear first. If reaction temperature is more important, specify sorting instructions in the following order:

Sort each RXN>VARIATION by >CONDITIONS>TEMP from low to high

Sort each RXN>VARIATION by >CONDITIONS>TIME from low to high

In this example, ISIS sorts the variation subrecords so that variations with the lowest reaction temperatures appear first. If several variations have the same reaction temperatures, ISIS places the variations with the shortest reaction times first.

You can save a set of sorting instructions within your database as a database object. You can also export a set of sorting instructions to a text file on hard disk or floppy. For information on saving sorting instructions, see the step-by-step instructions. Alternatively, click Help > Index, and search for sorting instructions, saving. For information on exporting sorting instructions, see the step-by-step instructions. Alternatively, click Help > Index, and search for sorting instructions, exporting.

100.1.6 Calculated Fields (Remote Databases Only)

In remote databases, you can create calculated fields that allow you to perform calculations on a set of data. For example:

*	Calculate the average or median of several activity measurements of a compound.

*	Count the number of bottles of each compound.

*	Calculate the sum of the yields of all the products of a reaction.

*	Determine the maximum or minimum value in a series, such as the maximum of several activity measurements or the earliest date of synthesis.

The data in a calculated field is not actually stored in the database, but is calculated from existing data. Calculated fields are listed in the database definition with the other fields. You can display the values from calculated fields on your form or use them to sort your search results.

For example, your molecule database might contain test results for the lethality of a compound (expressed as 50% lethal dose, or LD50). In the following example, the parent field LETHAL points to several LD50 values in the child field LD50_RESULT. The calculated field AVG_LD50_RESULT contains the average of all the LD50 values in LD50_RESULT (parentheses around AVG_LD50_RESULT indicate that it is a calculated field):

For information on creating calculated fields, see the step-by-step instructions. Alternatively, click Help > Index, and search for calculated fields, creating.

Note: A calculated field combines multiple instances of data from the same database field. If you want to create calculated values that combine data from different database fields, you need to create a form calculation. A form calculation takes data values from boxes or columns in the form that contain real numbers or integers and performs mathematical operations on the data to obtain a result. The mathematical operations include adding, subtracting multiplying, and dividing data. You see the result when you conduct a search and view the data in the Browse mode. However, you cannot use this data to sort search results. For more information on form calculations, see the step-by-step instructions. Alternatively, choose Help > Index, and search for forms, calculation.

For more information and examples of calculated fields, see the Request-A-Document Calculated Fields: Concepts/Examples.

100.1.7 Derived Data

For some types of searches, ISIS derives specific kinds of data from the reactions or structures that it retrieves during the search. You can display this derived data in a form and use it for sorting, just like data in database fields. The fields that contain derived data also appear in the database definition.

Reaction Similarity (RSim) searches, Molecule Similarity (MSim) searches, and Conformationally Flexible Substructure (CFS) searches all produce derived data. For more information on derived data, see the step-by-step instructions for the search of your choice.

Note: If you want to sort by derived data, we strongly recommend that you define your sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search ISIS must repeat the search to calculate the data.

100.1.8 Performance Considerations in Sorting

The time required for sorting depends on the factors described below.

Number of Records or Subrecords

The time required for sorting depends on the number of records (or subrecords) that you sort. The time required increases approximately as N log N, where N is the number of records (or subrecords) that you sort.

Calculated Fields

Sorting by data in calculated fields can require more time than sorting by data in other fields that are at the same level in the database hierarchy, because ISIS requires time to perform the calculations.

Number of Hierarchical Levels

Generally, the more hierarchical levels that separate a parent field from a given child field in the sorting instruction, the more time ISIS requires to sort by that child field. For example, sorting reaction records (RXN parent field) by RXN>VARIATION>PRODUCT>YIELD can require more time than sorting by RXN>RXNREGNO. This is because ISIS automatically creates hidden calculated fields that it uses to sort by data at lower levels of the hierarchy. Consequently, ISIS requires time to perform the calculations for the hidden calculated fields.

ISIS uses the following rules to create hidden calculated fields from sorting instructions:

*	If the order of sorting is high to low, ISIS calculates the maximum value of the field at each level of the database.

*	If the order of sorting is low to high, ISIS calculates the minimum value of the field at each level of the database.

For example, consider the following sorting instruction:

Sort each RXN by >VARIATION>PRODUCT>YIELD from high to low

To execute this sorting instruction, ISIS automatically creates two hidden calculated fields:

*	The first hidden field is a child of VARIATION, and contains the maximum value of RXN>VARIATION>PRODUCT>YIELD for each variation.

*	The second hidden field is a child of RXN, and contains the maximum value of the first calculated field for each reaction.

The following figure shows these hidden fields, which we call MAX1 and MAX2 (Parentheses () around the names show that they are calculated fields, and dotted lines in the hierarchy show that the fields are hidden):

ISIS deletes hidden calculated fields immediately after sorting. Therefore, you never see hidden calculated fields in the database definition.

Using Calculated Fields to Decrease Sorting Times

If you sort both records and subrecords by the same data, you can reduce sorting times by creating calculated fields at lower levels in the database hierarchy. For example, you might want to sort both reactions and variation subrecords by product yield. The sorting instructions are:

Sort each RXN by >VARIATION>PRODUCT>YIELD from high to low

Sort each RXN>VARIATION by >PRODUCT>YIELD from high to low

To execute the first sorting instruction, ISIS creates one hidden calculated field that contains the maximum value of YIELD (MAX1 in the previous example), and another that contains the maximum value of MAX1 (MAX2 in the previous example). To execute the second sorting instruction, ISIS creates a calculated field that contains the maximum value of YIELD. This hidden field contains the same data that is in the MAX1 hidden field. Consequently, ISIS creates the MAX1 field twice: once when executing the first sorting instruction and once when executing the second sorting instruction. To eliminate this duplication, and to decrease sorting time, create the calculated field MAX1 explicitly (in the following figure, the solid line in the hierarchy indicates that MAX1 is not hidden):

Then, use the calculated field MAX1 in the sorting instructions:

Sort each RXN by >VARIATION>MAX1 from high to low

Sort each RXN>VARIATION by >MAX1 from high to low

To execute these sorting instructions, ISIS performs the calculations for the MAX1 field only once, and uses this information for sorting both reactions and variations.

100.1.9 Saving and Exporting Sorted Search Results

If you save or export search results, ISIS preserves the order of the sorted records. However, ISIS doe not preserve the order of variation subrecords or other subrecords that you sort. For information on saving a list of records, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for search results, saving remote. For information on exporting a list of records, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for search results, exporting remote.

You can preserve the sorted order of both the records and subrecords by exporting your search results to a local database. For more information, see the step-by-step instructions. Alternatively, choose Help > Index, and search for search results, exporting to local database.

100.2 Sorting Examples

This section contains typical examples of sorting search results from reaction databases. These examples use the ISISRX demo database.

100.2.1 Sorting Reactions by Similarity Data (RSim Search Only)

In a Reaction Similarity (RSim) search, ISIS can derive two types of data on how similar the reactions you retrieve are to your reaction query. The type of similarity can be:

*	Structural Similarity: Physical resemblance to the substrate molecules in your query.

*	Transformational Similarity: Similar reacting centers.

You can sort your reaction records by either or both types of similarity.

Note: The similarity data that ISIS creates during an RSim search disappears when you perform another search. To ensure that similarity data is available for sorting, we strongly recommend that you sort your search results immediately after the search. To do this, we recommend that you define your sorting instructions before the search, and then sort your search results automatically after the search. For information on automatic sorting, see the step-by-step instructions for the RSim search. Alternatively, choose Help > Index, and search for RSim, how to/examples.

Sorting by Structural Similarity

In some RSim searches, you are primarily interested in the types of molecules that participate in a reaction, and are less interested in finding a specific transformation. For example, you might want to find alternate synthetic routes to a particular product. You might also want to find reactions with similar molecules but different reacting centers. When you perform the search, you specify a high value of structural similarity (80, for example) and a low value of transformational similarity (20, for example). You can then sort your search results by structural similarity. The following sorting instruction sorts your search results so that reactions with the highest structural similarity to the query appear first:

Sort each RXN by >RXNSTRUCTURESIMILARITY from high to low

Sorting by Transformational Similarity

In some RSim searches, you are primarily interested in a specific transformation, and less interested in the types of molecules that participate in the reaction. When you perform the search, you specify a low value of structural similarity (20, for example) and a high value of transformational similarity (80, for example). You can then sort your search results by transformational similarity. The following sorting instruction sorts your search results so that reactions with the highest transformational similarity to the query appear first:

Sort each RXN by >RXNCENTERSIMILARITY from high to low

Sorting by Both Structural and Transformational Similarity

When you sort your search results by both kinds of similarity, you must first decide which type of similarity is more important, and then specify that type of similarity first in the sorting instructions:

*	If structural similarity is more important, use the following sorting instructions, in this order:

Sort each RXN by >RXNSTRUCTURESIMILARITY from high to low

Sort each RXN by >RXNCENTERSIMILARITY from high to low

ISIS sorts all reaction records by structural similarity. If two reactions have the same structural similarity, ISIS places the reaction with higher transformational similarity first.

*	If transformational similarity is more important, use the following sorting instructions, in this order:

Sort each RXN by >RXNCENTERSIMILARITY from high to low

Sort each RXN by >RXNSTRUCTURESIMILARITY from high to low

100.2.2 Sorting by the Yield of the Principal Product

If the reactions on your list have only one principal product, you can sort reaction records so that reactions with the highest yield appear first:

Sort each RXN by >VARIATION>PRODUCT>YIELD from high to low

100.2.3 Sorting by the Total Yield of a Mixture of Stereoisomers (Remote Databases Only)

If the reactions on your list produce a mixture of stereoisomers as the product, you might want to sort by the total yield of all stereoisomers. To do this, you need to define a calculated field that contains the sum of the yields of individual products. In the following database hierarchy, the calculated field TOTAL_PROD_YIELD contains the sum of the yields of individual stereoisomers within a variation:

To sort by total yield of all stereoisomers, use the following sorting instruction:

Sort each RXN by >VARIATION>TOTAL_PROD_YIELD from high to low

100.2.4 Sorting by Reaction Conditions

You can sort reaction records by one or more reaction conditions, such as temperature, reaction time, and pressure. For example:

*	You want to sort reaction records so that reactions that require the shortest reaction times appear first. To do this, use the following sorting instruction:

Sort each RXN by >VARIATION>CONDITIONS>TIME from low to high

*	You want to sort reaction records so that reactions that require the lowest reaction temperatures appear first. To do this, use the following sorting instruction:

Sort each RXN by >VARIATION>CONDITIONS>TEMP from low to high

*	You want to sort reaction records so that reactions with the least extreme reaction conditions appear first. That is, you want reactions with the lowest temperatures, shortest reaction times, and lowest pressures to appear first. Of the three types of data, temperature is the most important and pressure the least important. To do this, use the following sorting instructions, in this order:

Sort each RXN by >VARIATION>CONDITIONS>TEMP from low to high

Sort each RXN by >VARIATION>CONDITIONS>TIME from low to high

Sort each RXN by >VARIATION>CONDITIONS>PRESSURE from low to high

100.2.5 Sorting by a Combination of Similarity and Other Data (RSim Search Only)

You can sort the results of an RSim search by any combination of structural similarity, transformational similarity, and data in database fields. For example, you might be primarily interested in reactions that are highly similar to the query and that take place at low reaction temperatures. Transformational similarity to the query is more important, so you place the sorting instruction for that data first:

Sort each RXN by >RXNCENTERSIMILARITY from high to low

Sort each RXN by >VARIATION>CONDITIONS>TEMP from low to high

ISIS sorts these search results so that reactions with the highest transformational similarity appear first. If several reactions have the same transformational similarity, you want the reactions with the lowest reaction temperatures to appear first within this group of reactions. To do this, use the following sorting instructions, in this order:

100.2.8 Sorting Variation Subrecords by Yield, Reaction Conditions, and Other Data

You can sort the variation subrecords within each reaction. To do this, you specify the VARIATION parent field in the sorting instruction. For example:

*	You want to sort variation subrecords so that variations that were published most recently appear first:

Sort each RXN>VARIATION by >LITREF>JOURNAL_YEAR from high to low

*	You want to sort variation subrecords so that variations with the least extreme reaction conditions appear first. That is, you want variations with the lowest temperatures, shortest reaction times, and lowest pressures to appear first. Of the three types of data, temperature is the most important and pressure the least important. To do this, use the following sorting instructions, in this order:

Sort each RXN>VARIATION by >CONDITIONS>TEMP from low to high

Sort each RXN>VARIATION by >CONDITIONS>TIME from low to high

Sort each RXN>VARIATION by >CONDITIONS>PRESSURE from low to high

*	You have a list of reactions whose products are a mixture of stereoisomers. You want to sort variation subrecords so that variations with the highest yield of a mixture of stereoisomers appear first (the calculated field TOTAL_PROD_YIELD contains the sum of the yields of individual stereoisomers):

Sort each RXN>VARIATION by >TOTAL_PROD_YIELD from high to low

You can also sort other kinds of subrecords within each reaction. For example, if the reactions on your list produce a mixture of stereoisomers as the product, you might want to sort the product subrecords within each variation so that stereoisomers with the highest yields appear first within each variation subrecord:

Sort each RXN>VARIATION>PRODUCT by >YIELD from high to low

The following sorting instructions sort both variation subrecords and product subrecords by yield (the calculated field TOTAL_PROD_YIELD contains the sum of the yields of individual stereoisomers):

Sort each RXN>VARIATION by >TOTAL_PROD_YIELD from high to low

Sort each RXN>VARIATION>PRODUCT by >YIELD from high to low

100.2.9 Sorting Both Reaction Records and Variation Subrecords

You can sort both reaction records and the variation subrecords within each reaction. For example:

*	You want to sort reaction records and variation subrecords so that those with the lowest reaction temperatures appear first. To do this, use the following sorting instructions:

Sort each RXN by >VARIATION>CONDITIONS>TEMP from low to high

Sort each RXN>VARIATION by >CONDITIONS>TEMP from low to high

Note: For faster sorting times, you can define the calculated field RXN>VARIATION>MIN_TEMP that contains the minimum reaction temperature for each variation. Then, sort reactions and variations by MIN_TEMP:

Sort each RXN by >VARIATION>MIN_TEMP from low to high

Sort each RXN>VARIATION by >MIN_TEMP from low to high

If you do not create the MIN_TEMP calculated field, ISIS creates the equivalent hidden calculated field twice: once when executing the first sorting instruction and once when executing the second sorting instruction. This increases sorting time. For more information on hidden calculated fields, see Section 100.1.6.

*	You want to sort reaction records whose products are a mixture of stereoisomers. You want reactions with the highest total product yield to appear first. If several reactions have the same total product yield, you want reactions with the lowest reaction temperature to appear first. Within each reaction record, you want the variations with the highest total product yield to appear first. To do this, use the following sorting instructions:

Sort each RXN by >VARIATION>TOTAL_PROD_YIELD from high to low

Sort each RXN by >VARIATION>CONDITIONS>TEMP from low to high

Sort each RXN>VARIATION by >TOTAL_PROD_YIELD from high to low


Reaction Components: Sorting Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This request-a-document contains:

*	Basic Concepts	101.1

*	Sorting Examples	101.2

We recommend that you print this 10-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

101.1 Basic Concepts

101.1.1 Flat and Hierarchical Databases

ISIS databases can be either flat or hierarchical. In the following example, the database organization is flat, because the database contains only one level of data:

In this example, MOL is a parent field. Parent fields do not store data, but point to one or more child fields that contain the actual data. In this example, the child fields are STRUCTURE, CAS_NUMBER, MOLECULE_NAME, BOILING_POINT, and DATE. Each record has only one set of data associated with it.

However, your database might have more than one set of data that is associated with a molecule or reaction. Each set of data becomes a branch in a hierarchical database. The following is a portion of a hierarchical reaction database:

In this example, one reaction has several variations associated with it. Each variation, in turn, has several associated literature references and reaction conditions. The result is a hierarchy of three levels. The highest level in the database hierarchy has data associated with a specific reaction: the reaction (RXNSTRUCTURE) and its ID number (RXNREGNO). The middle level in the hierarchy provides data that is associated with a specific variation of the original reaction, such as the variation number (VARIATION_NO). The lowest level in the hierarchy provides the text of a specific literature reference for a given variation (LITTEXT_DATA), and data on reaction conditions (TIME, TEMP, PRESSURE).

Each level of the database has a parent field that points to one or more child fields that store data. In this example, RXN, VARIATION, CONDITIONS, and LITTEXT are parent fields at each level of the hierarchy.

101.1.2 Subrecords

A hierarchical database contains subrecords (subordinate records) that contain separate sets of data within the main record. For example:

*	In a reaction database, each reaction might have several variations associated with it. For example, the yield of a product might vary according to reaction conditions such as reaction temperature, catalyst, and solvent. This information is stored in the variation subrecords within each reaction.

*	In a molecule database, you might have several bottles of each compound. Each batch has its own set of associated test results. Information on each bottle is stored in the bottle subrecords within each molecule record.

Subrecords are defined by parent fields at lower levels of the database. For example, variation subrecords in a reaction database are defined by the VARIATION parent field. Each set of literature references (LITTEXT parent field) or reaction conditions (CONDITIONS parent field) is a subrecord within a variation subrecord:

You can sort subrecords. For example, you might want to sort bottle subrecords within each molecule record so that bottles with the highest amounts are displayed first:

101.1.3 Sorting in Hierarchical Databases

In remote databases only, you can sort records or subrecords by any child field below it in the hierarchy. For example, you can sort reaction records (RXN parent field) by reaction temperature (RXN>VARIATION>CONDITIONS>TEMP).

In local databases, you can sort record or subrecords solely by child fields that are directly attached to the corresponding parent field. For example, you can sort reaction records (RXN parent field) by RXNREGNO, or variation subrecords (VARIATION parent field) by VARIATION_NO.

You can sort records and subrecords by a maximum of three child fields.

You can sort records and subrecords by any of the following types of data: date, integer, real, fixed text, variable text, and range. You cannot sort by the following types of data: structure, reaction, or sketch.

101.1.4 Order of Sorting

The order of sorting can be either of the following:

*	Low to high places the smallest values first (ascending order). Fixed- and variable-text data is sorted in ascending alphanumeric order.

*	High to low places the largest values first (descending order). Fixed- and variable-text data is sorted in descending alphanumeric order.

101.1.5 Sorting Instructions

To specify how to sort your search results, you must create sorting instructions. Each sorting instruction has the following syntax:

Sort each parent-field by child-field from order

Parent-field specifies the records or subrecords to sort, child-field is the field that contains the data by which to sort, and order is either high to low or low to high.

For example, the following sorting instruction sorts reaction records (RXN parent field) so that those with the lowest reaction temperatures appear first:

Sort each RXN by >VARIATION>CONDITIONS>TEMP from low to high

The following sorting instruction sorts variation subrecords (VARIATION parent field) so that variations with the lowest reaction temperatures appear first:

Sort each RXN>VARIATION by >CONDITIONS>TEMP from low to high

The order in which you specify sorting instructions affects sorting. ISIS sorts your records as follows:

1.	ISIS applies the first sorting instruction to all records.

2.	If several records have the same value for the field specified in the first sorting instruction, ISIS uses the second sorting instruction to decide the order.

3.	If several records have the same value for the fields specified in the first two sorting instructions, ISIS uses the third sorting instruction to decide the order.

Consequently, you generally want to place the sorting instruction with the most important data first, so that ISIS sorts all records by that data.

For example, you might want to sort variation subrecords so that variations with the least extreme reaction conditions (lowest reaction temperatures and shortest reaction times) appear first. If reaction temperature is more important, specify sorting instructions, in the following order:

Sort each RXN>VARIATION by >CONDITIONS>TEMP from low to high

Sort each RXN>VARIATION by >CONDITIONS>TIME from low to high

In this example, ISIS sorts the variation subrecords so that variations with the lowest reaction temperatures appear first. If several variations have the same reaction temperatures, ISIS places the variations with the shortest reaction times first.

You can save a set of sorting instructions within your database as a database object. You can also export a set of sorting instructions to a text file on hard disk or floppy. For information on saving sorting instructions, see the step-by-step instructions. Alternatively, click Help > Index, and search for sorting instructions, saving. For information on exporting sorting instructions, see the step-by-step instructions. Alternatively, click Help > Index, and search for sorting instructions, exporting.

101.1.6 Calculated Fields (Remote Databases Only)

In remote databases, you can create calculated fields that allow you to perform calculations on a set of data. For example:

*	Calculate the average or median of several activity measurements of a compound.

*	Count the number of bottles of each compound.

*	Calculate the sum of the yields of all the products of a reaction.

*	Determine the maximum or minimum value in a series, such as the maximum of several activity measurements or the earliest date of synthesis.

The data in a calculated field is not actually stored in the database, but is calculated from existing data. Calculated fields are listed in the database definition with the other fields. You can display the values from calculated fields on your form or use them to sort your search results.

For example, your molecule database might contain test results for the lethality of a compound (expressed as 50% lethal dose, or LD50). In the following example, the parent field LETHAL points to several LD50 values in the child field LD50_RESULT. The calculated field AVG_LD50_RESULT contains the average of all the LD50 values in LD50_RESULT (parentheses around AVG_LD50_RESULT indicate that it is a calculated field):

For information on creating calculated fields, see the step-by-step instructions. Alternatively, click Help > Index, and search for calculated fields, creating.

Note: A calculated field combines multiple instances of data from the same database field. If you want to create calculated values that combine data from different database fields, you need to create a form calculation. A form calculation takes data values from boxes or columns in the form that contain real numbers or integers and performs mathematical operations on the data to obtain a result. The mathematical operations include adding, subtracting multiplying, and dividing data. You see the result when you conduct a search and view the data in the Browse mode. However, you cannot use this data to sort search results. For more information on form calculations, see the step-by-step instructions. Alternatively, choose Help > Index, and search for forms, calculation.

For more information and examples of calculated fields, see the Request-A-Document Calculated Fields: Concepts/Examples.

101.1.7 Derived Data

For some types of searches, ISIS derives specific kinds of data from the reactions or structures that it retrieves during the search. You can display this derived data in a form and use it for sorting, just like data in database fields. The fields that contain derived data also appear in the database definition.

Reaction Similarity (RSim) searches, Molecule Similarity (MSim) searches, and Conformationally Flexible Substructure (CFS) searches all produce derived data. For more information on derived data, see the step-by-step instructions for the search of your choice.

Note: If you want to sort by derived data, we strongly recommend that you define your sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search ISIS must repeat the search to calculate the data.

101.1.8 Performance Considerations in Sorting

The time required for sorting depends on the factors described below.

Number of Records or Subrecords

The time required for sorting depends on the number of records (or subrecords) that you sort. The time required increases approximately as N log N, where N is the number of records (or subrecords) that you sort.

Calculated Fields

Sorting by data in calculated fields can require more time than sorting by data in other fields that are at the same level in the database hierarchy, because ISIS requires time to perform the calculations.

Number of Hierarchical Levels

Generally, the more hierarchical levels that separate a parent field from a given child field in the sorting instruction, the more time ISIS requires to sort by that child field. For example, sorting reaction records (RXN parent field) by RXN>VARIATION>PRODUCT>YIELD can require more time than sorting by RXN>RXNREGNO. This is because ISIS automatically creates hidden calculated fields that it uses to sort by data at lower levels of the hierarchy. Consequently, ISIS requires time to perform the calculations for the hidden calculated fields.

ISIS uses the following rules to create hidden calculated fields from sorting instructions:

*	If the order of sorting is high to low, ISIS calculates the maximum value of the field at each level of the database.

*	If the order of sorting is low to high, ISIS calculates the minimum value of the field at each level of the database.

For example, consider the following sorting instruction:

Sort each RXN by >VARIATION>PRODUCT>YIELD from high to low

To execute this sorting instruction, ISIS automatically creates two hidden calculated fields:

*	The first hidden field is a child of VARIATION, and contains the maximum value of RXN>VARIATION>PRODUCT>YIELD for each variation.

*	The second hidden field is a child of RXN, and contains the maximum value of the first calculated field for each reaction.

The following figure shows these hidden fields, which we call MAX1 and MAX2 (Parentheses () around the names show that they are calculated fields, and dotted lines in the hierarchy show that the fields are hidden):

ISIS deletes hidden calculated fields immediately after sorting. Therefore, you never see hidden calculated fields in the database definition.

Using Calculated Fields to Decrease Sorting Times

If you sort both records and subrecords by the same data, you can reduce sorting times by creating calculated fields at lower levels in the database hierarchy. For example, you might want to sort both reactions and variation subrecords by product yield. The sorting instructions are:

Sort each RXN by >VARIATION>PRODUCT>YIELD from high to low

Sort each RXN>VARIATION by >PRODUCT>YIELD from high to low

To execute the first sorting instruction, ISIS creates one hidden calculated field that contains the maximum value of YIELD (MAX1 in the previous example), and another that contains the maximum value of MAX1 (MAX2 in the previous example). To execute the second sorting instruction, ISIS creates a calculated field that contains the maximum value of YIELD. This hidden field contains the same data that is in the MAX1 hidden field. Consequently, ISIS creates the MAX1 field twice: once when executing the first sorting instruction and once when executing the second sorting instruction. To eliminate this duplication, and to decrease sorting time, create the calculated field MAX1 explicitly (in the following figure, the solid line in the hierarchy indicates that MAX1 is not hidden):

Then, use the calculated field MAX1 in the sorting instructions:

Sort each RXN by >VARIATION>MAX1 from high to low

Sort each RXN>VARIATION by >MAX1 from high to low

To execute these sorting instructions, ISIS performs the calculations for the MAX1 field only once, and uses this information for sorting both reactions and variations.

101.1.9 Saving and Exporting Sorted Search Results

If you save or export search results, ISIS preserves the order of the sorted records. However, ISIS doe not preserve the order of variation subrecords or other subrecords that you sort. For information on saving a list of records, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for search results, saving remote. For information on exporting a list of records, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for search results, exporting remote.

You can preserve the sorted order of both the records and subrecords by exporting your search results to a local database. For more information, see the step-by-step instructions. Alternatively, choose Help > Index, and search for search results, exporting to local database.

101.2 Sorting Examples

A reaction component is a molecule that participates in a reaction as a reactant, product, solvent, or catalyst. This section contains typical examples for sorting results of searches for reaction components. These examples use the ISISRX demo database.

101.2.1 Sorting by Structural Similarity (MSim Search Only)

When you execute a Molecule Similarity (MSim) search for a particular reaction component, ISIS calculates the value of structural similarity for the corresponding reaction component in the reactions that it retrieves. For example, you perform an MSim search to find reaction records with products that are similar to the product in your query. You want to sort the reaction records so that products with the highest similarity to the product molecule in your query appear first on the list. To do this, use the following sorting instruction:

Sort each RXN by >PRODUCT>MOL>MOLSIMILARITY from high to low

Note: The similarity data that ISIS creates during an MSim search disappears when you perform another search. To ensure that similarity data is available for sorting, we strongly recommend that you sort your search results immediately after the search. To do this, we recommend that you define your sorting instructions before the search, and sort your search results automatically after the search. For information on automatic sorting, see the step-by-step instructions for the MSim search. Alternatively, choose Help > Index, and search for MSim, how to/examples.

101.2.2 Sorting by a Combination of Similarity and Other Data (MSim Search Only)

You can sort the results of an MSim search by any combination of structural similarity and data in database fields. For example, you perform an MSim search to find reaction records with products that are similar to the product in your query. You are interested in reactions whose products are highly similar to the product molecule in your query, and that have low reaction temperatures. You are more interested in similarity than in reaction conditions. To do this, use the following sorting instructions, in this order:

Sort each RXN by >PRODUCT>MOL>MOLSIMILARITY from high to low

Sort each RXN by >VARIATION>CONDITIONS>TEMP from low to high

101.2.3 Sorting by the Yield of the Principal Product

If the reactions on your list have only one principal product, you can sort reaction records so that reactions with the highest yields appear first:

Sort each RXN by >VARIATION>PRODUCT>YIELD from high to low

101.2.4 Sorting by the Total Yield of a Mixture of Stereoisomers

If the reactions that you retrieve can produce a mixture of stereoisomers as the product, you might want to sort by the total yield over all stereoisomers. To do this, you need to define a calculated field that contains the sum of the yields of individual products. In the following database hierarchy, the calculated field TOTAL_PROD_YIELD contains the sum of the yields of individual stereoisomers within a variation:

To sort by total yield of all stereoisomers, use the following sorting instruction:

Sort each RXN by >VARIATION>TOTAL_PROD_YIELD from high to low

101.2.4 Sorting by Reaction Conditions

You can sort reaction records by one or more reaction conditions, such as temperature, reaction time, and pressure. For example:

*	You want to sort reaction records so that reactions that require the shortest reaction times appear first. To do this, use the following sorting instruction:

Sort each RXN by >VARIATION>CONDITIONS>TIME from low to high

*	You want to sort reaction records so that reactions that require the lowest reaction temperatures appear first. To do this, use the following sorting instruction:

Sort each RXN by >VARIATION>CONDITIONS>TEMP from low to high

*	You want to sort reaction records so that reactions with the lowest reaction temperatures appear first. If several reactions have the same reaction temperature, you want the reactions with the shortest reaction times to appear first. To do this, use the following sorting instructions, in this order:

Sort each RXN by >VARIATION>CONDITIONS>TEMP from low to high

Sort each RXN by >VARIATION>CONDITIONS>TIME from low to high

101.2.6 Sorting Variation Subrecords by Yield, Reaction Conditions, and Other Data

You can sort the variation subrecords within each reaction. To do this, you specify the VARIATION parent field in the sorting instruction. For example:

*	You want to sort variation subrecords so that variations that were published most recently appear first:

Sort each RXN>VARIATION by >LITREF>JOURNAL_YEAR from high to low

*	You have a list of reactions whose products are a mixture of stereoisomers. You want to sort variation subrecords so that variations with the highest yield of all stereoisomers appear first (the calculated field TOTAL_PROD_YIELD contains the sum of the yields of individual stereoisomers):

Sort each RXN>VARIATION by >TOTAL_PROD_YIELD from high to low

*	You want to sort variation subrecords so that variations with the lowest reaction temperatures appear first. If several variations have the same reaction temperature, you want the variations with the shortest reaction times to appear first. To do this, use the following sorting instructions, in this order:

Sort each RXN>VARIATION by >CONDITIONS>TEMP from low to high

Sort each RXN>VARIATION by >CONDITIONS>TIME from low to high

You can also sort other kinds of subrecords within each reaction. For example, if the reactions on your list produce a mixture of stereoisomers as the product, you might want to sort the product subrecords within each variation so that stereoisomers with the highest yields appear first within each variation subrecord:

Sort each RXN>VARIATION>PRODUCT by >YIELD from high to low

The following sorting instructions sort variation subrecords by total product subrecords by yield:

Sort each RXN>VARIATION by >TOTAL_PROD_YIELD from high to low

Sort each RXN>VARIATION>PRODUCT by >YIELD from high to low

101.2.7 Sorting Both Reaction Records and Variation Subrecords

You can sort both reaction records and the variation subrecords within each reaction. For example:

*	You want to sort reaction records and variation subrecords so that those with the lowest reaction temperatures appear first. To do this, use the following sorting instructions:

Sort each RXN by >VARIATION>CONDITIONS>TEMP from low to high

Sort each RXN>VARIATION by >CONDITIONS>TEMP from low to high

*	You want to sort reaction records so that reactions with the highest total product yield appear first. If several reactions have the same total product yield, you want reactions with the lowest reaction temperature to appear first. Within each reaction record, you want the variations with the highest total product yield to appear first.

Sort each RXN by >VARIATION>TOTAL_PROD_YIELD from high to low

Sort each RXN by >VARIATION>CONDITIONS>TEMP from low to high

Sort each RXN>VARIATION by >TOTAL_PROD_YIELD from high to low


Molecules: Sorting Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This request-a-document contains:

*	Basic Concepts	102.1

*	Sorting Examples	102.2

We recommend that you print this 11-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

102.1 Basic Concepts

102.1.1 Flat and Hierarchical Databases

ISIS databases can be either flat or hierarchical. In the following example, the database organization is flat, because the database contains only one level of data:

In this example, MOL is a parent field. Parent fields do not store data, but point to one or more child fields that contain the actual data. In this example, the child fields are STRUCTURE, CAS_NUMBER, MOLECULE_NAME, BOILING_POINT, and DATE. Each record has only one set of data associated with it.

However, your database might have more than one set of data that is associated with a molecule or reaction. Each set of data becomes a branch in a hierarchical database. The following is a portion of a hierarchical reaction database:

In this example, one reaction has several variations associated with it. Each variation, in turn, has several associated literature references and reaction conditions. The result is a hierarchy of three levels. The highest level in the database hierarchy has data associated with a specific reaction: the reaction (RXNSTRUCTURE) and its ID number (RXNREGNO). The middle level in the hierarchy provides data that is associated with a specific variation of the original reaction, such as the variation number (VARIATION_NO). The lowest level in the hierarchy provides the text of a specific literature reference for a given variation (LITTEXT_DATA), and data on reaction conditions (TIME, TEMP, PRESSURE).

Each level of the database has a parent field that points to one or more child fields that store data. In this example, RXN, VARIATION, CONDITIONS, and LITTEXT are parent fields at each level of the hierarchy.

102.1.2 Subrecords

A hierarchical database contains subrecords (subordinate records) that contain separate sets of data within the main record. For example:

*	In a reaction database, each reaction might have several variations associated with it. For example, the yield of a product might vary according to reaction conditions such as reaction temperature, catalyst, and solvent. This information is stored in the variation subrecords within each reaction.

*	In a molecule database, you might have several bottles of each compound. Each batch has its own set of associated test results. Information on each bottle is stored in the bottle subrecords within each molecule record.

Subrecords are defined by parent fields at lower levels of the database. For example, variation subrecords in a reaction database are defined by the VARIATION parent field. Each set of literature references (LITTEXT parent field) or reaction conditions (CONDITIONS parent field) is a subrecord within a variation subrecord:

You can sort subrecords. For example, you might want to sort bottle subrecords within each molecule record so that bottles with the highest amounts are displayed first:

102.1.3 Sorting in Hierarchical Databases

In remote databases only, you can sort records or subrecords by any child field below it in the hierarchy. For example, you can sort reaction records (RXN parent field) by reaction temperature (RXN>VARIATION>CONDITIONS>TEMP).

In local databases, you can sort record or subrecords solely by child fields that are directly attached to the corresponding parent field. For example, you can sort reaction records (RXN parent field) by RXNREGNO, or variation subrecords (VARIATION parent field) by VARIATION_NO.

You can sort records and subrecords by a maximum of three child fields.

You can sort records and subrecords by any of the following types of data: date, integer, real, fixed text, variable text, and range. You cannot sort by the following types of data: structure, reaction, or sketch.

102.1.4 Order of Sorting

The order of sorting can be either of the following:

*	Low to high places the smallest values first (ascending order). Fixed- and variable-text data is sorted in ascending alphanumeric order.

*	High to low places the largest values first (descending order). Fixed- and variable-text data is sorted in descending alphanumeric order.

102.1.5 Sorting Instructions

To specify how to sort your search results, you must create sorting instructions. Each sorting instruction has the following syntax:

Sort each parent-field by child-field from order

Parent-field specifies the records or subrecords to sort, child-field is the field that contains the data by which to sort, and order is either high to low or low to high.

For example, the following sorting instruction sorts reaction records (RXN parent field) so that those with the lowest reaction temperatures appear first:

Sort each RXN by >VARIATION>CONDITIONS>TEMP from low to high

The following sorting instruction sorts variation subrecords (VARIATION parent field) so that variations with the lowest reaction temperatures appear first:

Sort each RXN>VARIATION by >CONDITIONS>TEMP from low to high

The order in which you specify sorting instructions affects sorting. ISIS sorts your records as follows:

1.	ISIS applies the first sorting instruction to all records.

2.	If several records have the same value for the field specified in the first sorting instruction, ISIS uses the second sorting instruction to decide the order.

3.	If several records have the same value for the fields specified in the first two sorting instructions, ISIS uses the third sorting instruction to decide the order.

Consequently, you generally want to place the sorting instruction with the most important data first, so that ISIS sorts all records by that data.

For example, you might want to sort variation subrecords so that variations with the least extreme reaction conditions (lowest reaction temperatures and shortest reaction times) appear first. If reaction temperature is more important, specify sorting instructions, in the following order:

Sort each RXN>VARIATION by >CONDITIONS>TEMP from low to high

Sort each RXN>VARIATION by >CONDITIONS>TIME from low to high

In this example, ISIS sorts the variation subrecords so that variations with the lowest reaction temperatures appear first. If several variations have the same reaction temperatures, ISIS places the variations with the shortest reaction times first.

You can save a set of sorting instructions within your database as a database object. You can also export a set of sorting instructions to a text file on hard disk or floppy. For information on saving sorting instructions, see the step-by-step instructions. Alternatively, click Help > Index, and search for sorting instructions, saving. For information on exporting sorting instructions, see the step-by-step instructions. Alternatively, click Help > Index, and search for sorting instructions, exporting.

102.1.6 Calculated Fields (Remote Databases Only)

In remote databases, you can create calculated fields that allow you to perform calculations on a set of data. For example:

*	Calculate the average or median of several activity measurements of a compound.

*	Count the number of bottles of each compound.

*	Calculate the sum of the yields of all the products of a reaction.

*	Determine the maximum or minimum value in a series, such as the maximum of several activity measurements or the earliest date of synthesis.

The data in a calculated field is not actually stored in the database, but is calculated from existing data. Calculated fields are listed in the database definition with the other fields. You can display the values from calculated fields on your form or use them to sort your search results.

For example, your molecule database might contain test results for the lethality of a compound (expressed as 50% lethal dose, or LD50). In the following example, the parent field LETHAL points to several LD50 values in the child field LD50_RESULT. The calculated field AVG_LD50_RESULT contains the average of all the LD50 values in LD50_RESULT (parentheses around AVG_LD50_RESULT indicate that it is a calculated field):

For information on creating calculated fields, see the step-by-step instructions. Alternatively, click Help > Index, and search for calculated fields, creating.

Note: A calculated field combines multiple instances of data from the same database field. If you want to create calculated values that combine data from different database fields, you need to create a form calculation. A form calculation takes data values from boxes or columns in the form that contain real numbers or integers and performs mathematical operations on the data to obtain a result. The mathematical operations include adding, subtracting multiplying, and dividing data. You see the result when you conduct a search and view the data in the Browse mode. However, you cannot use this data to sort search results. For more information on form calculations, see the step-by-step instructions. Alternatively, choose Help > Index, and search for forms, calculation.

For more information and examples of calculated fields, see the Request-A-Document Calculated Fields: Concepts/Examples.

102.1.7 Derived Data

For some types of searches, ISIS derives specific kinds of data from the reactions or structures that it retrieves during the search. You can display this derived data in a form and use it for sorting, just like data in database fields. The fields that contain derived data also appear in the database definition.

Reaction Similarity (RSim) searches, Molecule Similarity (MSim) searches, and Conformationally Flexible Substructure (CFS) searches all produce derived data. For more information on derived data, see the step-by-step instructions for the search of your choice.

Note: If you want to sort by derived data, we strongly recommend that you define your sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search ISIS must repeat the search to calculate the data.

102.1.8 Performance Considerations in Sorting

The time required for sorting depends on the factors described below.

Number of Records or Subrecords

The time required for sorting depends on the number of records (or subrecords) that you sort. The time required increases approximately as N log N, where N is the number of records (or subrecords) that you sort.

Calculated Fields

Sorting by data in calculated fields can require more time than sorting by data in other fields that are at the same level in the database hierarchy, because ISIS requires time to perform the calculations.

Number of Hierarchical Levels

Generally, the more hierarchical levels that separate a parent field from a given child field in the sorting instruction, the more time ISIS requires to sort by that child field. For example, sorting reaction records (RXN parent field) by RXN>VARIATION>PRODUCT>YIELD can require more time than sorting by RXN>RXNREGNO. This is because ISIS automatically creates hidden calculated fields that it uses to sort by data at lower levels of the hierarchy. Consequently, ISIS requires time to perform the calculations for the hidden calculated fields.

ISIS uses the following rules to create hidden calculated fields from sorting instructions:

*	If the order of sorting is high to low, ISIS calculates the maximum value of the field at each level of the database.

*	If the order of sorting is low to high, ISIS calculates the minimum value of the field at each level of the database.

For example, consider the following sorting instruction:

Sort each RXN by >VARIATION>PRODUCT>YIELD from high to low

To execute this sorting instruction, ISIS automatically creates two hidden calculated fields:

*	The first hidden field is a child of VARIATION, and contains the maximum value of RXN>VARIATION>PRODUCT>YIELD for each variation.

*	The second hidden field is a child of RXN, and contains the maximum value of the first calculated field for each reaction.

The following figure shows these hidden fields, which we call MAX1 and MAX2 (Parentheses () around the names show that they are calculated fields, and dotted lines in the hierarchy show that the fields are hidden):

ISIS deletes hidden calculated fields immediately after sorting. Therefore, you never see hidden calculated fields in the database definition.

Using Calculated Fields to Decrease Sorting Times

If you sort both records and subrecords by the same data, you can reduce sorting times by creating calculated fields at lower levels in the database hierarchy. For example, you might want to sort both reactions and variation subrecords by product yield. The sorting instructions are:

Sort each RXN by >VARIATION>PRODUCT>YIELD from high to low

Sort each RXN>VARIATION by >PRODUCT>YIELD from high to low

To execute the first sorting instruction, ISIS creates one hidden calculated field that contains the maximum value of YIELD (MAX1 in the previous example), and another that contains the maximum value of MAX1 (MAX2 in the previous example). To execute the second sorting instruction, ISIS creates a calculated field that contains the maximum value of YIELD. This hidden field contains the same data that is in the MAX1 hidden field. Consequently, ISIS creates the MAX1 field twice: once when executing the first sorting instruction and once when executing the second sorting instruction. To eliminate this duplication, and to decrease sorting time, create the calculated field MAX1 explicitly (in the following figure, the solid line in the hierarchy indicates that MAX1 is not hidden):

Then, use the calculated field MAX1 in the sorting instructions:

Sort each RXN by >VARIATION>MAX1 from high to low

Sort each RXN>VARIATION by >MAX1 from high to low

To execute these sorting instructions, ISIS performs the calculations for the MAX1 field only once, and uses this information for sorting both reactions and variations.

102.1.9 Saving and Exporting Sorted Search Results

If you save or export search results, ISIS preserves the order of the sorted records. However, ISIS doe not preserve the order of variation subrecords or other subrecords that you sort. For information on saving a list of records, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for search results, saving remote. For information on exporting a list of records, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for search results, exporting remote.

You can preserve the sorted order of both the records and subrecords by exporting your search results to a local database. For more information, see the step-by-step instructions. Alternatively, choose Help > Index, and search for search results, exporting to local database.

102.2 Sorting Examples

This section contains typical examples of sorting molecule records.

102.2.1 Sorting Molecule Records by Structural Similarity (MSim Search Only)

In a Molecule Similarity (MSim) search, you specify the structural similarity value for the molecule in your query. For each molecule that ISIS retrieves, ISIS calculates the structural similarity of that molecule to the molecule in your query. You can use these structural similarity values to sort your search results.

You can perform an MSim search in a database hierarchy with 2D structures at the top level:

The similarity data that ISIS derives during the search is in the derived field MOLSIMILARITY. To sort molecule records so that molecules with the highest similarity to the query molecule appear first, you use the following sorting instruction:

Sort each MOL by >MOLSIMILARITY from high to low

If you are performing a similarity search as part of a series of 2D and 3D searches, you might have a database hierarchy with 3D structures (models) at the top level:

To sort 3D structure records so that molecules with the highest similarity to the query appear first, use the following sorting instruction:

Sort each MODEL by >MOL>MOLSIMILARITY from high to low

Notes (1) To determine the type of database hierarchy that you have, print or view a list of the fields in your database. To do this, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for database fields, viewing. (2) The similarity data that ISIS creates during an MSim search disappears when you perform another search. Therefore, if you want to sort your search results by similarity data, we strongly recommend that you sort immediately after the search. For more information, follow the step-by-step instructions for the MSim search. Alternatively, choose Help > Index, and search for MSim, how-to/examples.

102.2.2 Sorting Molecule Records by Molecular Weight

You can sort molecule records by data in any database field. For example, you might perform a Search By Form (SBF) to find records with a specific type of biological activity. You might want to sort your records so that compounds with the lowest molecular weight appear first on the list. Use the following sorting instruction:

Sort each MOL by >MOL.WEIGHT from low to high

If your database has 3D structures (models) at the top level of the hierarchy, use the following sorting instruction:

Sort each MODEL by >MOL>MOL.WEIGHT from low to high

102.2.3 Sorting Molecule Records by Total Available Amount of a Compound

You can sort molecule records by data in calculated fields. For example, you might know that you have several bottles of each compound on your list. You now want to sort your search results so that compounds with the highest total amount appear first on your list.

Your database structure might be similar to that of the ISISDEMO demo database:

The highest level of the hierarchy contains data that is associated with a specific molecule, such as the molecular structure and corporate ID. The second level of the hierarchy (DEMO_INVENTORY parent field) contains data that is associated with each bottle of that compound, such as the bottle ID, the location (STOCKROOM), and the amount in of the compound in the bottle (BOTTLE_AMT). The third level of the hierarchy (DEMO_CHECKOUT parent field) contains information on the checkout record of each bottle, such as the chemist who used it and the dates that the bottle was checked in and checked out (CHECK_IN and CHECK_OUT, respectively).

To find the total amount of each compound, you need to find the sum of the amounts in the individual bottles. This data is in the field BOTTLE_AMT. To obtain the total amount, you define the calculated field TOTAL_AMOUNT as the sum of the values of BOTTLE_AMT. TOTAL_AMOUNT is a child of MOL, because each compound has only one total amount associated with it:

To sort search results so that compounds with the highest total amounts appear first, use the following sorting instruction:

Sort each MOL by >TOTAL_AMT from high to low

102.2.4 Sorting Molecule Records by Activity Index and Molecular Weight

MDL databases such as MDDR contain an activity index that classifies compounds according to the type of biological activity. You can sort molecule records so that compounds with similar activity are grouped together on your list. Within each set of compounds with the same activity, you might want compounds with the lowest molecular weights to appear first. To do this, you specify the sorting instruction for activity index first:

Sort each MOL by >ACTIVITY>ACTIVITY_INDEX from low to high

Sort each MOL by >MOL.WEIGHT from low to high

If your database has 3D structures (models) at the top of the hierarchy, use the following sorting instructions:

Sort each MODEL by >MOL>ACTIVITY>ACTIVITY_INDEX from low to high

Sort each MODEL by >MOL>MOL.WEIGHT from low to high

102.2.5 Sorting Molecule Records by a Combination of Structural Similarity and Other Data (MSim Search Only)

You might want to sort the molecule records from an MSim search by both structural similarity and the data in one or more database fields. For example, you might want to sort search results from the MDL database MDDR by similarity and activity index. You want compounds with similar activity indexes to appear together on the list, and you want compounds with the highest structural similarity to the query molecule to appear first. Activity index is more important than similarity, so you use the following sorting instructions, in this order:

Sort each MOL by >ACTIVITY>ACTIVITY_INDEX from low to high

Sort each MOL by >MOLSIMILARITY from high to low

If your database has 3D structures (models) at the top of the hierarchy, use the following sorting instructions:

Sort each MODEL by >MOL>ACTIVITY>ACTIVITY_INDEX from low to high

Sort each MODEL by >MOL>MOLSIMILARITY from high to low

102.2.6 Sorting Subrecords Within Each Molecule Record

A subrecord (subordinate record) is a portion of the data within a record that is grouped under a specific parent field in the database hierarchy. For example, the following is a portion of the hierarchy of the ISISDEMO demo database:

In this hierarchy, you can have several bottles of each compound. Each bottle can be checked out multiple times by different chemists. Each compound can also have several different names. The highest level in the database hierarchy (MOL) has data on a specific compound. The middle level of the hierarchy has two branches. The first branch (ALTERNATE_NAMES) provides the alternate names of the compound. The other branch of the hierarchy (DEMO_INVENTORY) provides data on a specific bottle of each compound, such as bottle ID, the amount of compound in each bottle (BOTTLE_AMT), and the purchase date. This branch of the hierarchy has a third level of information (DEMO_CHECKOUT) that provides the dates that each CHEMIST checked out a particular bottle (CHECK_IN and CHECK_OUT, respectively).

The parent fields in the two main branches of the hierarchy (ALTERNATE_NAMES and DEMO_INVENTORY) define subrecords within the main database hierarchy. The DEMO_CHECKOUT parent field, in turn, defines subrecords within the DEMO_INVENTORY subrecords.

Sorting Alternate Names in Alphanumeric Order

If you have a table in your form that displays the alternate names for each compound, you might want to display these names in alphanumeric order. To do this, create a sorting instruction that sorts the ALTERNATE_NAMES subrecords by NAME:

Sort each ALTERNATE_NAMES by >NAME from low to high

Sorting Bottles by Amount

You might want to sort the bottles in the DEMO_INVENTORY subrecords so that bottles that contain the largest amounts appear first. The following sorting instruction does this:

Sort each DEMO_INVENTORY by >BOTTLE_AMT from high to low


3D Structures: Sorting Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This request-a-document contains:

*	Basic Concepts	103.1

*	Sorting Examples	103.2

We recommend that you print this 10-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

103.1 Basic Concepts

103.1.1 Flat and Hierarchical Databases

ISIS databases can be either flat or hierarchical. In the following example, the database organization is flat, because the database contains only one level of data:

In this example, MOL is a parent field. Parent fields do not store data, but point to one or more child fields that contain the actual data. In this example, the child fields are STRUCTURE, CAS_NUMBER, MOLECULE_NAME, BOILING_POINT, and DATE. Each record has only one set of data associated with it.

However, your database might have more than one set of data that is associated with a molecule or reaction. Each set of data becomes a branch in a hierarchical database. The following is a portion of a hierarchical reaction database:

In this example, one reaction has several variations associated with it. Each variation, in turn, has several associated literature references and reaction conditions. The result is a hierarchy of three levels. The highest level in the database hierarchy has data associated with a specific reaction: the reaction (RXNSTRUCTURE) and its ID number (RXNREGNO). The middle level in the hierarchy provides data that is associated with a specific variation of the original reaction, such as the variation number (VARIATION_NO). The lowest level in the hierarchy provides the text of a specific literature reference for a given variation (LITTEXT_DATA), and data on reaction conditions (TIME, TEMP, PRESSURE).

Each level of the database has a parent field that points to one or more child fields that store data. In this example, RXN, VARIATION, CONDITIONS, and LITTEXT are parent fields at each level of the hierarchy.

103.1.2 Subrecords

A hierarchical database contains subrecords (subordinate records) that contain separate sets of data within the main record. For example:

*	In a reaction database, each reaction might have several variations associated with it. For example, the yield of a product might vary according to reaction conditions such as reaction temperature, catalyst, and solvent. This information is stored in the variation subrecords within each reaction.

*	In a molecule database, you might have several bottles of each compound. Each batch has its own set of associated test results. Information on each bottle is stored in the bottle subrecords within each molecule record.

Subrecords are defined by parent fields at lower levels of the database. For example, variation subrecords in a reaction database are defined by the VARIATION parent field. Each set of literature references (LITTEXT parent field) or reaction conditions (CONDITIONS parent field) is a subrecord within a variation subrecord:

You can sort subrecords. For example, you might want to sort bottle subrecords within each molecule record so that bottles with the highest amounts are displayed first:

103.1.3 Sorting in Hierarchical Databases

In remote databases only, you can sort records or subrecords by any child field below it in the hierarchy. For example, you can sort reaction records (RXN parent field) by reaction temperature (RXN>VARIATION>CONDITIONS>TEMP).

In local databases, you can sort record or subrecords solely by child fields that are directly attached to the corresponding parent field. For example, you can sort reaction records (RXN parent field) by RXNREGNO, or variation subrecords (VARIATION parent field) by VARIATION_NO.

You can sort records and subrecords by a maximum of three child fields.

You can sort records and subrecords by any of the following types of data: date, integer, real, fixed text, variable text, and range. You cannot sort by the following types of data: structure, reaction, or sketch.

103.1.4 Order of Sorting

The order of sorting can be either of the following:

*	Low to high places the smallest values first (ascending order). Fixed- and variable-text data is sorted in ascending alphanumeric order.

*	High to low places the largest values first (descending order). Fixed- and variable-text data is sorted in descending alphanumeric order.

103.1.5 Sorting Instructions

To specify how to sort your search results, you must create sorting instructions. Each sorting instruction has the following syntax:

Sort each parent-field by child-field from order

Parent-field specifies the records or subrecords to sort, child-field is the field that contains the data by which to sort, and order is either high to low or low to high.

For example, the following sorting instruction sorts reaction records (RXN parent field) so that those with the lowest reaction temperatures appear first:

Sort each RXN by >VARIATION>CONDITIONS>TEMP from low to high

The following sorting instruction sorts variation subrecords (VARIATION parent field) so that variations with the lowest reaction temperatures appear first:

Sort each RXN>VARIATION by >CONDITIONS>TEMP from low to high

The order in which you specify sorting instructions affects sorting. ISIS sorts your records as follows:

1.	ISIS applies the first sorting instruction to all records.

2.	If several records have the same value for the field specified in the first sorting instruction, ISIS uses the second sorting instruction to decide the order.

3.	If several records have the same value for the fields specified in the first two sorting instructions, ISIS uses the third sorting instruction to decide the order.

Consequently, you generally want to place the sorting instruction with the most important data first, so that ISIS sorts all records by that data.

For example, you might want to sort variation subrecords so that variations with the least extreme reaction conditions (lowest reaction temperatures and shortest reaction times) appear first. If reaction temperature is more important, specify sorting instructions, in the following order:

Sort each RXN>VARIATION by >CONDITIONS>TEMP from low to high

Sort each RXN>VARIATION by >CONDITIONS>TIME from low to high

In this example, ISIS sorts the variation subrecords so that variations with the lowest reaction temperatures appear first. If several variations have the same reaction temperatures, ISIS places the variations with the shortest reaction times first.

You can save a set of sorting instructions within your database as a database object. You can also export a set of sorting instructions to a text file on hard disk or floppy. For information on saving sorting instructions, see the step-by-step instructions. Alternatively, click Help > Index, and search for sorting instructions, saving. For information on exporting sorting instructions, see the step-by-step instructions. Alternatively, click Help > Index, and search for sorting instructions, exporting.

103.1.6 Calculated Fields (Remote Databases Only)

In remote databases, you can create calculated fields that allow you to perform calculations on a set of data. For example:

*	Calculate the average or median of several activity measurements of a compound.

*	Count the number of bottles of each compound.

*	Calculate the sum of the yields of all the products of a reaction.

*	Determine the maximum or minimum value in a series, such as the maximum of several activity measurements or the earliest date of synthesis.

The data in a calculated field is not actually stored in the database, but is calculated from existing data. Calculated fields are listed in the database definition with the other fields. You can display the values from calculated fields on your form or use them to sort your search results.

For example, your molecule database might contain test results for the lethality of a compound (expressed as 50% lethal dose, or LD50). In the following example, the parent field LETHAL points to several LD50 values in the child field LD50_RESULT. The calculated field AVG_LD50_RESULT contains the average of all the LD50 values in LD50_RESULT (parentheses around AVG_LD50_RESULT indicate that it is a calculated field):

For information on creating calculated fields, see the step-by-step instructions. Alternatively, click Help > Index, and search for calculated fields, creating.

Note: A calculated field combines multiple instances of data from the same database field. If you want to create calculated values that combine data from different database fields, you need to create a form calculation. A form calculation takes data values from boxes or columns in the form that contain real numbers or integers and performs mathematical operations on the data to obtain a result. The mathematical operations include adding, subtracting multiplying, and dividing data. You see the result when you conduct a search and view the data in the Browse mode. However, you cannot use this data to sort search results. For more information on form calculations, see the step-by-step instructions. Alternatively, choose Help > Index, and search for forms, calculation.

For more information and examples of calculated fields, see the Request-A-Document Calculated Fields: Concepts/Examples.

103.1.7 Derived Data

For some types of searches, ISIS derives specific kinds of data from the reactions or structures that it retrieves during the search. You can display this derived data in a form and use it for sorting, just like data in database fields. The fields that contain derived data also appear in the database definition.

Reaction Similarity (RSim) searches, Molecule Similarity (MSim) searches, and Conformationally Flexible Substructure (CFS) searches all produce derived data. For more information on derived data, see the step-by-step instructions for the search of your choice.

Note: If you want to sort by derived data, we strongly recommend that you define your sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search ISIS must repeat the search to calculate the data.

103.1.8 Performance Considerations in Sorting

The time required for sorting depends on the factors described below.

Number of Records or Subrecords

The time required for sorting depends on the number of records (or subrecords) that you sort. The time required increases approximately as N log N, where N is the number of records (or subrecords) that you sort.

Calculated Fields

Sorting by data in calculated fields can require more time than sorting by data in other fields that are at the same level in the database hierarchy, because ISIS requires time to perform the calculations.

Number of Hierarchical Levels

Generally, the more hierarchical levels that separate a parent field from a given child field in the sorting instruction, the more time ISIS requires to sort by that child field. For example, sorting reaction records (RXN parent field) by RXN>VARIATION>PRODUCT>YIELD can require more time than sorting by RXN>RXNREGNO. This is because ISIS automatically creates hidden calculated fields that it uses to sort by data at lower levels of the hierarchy. Consequently, ISIS requires time to perform the calculations for the hidden calculated fields.

ISIS uses the following rules to create hidden calculated fields from sorting instructions:

*	If the order of sorting is high to low, ISIS calculates the maximum value of the field at each level of the database.

*	If the order of sorting is low to high, ISIS calculates the minimum value of the field at each level of the database.

For example, consider the following sorting instruction:

Sort each RXN by >VARIATION>PRODUCT>YIELD from high to low

To execute this sorting instruction, ISIS automatically creates two hidden calculated fields:

*	The first hidden field is a child of VARIATION, and contains the maximum value of RXN>VARIATION>PRODUCT>YIELD for each variation.

*	The second hidden field is a child of RXN, and contains the maximum value of the first calculated field for each reaction.

The following figure shows these hidden fields, which we call MAX1 and MAX2 (Parentheses () around the names show that they are calculated fields, and dotted lines in the hierarchy show that the fields are hidden):

ISIS deletes hidden calculated fields immediately after sorting. Therefore, you never see hidden calculated fields in the database definition.

Using Calculated Fields to Decrease Sorting Times

If you sort both records and subrecords by the same data, you can reduce sorting times by creating calculated fields at lower levels in the database hierarchy. For example, you might want to sort both reactions and variation subrecords by product yield. The sorting instructions are:

Sort each RXN by >VARIATION>PRODUCT>YIELD from high to low

Sort each RXN>VARIATION by >PRODUCT>YIELD from high to low

To execute the first sorting instruction, ISIS creates one hidden calculated field that contains the maximum value of YIELD (MAX1 in the previous example), and another that contains the maximum value of MAX1 (MAX2 in the previous example). To execute the second sorting instruction, ISIS creates a calculated field that contains the maximum value of YIELD. This hidden field contains the same data that is in the MAX1 hidden field. Consequently, ISIS creates the MAX1 field twice: once when executing the first sorting instruction and once when executing the second sorting instruction. To eliminate this duplication, and to decrease sorting time, create the calculated field MAX1 explicitly (in the following figure, the solid line in the hierarchy indicates that MAX1 is not hidden):

Then, use the calculated field MAX1 in the sorting instructions:

Sort each RXN by >VARIATION>MAX1 from high to low

Sort each RXN>VARIATION by >MAX1 from high to low

To execute these sorting instructions, ISIS performs the calculations for the MAX1 field only once, and uses this information for sorting both reactions and variations.

103.1.9 Saving and Exporting Sorted Search Results

If you save or export search results, ISIS preserves the order of the sorted records. However, ISIS doe not preserve the order of variation subrecords or other subrecords that you sort. For information on saving a list of records, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for search results, saving remote. For information on exporting a list of records, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for search results, exporting remote.

You can preserve the sorted order of both the records and subrecords by exporting your search results to a local database. For more information, see the step-by-step instructions. Alternatively, choose Help > Index, and search for search results, exporting to local database.

103.2 Sorting Examples

This section contains typical examples of sorting 3D structure records. The following figure shows part of the hierarchy of a 3D database:

The top level of the hierarchy (MODEL) contains data that is associated with a specific 3D structure, such as the modeling program that produced the 3D structure (MODEL_SOURCE) and data that is derived from the 3D structure during a CFS search (CFS_RMS, CFS_VDW, and CFS_TDF).

Each 3D model is associated with a single 2D structure. The middle level in the hierarchy (MOL) provides data that is associated with the compound rather than a specific 3D representation of that compound, such as the unique company ID number (CORP_ID) and molecular weight (MOL_WEIGHT).

The lowest level of the hierarchy provides data on the names of the compound and on the different types of activity for which the compound has been tested. Each compound might have several names (NAME) and several different types of activity (ACTIVITY_INDEX).

Each example in this section shows the sorting instructions that you use to sort search results from this database.

103.2.1 Sorting by CFS Data (CFS Only)

In a Conformationally Flexible Substructure (CFS) search, you can specify how ISIS fits 3D structures in the database to the constraints in your query. Also, ISIS can derive three types of data during the CFS search:

*	CFS_TDF: The torsional degrees of freedom (number of rotatable bonds) on the paths that connect the mapped atoms in the fitted 3D structure (Mapped atoms are the atoms in the 3D structure that correspond to atoms in the query). The higher the TDF, the more flexible the molecule is in the region that matches the query.

*	CFS_RMS: The root mean square (RMS) value for the goodness-of-fit to the 3D features that you specify in your query. The lower the RMS deviation, the better the fitted 3D structure fits the query.

*	CFS_VDW: The difference in van der Waals nonbonded interaction energy between the fitted conformation and the conformation that is stored in the database.

Note: The derived data that ISIS creates during a CFS search disappears when you perform another search. Therefore, we strongly recommend that you define your sorting instructions before the search and sort your search results automatically after the search. For more information on CFS searching, study the Request-A-Document CFS Searching Concepts/Examples.

A fourth derived data field, CFS_FITTER, stores the name of the fitter (Simplex or Derivative) that ISIS used in the search. This data is the same for all records from a CFS search, so it is not suitable for sorting. You can, however, display this information on your form.

You can also sort your CFS search results by data in one or more database fields, just as you would in other types of molecule searches.

Sorting by van der Waals Energy Difference

You might want to sort your search results so that fitted 3D structures with the lowest values in van der Waals interaction energy appear first on the list. The following sorting instruction does this:

Sort each MODEL by >CFS_VDW from low to high

Sorting by Torsional Degrees of Freedom

You might want to sort your search results so that 3D structures that are more rigid in the region that matches the query appear first on the list. The following sorting instruction does this:

Sort each MODEL by >CFS_TDF from low to high

Sorting by RMS Deviation

You might want to sort your search results so that fitted 3D structures that best fit the query appear first on the list. The following sorting instruction does this:

Sort each MODEL by >CFS_RMS from low to high

Note: To sort by RMS deviation, your query must contain only the following 3D components: atoms, ring centroids, angles defined by three atoms or ring centroids, and distances defined by two atoms or ring centroids. For more information on RMS deviation, study the Request-A-Document CFS Searching Concepts/Examples.

Sorting by a Combination of CFS Data

If you want to sort your search results by more than one kind of CFS data, you must decide which data is more important to you, and specify that type of data first in the sorting instructions.

For example, in the initial CFS search, you might want to sort by both torsional degrees of freedom (TDF) and RMS deviation. If TDF is more important, use the following sorting instructions in this order:

Sort each MODEL by >CFS_TDF from low to high

Sort each MODEL by >CFS_RMS from low to high

If RMS deviation is more important, use the following sorting instructions, in this order:

Sort each MODEL by >CFS_RMS from low to high

Sort each MODEL by >CFS_TDF from low to high

If you conduct a CFS search with bump checking (bump-checking CFS search), you can sort by all three types of CFS data. For example, you might be interested in structures that are relatively rigid in the region that matches the query. Therefore, you want to sort search results so that fitted 3D structures with the smallest number of rotatable bonds (TDF) appear first. If two 3D structures have the same TDF, you want structures with the smallest van der Waals energy difference to appear first. If any fitted 3D structures have the same van der Waals energy difference, you want 3D structures with the lowest RMS deviation to appear first. To do this, use the following sorting instructions.

Sort each MODEL by >CFS_TDF from low to high

Sort each MODEL by >CFS_VDW from low to high

Sort each MODEL by >CFS_RMS from low to high

Note: If you want to sort by RMS deviation in either the initial or bump-checking CFS searches, your query must contain only the following 3D components: atoms, ring centroids, angles defined by three atoms or ring centroids, and distances defined by two atoms or ring centroids. For more information on RMS deviation, study the Request-A-Document CFS Searching Concepts/Examples.

103.2.3 Sorting by Activity Index

MDL databases such as MDDR-3D contain an activity index that classifies compounds according to biological activity. You can sort 3D structure records so that compounds with similar activity are grouped together on your list:

Sort each MODEL by >MOL>ACTIVITY>ACTIVITY_INDEX from low to high

103.2.4 Sorting by Activity Index and Molecular Weight

MDL databases such as MDDR-3D contain an activity index that classifies compounds according to biological activity. You can sort 3D structure records so that compounds with similar activity are grouped together on your list. Within each set of compounds with the same activity, you might want compounds with the lowest molecular weights to appear first. To do this, you specify the sorting instruction for activity index first:

Sort each MODEL by >MOL>ACTIVITY>ACTIVITY_INDEX from low to high

Sort each MODEL by >MOL>MOL.WEIGHT from low to high


Local Databases: Sorting Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This request-a-document contains:

*	Basic Concepts	104.1

*	Sorting Examples	104.2

We recommend that you print this 4-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

104.1 Basic Concepts

104.1.1 Flat and Hierarchical Databases

ISIS databases can be either flat or hierarchical. In the following example, the database organization is flat, because the database contains only one level of data:

In this example, ROOT is a parent field. Parent fields do not store data, but point to one or more child fields that contain the actual data. The child fields are STRUCTURE, CAS_NUMBER, MOLECULE_NAME, BOILING_POINT, and DATE. You can sort your search results by data in any of these child fields.

However, your database might have more than one set of data that is associated with a molecule or reaction. Each set of data becomes a level in a hierarchical database. The following is a portion of a hierarchical reaction database:

In this example, one reaction has several variations associated with it. Each variation, in turn, has several associated literature references and reaction conditions. The result is a hierarchy of three levels. The highest level in the database hierarchy has data associated with a specific reaction: the reaction (RXNSTRUCTURE) and its ID number (RXNREGNO). The middle level in the hierarchy contains data that is associated with a specific variation of the original reaction, such as the variation number (VARIATION_NO). The lowest level in the hierarchy contains the text of a specific literature reference for a given variation (LITTEXT_DATA), and data on reaction conditions (TIME, TEMP, PRESSURE).

Each level of the database has a parent field that points to one or more child fields that store data. In this example, RXN, VARIATION, CONDITIONS, and LITTEXT are parent fields at specific levels of the hierarchy. Parent fields define subrecords (subordinate records) that contain separate sets of data. For example, each variation of information on a specific reaction is a subrecord within a reaction record. In this example, the reaction record can vary by literature references or reaction conditions. Each set of literature references or reaction conditions is a subrecord within a variation subrecord.

You can sort your search results by any child field of RXN. For example, you can sort reaction records so that records with the highest ID numbers (RXNREGNO) appear first, or you can sort variation subrecords by variation number (VARIATION_NO).

In remote databases only, you can sort a parent field by any child field below it in the hierarchy. For example, you can sort reaction records (RXN parent field) by reaction temperature (RXN>VARIATION>CONDITIONS>TEMP).

In local databases, you can sort a parent field solely by child fields that are directly attached to that parent.

You can sort each record or subrecord by a maximum of three child fields.

You can sort records and subrecords by any of the following types of data: date, integer, real, fixed text, variable text, and range. You cannot sort by the following types of data: structure, reaction, or sketch.

104.1.2 Order of Sorting

The order of sorting can be either of the following:

*	Low to high places the smallest values first (ascending order). Fixed- and variable-text data is sorted in ascending alphanumeric order.

*	High to low places the largest values first (descending order). Fixed- and variable-text data is sorted in descending alphanumeric order.

104.1.3 Sorting Instructions

To specify how to sort your search results, you must create sorting instructions. Each sorting instruction has the following syntax:

Sort each parent-field by child-field from order

Parent-field specifies the records or subrecords to sort, child-field is the field that contains the data by which to sort, and order is either high to low or low to high.

For example, the following sorting instruction sorts reaction records (RXN parent field) so that those with the lowest reaction temperatures appear first:

Sort each RXN by >VARIATION>CONDITIONS>TEMP from low to high

The following sorting instruction sorts variation subrecords (VARIATION parent field) so that variations with the lowest reaction temperatures appear first:

Sort each RXN>VARIATION by >CONDITIONS>TEMP from low to high

The order in which you specify sorting instructions affects sorting. ISIS sorts your records as follows:

1.	ISIS applies the first sorting instruction to all records.

2.	If several records have the same value for the field specified in the first sorting instruction, ISIS uses the second sorting instruction to decide the order.

3.	If several records have the same value for the fields specified in the first two sorting instructions, ISIS uses the third sorting instruction to decide the order.

Consequently, you generally want to place the sorting instruction with the most important data first, so that ISIS sorts all records by that data.

For example, you might want to sort variation subrecords so that variations with the least extreme reaction conditions (lowest reaction temperatures and shortest reaction times) appear first. If reaction temperature is more important, specify sorting instructions, in the following order:

Sort each RXN>VARIATION by >CONDITIONS>TEMP from low to high

Sort each RXN>VARIATION by >CONDITIONS>TIME from low to high

In this example, ISIS sorts the variation subrecords so that variations with the lowest reaction temperatures appear first. If several variations have the same reaction temperatures, ISIS places the variations with the shortest reaction times first.

You can save a set of sorting instructions within your database as a database object. You can also export a set of sorting instructions to a text file on hard disk or floppy. For information on saving sorting instructions, see the step-by-step instructions. Alternatively, click Help > Index, and search for sorting instructions, saving. For information on exporting sorting instructions, see the step-by-step instructions. Alternatively, click Help > Index, and search for sorting instructions, exporting.

104.1.4 Saving and Exporting Sorted Search Results

If you save or export search results, ISIS preserves the order of the sorted records. However, ISIS doe not preserve the order of variation subrecords or other subrecords that you sort. For information on saving a list of records, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for search results, saving local. For information on exporting a list of records, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for search results, exporting local.

You can preserve the sorted order of both the records and subrecords by exporting your search results to a local database. For more information, see the step-by-step instructions. Alternatively, choose Help > Index, and search for search results, exporting to local database.

104.2 Sorting Examples

You can sort any parent field in a local database by data in up to three of its child fields. The child field must be directly attached to the parent field that you want to sort. For example, in the following hierarchical molecule database, you can sort molecule records (MOL) by molecular weight, and bottle subrecords (BOTTLE) by the amount in each bottle:

To sort molecule records so that molecules with the lowest molecular weights appear first, use the following sorting instruction:

Sort each MOL by >MOLECULAR_WT from low to high

To sort subrecords so that bottles that contain the highest amounts appear first, use the following sorting instruction:

Sort each MOL>BOTTLE by >BOTTLE_AMT from high to low


Printing All the Data, and Only the Data, That You Want

Click [image] to print, or click [image] to close this Request-A-Document.

This request-a-document contains:

*	Printing Search Results from Flat Databases	107.1

*	Printing Search Results from Hierarchical Databases	107.2

*	How Form Design Affects Printing	107.3

*	Advanced Printing Concepts	107.4

We recommend that you print this 10-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

107.1 Printing Search Results from Flat Databases

A flat database has solely one level of data. For example:

Printing search results from flat databases is very simple, because you do not need to choose the level and branch of the database hierarchy from which to print data. ISIS prints all data within the form for each record.

Note: The information in the remainder of this document applies solely to hierarchical databases. If your database is flat, you can ignore the remainder of this document.

107.2 Printing Search Results From Hierarchical Databases

Most ISIS databases are hierarchical, that is, they contain multiple levels of data. The type and amount of data that ISIS prints from a hierarchical database depends upon subtle interactions between the currently-selected box or table, the design of your form, and the structure of your database.

Printing search results from a hierarchical database is a two-step process:

1.	Click the form box or table that contains the data that you want to print. Generally, this is the data that is most important to you.

2.	Print the data.

If you want to print data from other branches of the hierarchy, you must click a box or table that is connected to a field in that branch of the hierarchy.

The box or table that you select establishes the ending context for printing. The ending context defines the level and branch of the database hierarchy that contains the data that you want to print. For more information, see the section, "107.4.2 The Ending Context".

Note: You can print the ending context in the header or footer of the page when you print your search results. For more information on inserting text into a header or footer, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for footers, changing text of or headers, changing text of.

Study the following examples to understand how ISIS prints hierarchical data.

107.2.1 Printing Example 1: Printing All Data From the Lowest Level of the Database

The following is a portion of the hierarchy of a molecule database:

In this example, the database might contain several batches of one compound. Each batch, in turn, has several associated measurements of 50% lethal dose (LD50) and activity. The result is a hierarchy of three levels. The highest level of the database contains data that is associated with a compound, such as CORP_ID and MOLSTRUCTURE. The second level of the hierarchy contains data that is associated with a specific batch of the compound, such as BATCH_ID and CHEMIST. The lowest level in the hierarchy provides specific measurements of LD50 (LD50_RESULT) and activity (ACT_RESULT).

Each level of the database has a parent field that points to one or more child fields that store data. In this example, MOL, BATCH, LETHAL, and ACTIVITY are parent fields at each level of the hierarchy. The parent fields LETHAL and ACTIVITY are different branches of the hierarchy.

Parent fields define subrecords (subordinate records) that contain separate sets of data. For example, each batch (BATCH parent field) and its associated data is a subrecord within a molecule record. Each set of activity data or lethality data, in turn, is a subrecord within a batch.

You might use the following form to display and print data from this database:

The structure, corporate ID, batch number, and chemist name are in boxes. Test results for LD50 and activity are in simple tables that display three values at a time. (A simple table has one or more columns connected to fields that are grouped under the same parent field in the database.)

If you are primarily interested in activity, you probably want to print all activity data for every batch of every compound that you retrieve. To do this, click the table that contains activity measurements, then print the search results. The following figures show how ISIS prints the data for one record:

To print all the activity data, ISIS must print two forms for the first batch and two for the second. ISIS does not print all the LD50 data, because that data is in a different branch of the hierarchy. Instead, ISIS repeats the first three LD50 values when it prints the second set of activity values within each batch. To print all the LD50 data, you must select the table that contains the LD50 data. When you do this, ISIS prints all the LD50 values for each batch, but solely the first three activity values for each batch. If you want to print both activity and LD50 values from this form, you must print your search results twice: once for activity and once for LD50.

Note: To print both the activity and LD50 data simultaneously, you can create an uncoupled table in your form. For more information, see the section, "107.3 How Form Design Affects Printing".

107.2.2 Printing Example 2: Printing All Data From the Top Level of the Database

In many cases, you are not interested in data at lower levels of the database hierarchy. For example, you might be interested solely in the structures of the compounds that you retrieve. To print all the structures, you click the MOLSTRUCTURE box. Each record has only one structure associated with it, so ISIS prints only one form per record:

ISIS prints incomplete data for fields at lower levels of the database. The missing data is unimportant, because you want only the structures.

107.2.3 Printing Example 3: Printing All Data From an Intermediate Level of the Database

If you are primarily interested in the names of the chemists who prepared each batch of a compound, you select the box that is connected to the CHEMIST field. CHEMIST is a child field of the BATCH parent field, which is at the second level of the database. ISIS prints one form for each value of CHEMIST:

ISIS prints incomplete data for the ACT_RESULT and LD50_RESULT fields at the third level of the database. The missing data is unimportant, because you want solely the names of chemists.

107.3 How Form Design Affects Printing

The examples in this section show how you can design your form to ensure that you print all the data, and only the data, that you want.

107.3.1 Uncoupled Tables

An uncoupled table has its columns connected to fields that are located in different branches of the database hierarchy. You can use uncoupled tables to print data from different branches of the database hierarchy simultaneously. For example:

The data from the ACTIVITY branch of the hierarchy is uncoupled from the data in the LETHAL branch of the hierarchy. That is, the individual lethality and activity values are unrelated, although they are displayed in the same table. Both sets of data are related solely to the common parent fields BATCH and MOL.

The following figures show how ISIS prints the data when you select the uncoupled table:

107.3.2 Layered Tables

A layered table has its columns connected to fields that are from the same branch of the database hierarchy, but from sequential levels of the hierarchy. To ensure that you print all data from several levels of the database hierarchy, put data from all sequential levels of the hierarchy into a layered table. For example, the following is a portion of the hierarchy of a reaction database, with the portion of the form that prints the data on catalysts:

The table that contains CATALYST_NO and NAME is layered, because the fields are from sequential levels of the same branch of the hierarchy (that is, the branch that begins with the CATALYST_LINK parent field). The catalyst structure (MOLSTRUCTURE) at the middle level of this portion of the hierarchy is not part of the layered table, however. If you select the layered table when you print your search results, ISIS prints all the catalyst numbers and symbols, but prints the structure of solely the first catalyst:

To print the structures of all the catalysts, you must select the structure box. As ISIS prints each structure, ISIS places the corresponding catalyst number and name at the top of the group of subrecords within the layered table.

To ensure that you print all catalyst numbers, structures, and names, you can create a layered table that displays data from all three sequential child fields in this portion of the hierarchy: CATALYST_NO, MOLSTRUCTURE, and NAME. When you select the table that contains these fields, ISIS prints the data as follows:

Note: You might want to enlarge the table slightly, so that ISIS prints two catalysts on each form:

107.3.4 Printing Repeating Data in a Table

Repeating data occurs in layered tables. For any one record, the data for one level repeats itself in the table until all of the data at the lower level of the database hierarchy displays.

If you need more than one form to print all the data in a layered table, you might want to display the repeating data so that you can track the data across multiple forms. To change the properties of the layered table to display or hide repeating data, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for repeating data, showing or repeating data, hiding.

107.4 Advanced Printing Concepts

107.4.1 The Ending Context

Previous examples show how the currently-selected box or table defines the branch and level of the hierarchy from which to print data. The ending context is the parent field at the level and branch of the database hierarchy that you specify when you click a form box or table.

Note: ISIS displays the current value of the ending context in the Print dialog box when you print your search results.

The value of the ending context depends on whether you choose a box or table, and whether the table is simple, layered, or uncoupled. The following shows how ISIS defines the ending context for boxes and tables:

Form Object	Ending Context

Box	Parent of database field to which box is connected.

Simple Table	Parent of database fields in table. For example, if the table contains the fields RXN>VARIATION>CONDITIONS>TEMP, RXN>VARIATION>CONDITIONS>TIME, and RXN>VARIATION>CONDITIONS>PRESSURE, then the ending context is the parent field RXN>VARIATION>CONDITIONS.

Layered Table	Parent of database field at lowest level within the table. For example, if the table contains the fields MOL>CORP_ID and MOL>ACTIVITY>ACTIVITY_RESULT, then the ending context is the parent field MOL>ACTIVITY.

Uncoupled Table	Undefined, because more than one parent field can be at the lowest level in the table. The ending context is the text "(uncoupled table)".

Note: You can print the ending context in the header or footer of the page when you print your search results. For more information on changing the text of headers and footers, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for footers, changing text of or headers, changing text of.

107.4.2 Customizing Data Selection by Changing the Starting Context

Changing the starting context allows you to restrict the number of subrecords (subordinate records) that you print within each record.

The starting context defines the highest level of the database hierarchy from which ISIS prints every set of data in the branch that is defined by the ending context. When the starting context is at the highest level of the database (the default), ISIS prints every set of data for each record or subrecord in the branch of the hierarchy that contains the ending context. We say that ISIS prints data from the starting context to the ending context.

You generally want to keep the starting context at its default value so that ISIS prints all the data for the box or table (that is, for the ending context) that you select. In some cases, however, you might not want to print every set of data for each record. For example, you might want to print all activity data, but solely for the first batch of each compound. In a reaction database, you might want to print all literature references, but solely for the first variation of each reaction. To do this, you can change the starting context to a lower level of the database.

Caution: If you set the starting context incorrectly, you might print incomplete data without realizing that the data is incomplete. If you are not sure how to use the starting context, we strongly recommend that you use the default starting context. This ensures that ISIS prints all the data in the branch of the hierarchy that contains the data in the selected box or table (the ending context).

Use the following guidelines for changing the starting context:

1.	You can set the starting context to any parent field in the same branch of the hierarchy that contains the ending context. That is, the starting context can be any parent field from the top of the database to the ending context parent field.

2.	To print all the data at a specific level of the hierarchy, the starting context must be at the same level or higher.

3.	To print solely the first set of data at a specific level of the hierarchy, set the starting context to the parent field immediately below that level.

Study the following examples to see how the starting context affects the data that you print.

Consider the molecule database hierarchy from previous examples. When you click the table on your form that contains activity data (the ACT_RESULT) field, the ACTIVITY parent field becomes the ending context. You can set the starting context to the MOL, BATCH, or ACTIVITY parent fields. The default starting context is MOL, the highest level of the database:

Setting the starting context to the highest level of the database ensures that ISIS prints all activity data for every batch of every molecule record that you print. That is, ISIS prints all data from a starting context of MOL to an ending context of ACTIVITY.

If you set the starting context to BATCH, ISIS also prints all activity data for every batch of every molecule record that you print, because the batch data is at the same level as the BATCH parent field. That is, ISIS prints all data from the starting context of BATCH to the ending context of ACTIVITY:

If you set the starting context to ACTIVITY, however, ISIS prints all activity data, but solely for the first batch of every molecule. This is because ACTIVITY is immediately below the BATCH parent field in the database hierarchy. That is, ISIS prints all data from the starting context of ACTIVITY to the ending context of ACTIVITY:

To change the starting context, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for starting context, changing.

Note: You can print the starting context in the header or footer of the page when you print your search results. If you change the starting context, we strongly recommend that you print both the starting and ending contexts with your search results. For more information on changing the text of headers and footers, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for footers, changing text of, or headers, changing text of.


Calculated Fields: Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This request-a-document contains:

*	Basic Concepts	110.1

*	Examples of Calculated Fields	110.2

*	Form Calculation: Combining Data from Different Database Fields	110.3

We recommend that you print this 9-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on creating calculated fields, click here.

110.1 Basic Concepts

A calculated field contains data that is not stored in the database, but is calculated from a set of the same type of data. For example, if your molecule database contains several activity measurements of each compound, you can create a calculated field that contains the average of those measurements. You can display data from a calculated field in a form and/or use it to sort search results, just like the data in any other database field.

Notes: (1) Do not confuse calculated fields with form calculations. A form calculation takes numeric data from boxes or columns in the form performs mathematical operations on the data to obtain a result. You see the result when you conduct a search and view the data in the Browse mode. However, you cannot use the result of a form calculation to sort your search results. For more information on form calculations, see Section 110.3. (2) Calculated fields are also called aggregate fields, because they aggregate a set of data into a single value. (3) Calculated fields are only available for remote databases.

To understand calculated fields, you need to understand the structure of hierarchical databases in ISIS.

110.1.1 Flat and Hierarchical Databases

ISIS databases can be either flat or hierarchical. In the following example, the database organization is flat, because the database contains only one level of data:

In this example, MOL is a parent field. Parent fields do not store data, but point to one or more child fields that contain the actual data. In this example, the child fields are STRUCTURE, CAS_NUMBER, MOLECULE_NAME, BOILING_POINT, and DATE. Each record has only one set of data associated with it.

However, your database might have more than one set of data that is associated with a molecule or reaction. Each set of data becomes a branch in a hierarchical database. The following is a portion of a hierarchical reaction database:

In this example, one reaction has several variations associated with it. Each variation, in turn, has several associated literature references and reaction conditions. The result is a hierarchy of three levels. The highest level in the database hierarchy has data associated with a specific reaction: the reaction (RXNSTRUCTURE) and its ID number (RXNREGNO). The middle level in the hierarchy provides data that is associated with a specific variation of the original reaction, such as the variation number (VARIATION_NO). The lowest level in the hierarchy provides the text of a specific literature reference for a given variation (LITTEXT_DATA), and data on reaction conditions (TIME, TEMP, PRESSURE).

Each level of the database has a parent field that points to one or more child fields that store data. In this example, RXN, VARIATION, CONDITIONS, and LITTEXT are parent fields at each level of the hierarchy.

110.1.2 Calculated Fields

A calculated field contains data that is not stored in the database, but is calculated from multiple instances of the same type of data. For example, your molecule database might contain test results for the lethality of a compound (for example, 50% lethal dose, or LD50). In the following example, the parent field LETHAL points to several values in the child field LD50_RESULT. The calculated field AVG_LD50_RESULT contains the average of all the LD50 values in LD50_RESULT (names of calculated fields are enclosed in parentheses):

AVG_LD50_RESULT is a child of MOL, at the same level as the parent field LETHAL. This is because each molecule (MOL) can have only one average LD50 value (AVG_LD50_RESULT) associated with it. A calculated field is at the same level in the database hierarchy as the parent of the field that contains the data on which the calculation is performed. That is, the calculated field "promotes" the data to a higher level of the database by combining a set of data into a single value.

110.1.3 Calculation Types

We provide six types of calculations that you can use to create calculated fields. The following table shows the types of available calculations, the types of fields on which each calculation can be performed, and examples of each type of calculation:

For the Range field type, the Count calculation produces a single integer value. Other calculation types produce a range of two values. The following table shows how ISIS calculates the two values in the range:

Calculation Type	Range Calculated

Sum	Sum of all the first values in the range;
Sum of all the second values in the range

Average	Average of all the first values in the range;
Average of all the second values in the range

Median	Median of all the first values in the range;
Median of all the second values in the range

Maximum	Range that includes the highest first value. If several ranges include the highest first value, ISIS arbitrarily chooses one of the ranges.

Minimum	Range that includes the lowest second value. If several ranges include the lowest second value, ISIS arbitrarily chooses one of the ranges.

Note: Minimum and maximum calculations on a range are generally not useful, because the chosen value can be arbitrary. For example, you might want to find the maximum of the following set of ranges:

100 - 120
80 - 200
109 - 111
109 - 700
105 - 108

In this example, the highest first value is 109. When ISIS calculates the maximum range, however, it arbitrarily chooses one of the first four ranges. This is because each of the first four ranges includes the highest first value, 109. The fifth range (105 - 108) is excluded because it does not include the value 109. Consequently, we recommend that you use the maximum or minimum of a range only when you are sure that none of the ranges overlap, or when both values in the range are equal.

110.2 Examples of Calculated Fields

Study the examples in this section to decide which calculated fields you want to create in your database. In diagrams of database hierarchies, parentheses enclose the names of calculated fields.

For information on how to create a calculated field, see the step-by-step instructions. Alternatively, choose Help > Index, and search for calculated fields, creating. For information on connecting a field to a box or table column on your form, see the step-by-step instructions Alternatively, choose Help > Index, and search for forms, editing. For information on using calculated fields for sorting search results, see the step-by-step instructions for the search of your choice.

110.2.1 Example 1: Number of Bottles of a Compound

You have a list of search results from an MSim search of a molecule database. You know that you have several bottles of each compound on your list. You now want to display on your form the total number of bottles of each compound.

The following is a portion of the hierarchy of the molecule database:

Each compound might have several bottles associated with it. Each bottle, in turn, might be checked out several times by different chemists. The DEMO_INVENTORY parent field points to fields that contain information on individual bottles of a compound, such as the bottle ID, the location (STOCKROOM)< the supplier, and the amount within each bottle (BOTTLE_AMT). The DEMO_CHECKOUT parent field points to fields that contain the checkout record of each bottle, such as the chemist who used it and the dates that the bottle was checked in and checked out (CHECK_IN and CHECK_OUT, respectively).

To find the number of bottles of each compound, you define the calculated field COUNT_BOTTLE, which counts the number of bottle IDs. This calculated field is a child of MOL, because it contains the number of bottles of each compound:

To display the data on your form, you connect a box or table column to the calculated field.

110.2.2 Example 2: Total Available Amount of a Compound

In the molecule database from the previous example, you know that you have several bottles of each compound. You want to find the sum of the amounts in the individual bottles. Then, you want to sort your search results so that compounds with the highest total amounts appear first on the list. To do this, you define the calculated field TOTAL_AMT as the sum of the data in the BOTTLE_AMT field. This calculated field is a child of MOL, because each compound has only one total amount associated with it:

To sort search results, use the following sorting instruction:

Sort each MOL by >TOTAL_AMT from high to low

110.2.3 Example 3: Average LD50 Measurement

Your molecule database contains test results for the lethality of a compound (where lethality is 50% lethal dose, or LD50). Your database contains several measurements of LD50 for each compound in the database. You want to find the average value of LD50, then sort your search results so that compounds with the lowest average LD50 are first on the list.

In a 2D molecule database, the database hierarchy has two levels:

Each compound has several measurements of LD50 (LD50_RESULT) associated with it. To find the average of all the LD50 measurements of a compound, you define the calculated field AVG_LD50_RESULT. The calculated field is a child of MOL, because each compound has only one average LD50 measurement associated with it:

To sort your search results so that compounds with the lowest average LD50 appear first on the list, use the following sorting instruction:

Sort each MOL by >AVG_LD50_RESULT from low to high

In a 3D database, your hierarchy might look like this:

To sort your search results so that 3D structures with the lowest average LD50 appear first on the list, use the following sorting instruction:

Sort each MODEL by >MOL>AVG_LD50_RESULT from low to high

110.2.4 Example 4: Total Yield of a Mixture of Stereoisomers

In a reaction database, you might want to sort your search results so that reactions with the highest yields appear first on the list. If all the reactions produce a single product, then you simply sort your search results by product yield. If the reactions produce a mixture of stereoisomers, however, you might want to sort by the total yield of all stereoisomers.

The following is the portion of the reaction database hierarchy that contains information on product yields:

Each reaction can have several products, and the yield of each product can be different for each variation of the reaction. To sort reaction records by the total yield of a mixture of stereoisomers, you need the total yield of all products in the reaction. To do this, you create a calculated field that contains the sum of all the yields of the individual products:

The calculated field TOTAL_PROD_YIELD is a child of VARIATION, at the same level as the parent of the field that contains the yields of individual products. This is because each variation has only one total product yield associated with it.

Sort each RXN by >VARIATION>TOTAL_PROD_YIELD from high to low

110.2.5 Example 5: Maximum Product Yield Within a Reaction

In the previous example, you defined a calculated field that contains the total yield of all products of a reaction. You might also want to find the highest total product yield among all variations within each reaction. To do this, you create a calculated field called MAX_YIELD. MAXYIELD contains the maximum value of the calculated field TOTAL_PROD_YIELD:

The calculated field MAX_YIELD is a child of RXN, because each reaction can have only one maximum total product yield associated with it. To display the maximum yield on your form, connect a form box or table to the MAX_YIELD field.

You can also use the MAX_YIELD field in to sort your search results. The following sorting instruction sorts reactions so that reactions with the highest total product yield appear first on the list:

Sort each RXN by >MAX_YIELD from high to low

110.2.6 Example 6: Average Product Yield Within a Reaction

You might want to sort reaction records so that reactions with the highest average product yield over all variations appear first on the list. To do this, you create the calculated field TOTAL_PROD_YIELD, just as you did in the previous example. Then, you create a calculated field (AVG_YIELD) that contains the average total product yield (TOTAL_PROD_YIELD) for all variations of a reaction:

To sort your search results so that reactions with the highest average total product yield appear first on the list, use the following sorting instruction:

Sort each RXN by AVG_YIELD from high to low

110.3 Form Calculations: Combining Data from Different Database Fields

A calculated field performs calculations on multiple instances of data from the same database field. You cannot use a calculated field to combine data from different fields. To combine data from different fields, you need to create a form calculation.

A form calculation takes numeric data from boxes or columns in the form and performs mathematical operations on the data to obtain a result. The mathematical operations include adding, subtracting multiplying, and dividing data. You see the result when you conduct a search and view the data in the Browse mode.

For example, one field in your database might contain the molecular weight of a compound, while another field contains the molar concentration of a solution of that compound. If you want to convert molar concentration to grams per liter, you need to multiply the data in the molecular weight field by the data in the molar concentration field. To do this, you create a form box or table column that contains the formula for multiplying the molecular weight field by the molar concentration field.

Form calculations are available for both local and remote databases.

For more information on form calculation, see the step-by-step instructions. Alternatively, choose Help > Index, and search for forms, calculation.


ISIS/Base Dialog Boxes

Alignment Options

Box Properties --Border/Pattern

Box Properties --Chem Display

Box Properties --Data/Label

Box Properties --Field name

Box Properties --Floating Boxes

Box Properties --Function

Calculated fields

CFS Options

Configure Local Database

Configure Remote Database

Connection Options

Conversion Required

Copy Item to a New List

Copy Item

Create Database

Current Mol

Customized Data Selection

Duplicate ID

Duplicate Structure

Edit Database Definition

Export Fields

Field Vocabulary

Flexmatch Parameters

Form Upgrade

Formula Query

Header/Footer

Host Errors

Host Request

Hview List

Import RDFile

Import SDFile

ISIS/Base

List Logic

Modify Object

Modifying the Database Definition

Move Item To a New List

Move Item

Multiply Form Box

Network Connection

New Database

New Remote Database

Non-Unique Field Selection

Object Manager

Object Name

Open Form

Open List

Page Layout

Partition Form Box

Pick Text Item from Vocabulary

Polymer

Print

Query Builder

Query Restore Error

Query Restore Options

Ruler Settings

Save As Text File

Save List

Save Query

Select Object

Settings -- Atom Maps

Settings -- Border/Pattern

Settings -- Chem Display

Settings -- Form

Settings -- General

Settings -- Header/Footer

Settings -- Print

Settings -- Ruler Settings

Settings -- Search

Similarity Values

Sort

Table/Column Properties -- Border/Pattern

Table/Column Properties -- Chem Display

Table/Column Properties -- Data/Label

Table/Column Properties -- Field Name

Table/Column Properties -- Floating Boxes

Table/Column Properties -- Function

TCP/IP Network Information

Text Field Vocabulary

Upgrade Database

View Database Definition

Vocabulary


Alignment Options

Use this dialog to:

*	Align selected objects on a form.

Click any of the following item:

Horizontal

Vertical

For complete information on how to edit forms, click here.


Horizontal

None

To align multiple objects vertically, click [image] None.

Tops

To align the tops of multiple objects, click [image] Tops.

Tops/Bottom Centers

To align the centers of multiple objects, click [image] Tops/Bottoms Centers.

Bottoms

To align the bottoms of multiple objects, click [image] Bottoms.


Vertical

None

To align multiple objects horizontally, click [image] None.

Left Sides

To align the left sides of multiple objects, click [image] Left Sides.

Left/Right Centers

To align the centers of multiple objects, click [image] Left/Right Centers.

Right Sides

To align the right sides of multiple objects, click [image] Right Sides.


Form Upgrade

Use this dialog to:

*	Specify which forms to upgrade and how to upgrade them when you upgrade a database that was created with ISIS/Base versions 1.0, 1.01, or 1.1.

*	Specify how to upgrade an imported form that you created with ISIS/Base versions 1.0, 1.01, or 1.1.

You can upgrade all of your database forms together, or you can upgrade them individually. We recommend that you view and upgrade each form individually.

Click any of the following item:

Scale the size of the form down by 5%  (PC only)

Scale the size of the fonts to fit in the form  (PC only)

Scale, Scale All

Skip, Skip All


Scale the Size of the Form Down by 5% (PC Only)

To reduce the size of the form by 5%, set [image] Scale the size of the form down by 5%.


Scale the Size of the Fonts to Fit in the Form (PC Only)

To scale the size of the fonts so that the text fits on the form, set [image] Scale the size of the fonts to fit in the form.


Scale, Scale All

Scale

To scale the current form only, click Scale. After you upgrade all the forms, ISIS/Base returns to the default form for the database.

Scale All

To scale all of the forms, click Scale All. ISIS/Base returns to the default form for the database.


Skip, Skip All

Skip

To leave the current form as is, click Skip. The form is closed without any changes and is not scaled.

Skip All

To leave all forms as they are, click Skip All. None of the forms are scaled.


Formula Query

Use this dialog to:

*	Specify queries for exact formulas or subformulas and to conduct an FMLA search.

Note: You cannot include wildcards.

Click any of the following items:

Query

Exact match

Subformula

If you are not sure which query to specify, see Searching Concepts/Examples.


Searching Concepts/Examples

Click any of the following items:

Molecule records: remote database (FMLA) or local database (FMLA)

Reaction records: remote database (FMLA) or local (FMLA) database


Query

To enter a formula query, click the Query box and enter the formula.


Exact Match

To retrieve only structures that contain the atoms that are specified by the query, set [image] Exact match.


Subformula

To retrieve structures that include the atoms that are specified by the query, set [image] Subformula.


OK, Cancel

OK

To use the dialog box settings for the current ISIS/Base work session and close the dialog box, click OK. The settings that you change in the dialog box are not saved in the settings file when you exit ISIS/Base. To save the current settings when you exit ISIS/Base click Save.

Cancel

To cancel changes to the settings file and close the dialog box, click Cancel.


Host Errors

Use this dialog to:

*	Save the error message that ISIS/Host displays.

Click any of the following item:

OK

Save


OK

To close the dialog box without saving the error message that you see, click OK.


Save

To save the error message in a file, click Save.


Host Request

Use this dialog to:

*	Enter information that is requested by ISIS/Host that allows you to open a remote database.

 Requirements to use this dialog

Click any of the following item:

OK

Cancel


Requirements to Use This Dialog

To open a remote database, you need know your password. If you do not know your password, see your ISIS Administrator.


OK

To open the database, click OK.


Cancel

To close the dialog box without opening the database, click Cancel.


List Logic

Use this dialog to:

*	Create a list of search results that combines the results from different searches. You can intersect or merge two or more lists of search results. You can also subtract one or more lists of search results from another list.

Click any of the following item:

List 1

AND, OR, NOT

List 2

Apply, Cancel, Close

Note: You can combine any molecule list with another molecule list, or any reaction list with another reaction list. You cannot combine a molecule list with a reaction list.


List 1

List 1

To select a list, click the List1 box and then click the name of the list.

Description

Displays the description of the list that you entered when you created the list.

Permanent/Temporary

Displays whether the list is a permanent list or a temporary list.


List 2

List 2

To select a list, click the List2 box and then click the name of the list.

Description

Displays the description of the list that you entered when you created the list.

Permanent/Temporary

Displays whether the list is a permanent list or a temporary list.


AND, OR, NOT

AND

To create a list that includes all records contained in both lists, click [image] AND.

OR

To create a list that includes only records that are present on either list, click [image] OR.

NOT

To create a list that includes only those records that are in list one but not in list two, set [image] NOT.


Apply, Cancel, Close

Apply

To create a list from the selected lists that uses the logic that you specified, click Apply.

Cancel

To close the dialog box without creating the list, click Cancel.

Close

To close the dialog box and make the last created temporary list the current list, click Close.


Modify Object

Use this dialog to:

*	Modify the properties of the database object of your choice.

 Requirements to use this dialog

Click any of the following items:

Name

Description

Read-Only

Permanent/Temporary

If you are not sure which database objects you want to modify, see the ISIS/Base Search Types.


Name

To change the name of the object, click the Name box, and then enter a name.


Description

To change the description of the object, click the Description box, and then enter a new description. You can enter up to forty characters.


Read-Only

To specify that the object cannot be modified, set [image] Read-Only.


Permanent/Temporary

To specify that the object is permanent (saved in the database and exists after you close ISIS/Base), set [image] Permanent.

To specify that the database object is temporary (stored in the database solely for the current ISIS/Base session), set [image] Permanent.


Copy Item

Use this dialog to:

*	Copy the currently-displayed record to an existing list of search results.

Click any of the following items:

Target list

Description

Permanent/Temporary

Copy

For more information on how to manipulate search results, click here.


Target list

To specify the existing list that you want to copy the record to, select a list name.


Description

Displays the description of the list that you entered when you created the list.


Permanent/Temporary

Displays whether the list is a permanent list or a temporary list.


Copy

To copy the record to the selected list and close the dialog box, click Copy.


Move Item

Use this dialog to:

*	Move the currently-displayed record to an existing list of search results.

Click any of the following items:

Target list

Description

Permanent/Temporary

Move

For more information on how to manipulate search results, click here.

For information on how to restore moved records back to the original list, click here.


Target list

To specify the existing list that you want to move the record to, select a list name.


Description

Displays the description of the list that you entered when you created the list.


Permanent/Temporary

Displays whether the list is a permanent list or a temporary list.


Move

To move the record to the selected list and close the dialog box, click Move.


Copy Item to a New List

Use this dialog to:

*	Copy the currently-displayed record to a new list of search results.

Click any of the following items:

List name

Description

Permanent

Copy

For more information on how to manipulate search results, click here.


List name

To create a new list and copy the record to that list, click the List name box and enter a list name.


Description

To save a description of the list, click the Description box, and then enter the description. You can enter up to forty characters.


Permanent

To save the new list as a permanent list, set [image] Permanent.

To save the new list as a temporary list, set [image] Permanent.


Copy

To copy the record to the new list and close the dialog box, click Copy.


Move Item to a New List

Use this dialog to:

*	Move the currently-displayed record to a new list of search results.

Click any of the following items:

List name

Description

Permanent

Move

For more information on how to manipulate search results, click here.

For information on how to restore moved records back to the original list, click here.


List name

To create a new list and move the record to that list, click the List name box and enter a list name.


Description

To save a description of the list, click the Description box, and then enter the description. You can enter up to forty characters.


Permanent

To save the new list as a permanent list, set [image] Permanent.

To save the new list as a temporary list, set [image] Permanent.


Move

To move the record to the new list and close the dialog box, click Move.


Multiply Form Box

Use this dialog to:

*	Create exact copies of a selected box on a form. For information on how to create boxes, click here.

Click any of the following items:

Horizontal

Vertical


Horizontal

Repeats

To create copies of a box, click the Repeats box and enter the number of copies of the selected box that you want on the horizontal axis.

Spacing

To specify the horizontal space between the boxes, click the Spacing box and enter the distance between the boxes in inches or centimeters. To specify the unit of measurement, choose Options > Ruler Settings.


Vertical

Repeats

To create copies of a box, click the Repeats box and enter the number of copies of the selected box that you want on the vertical axis.

Spacing

To specify the vertical space between the boxes, click the Spacing box and enter the distance between the boxes in inches or centimeters. To specify the unit of measurement, choose Options > Ruler Settings.


New Database

Use this dialog to:

*	Access a remote database. You create a remote-access file (located on your workstation) that points to an Hview that is located on a remote host computer.

*	Create a local database.

 Requirements to use this dialog

Click any of the following items:

Remote

Local

Password

For information on other items, consult your system documentation.


Requirements to Use This Dialog

If you want to access a new remote database, you need to obtain network access information from your ISIS Administrator.


Remote

To create a new remote-access file (located on your workstation) that points to an Hview located on a remote host computer, set [image] Remote.


Local

To create a new database that is located on your workstation, set [image] Local.


Password

To specify a password for the local database or remote-access file, click the box and enter the password. This password can be a maximum of 13 characters. (Note that this is not a host password.)


New Database

Use this dialog to:

*	Access a remote database. You create a remote-access file (located on your workstation) that points to an Hview that is located on a remote host computer.

*	Create a local database.

 Requirements to use this dialog

Click any of the following items:

Remote

Local

Password

For information on other items, consult your system documentation.


New Remote Database

Use this dialog to:

*	Access a new remote database. You create a new remote-access file (located on your workstation) that points to an Hview located on a remote host computer.

 Requirements to use this dialog

Click any of the following items:

Network Connection

Hview name

SQL statement

SQL database access


Requirements to Use This Dialog

You need to obtain network access information from your ISIS Administrator.


Object Manager

Use this dialog to:

*	View and/or modify the properties of the database objects of your choice.

*	Delete any database object.

 Requirements to use this dialog

Click any of the following items:

Object Type

Description

Date

Time

Status

Close

Modify

Delete


Requirements to Use This Dialog

*	You can use this dialog solely if your database contains saved database objects.

*	Select the name in which the object was saved from the list of objects. You can now view, modify, or delete the object.


Object Type

Structures

Lists

Forms

Queries

Sorting Instructions

PL Programs


Structures

To display the names of the structures that are saved in the database, set [image] Structures.

Structures in this dialog refers to any searchable graphic data, such as molecules, 3D structures, fragments, submodels, atoms, reactions, or specific reaction components.


Lists

To display the names of the lists that are saved in the database, set [image] Lists.


Forms

To display the names of the forms that are saved in the database, set [image] Forms.


Queries

To display the names of the search queries that are saved in the database, set [image] Queries.


Sorting Instructions

To display the names of the sorting instructions that are saved in the database, set [image] Sorting instructions.


PL Programs

To display the names of the PL programs (Procedural Language) that are saved in the database, set [image] PL Programs.


Description

Displays the description of the selected item. This description is the text that you entered when you created the item.


Date

Displays the date that the selected item was created.


Time

Displays the time that the selected item was created.


Status

Displays the status of the selected item. The status shows you whether the object is Read-Only or Read-Write. If the object is Read-Only, you cannot save changes to the object under the same name.

In addition, for lists of search results, 2D or 3D structures, and search queries the status shows you if the object is Permanent or Temporary. For PL programs (Procedural Language), the status shows you whether the program is Executed on startup or Not executed on startup.


Close

To accept the changes to the object and close the dialog box, click Close.


Modify

To modify the name or description of a selected object, click Modify. Click in the Name or Description box, and enter your modifications. In addition, you can change the status of any object to [image] Read-Only. To return the status to read-write, you require the setting [image] Read-Only.

For queries and lists: To specify that a query or list is permanent (saved in the database and exists after you close ISIS/Base), set [image] Permanent.

To specify that the query or list is temporary (stored in the database solely for the current ISIS/Base session), set [image] Permanent.


Delete

To delete a selected object, click Delete. If the selected object is Read-Only (rather than Read-Write) or permanent, then Delete is disabled.

Caution: When you delete a selected object, you cannot retrieve it. We recommend that you backup your database or export the object to a file on disk before you delete the object.


Export Object

When you export an object as a file on disk, you store it outside of your database (rather than as an object within your database). Each type of object (a query, list, form, sorting instructions, and a PL program) is exported in a specific format. In addition, you export a molecule query as a molfile and a reaction query (or a reaction component with a reaction arrow) as a rxnfile.

You can share an exported file with ISIS users who access the database through a different remote-access file. Thus, any user who can access your exported file can import it into ISIS and use it.

Note: You can also share your exported queries with users of MACCS-II, REACCS, and CPSS or with any other program that accepts files in Connection Table File (CTfile) format.


Object Name

Use this dialog to:

*	Save an object in your database. You can later restore the object and either edit it or use it. If you save an object in a remote database, anyone who wants to restore the query must restore it through the same remote-access file.

Note: Alternatively, you can export the object to a file on disk that anyone can then import to any remote-access file and use.

Click any of the following items:

Name

Description

Permanent

Read-Only


Name

To enter a name for the object, click the Name box, and then enter a name (of eight or less characters). Do not include a file name extension.


Description

To enter a description of the object, click the Description box, and then enter a new description. You can enter up to forty characters.


Permanent

To specify that a query or list is permanent (saved in the database and exists after you close ISIS/Base), set [image] Permanent.

To specify that a query or list is temporary (stored in the database solely for the current ISIS/Base session), set [image] Permanent.


Read-Only

To save the object as a Read-only object in the database, set [image] Read-only. You will not be able to save changes to the object under the same name.


Partition Form Box

Use this dialog to:

*	Divide a selected form box into smaller boxes of equal size. For information on how to create boxes, click here.

Click any of the following items:

Vertical partitions

Horizontal partitions


Vertical partitions

To divide a selected box into several vertical boxes, click the Vertical partitions box and enter the number of vertical boxes that you want.


Horizontal partitions

To divide a selected box into several horizontal boxes, click the Horizontal partitions box and enter the number of horizontal boxes that you want.


Query Builder

Use this dialog to:

*	Create a set of all-text search queries with the AND, OR, and NOT boolean operators and conduct a single search.

*	Create an all-text search query for any search in ISIS. However, because the text format and syntax of the query are so complex, we recommend that you use another, simpler search. If you are not sure of the search that you need to use, see the ISIS/Base SearchSelector or the ISIS/Base Search Types.

 Requirements to use this dialog

Click any of the following items:

Database Fields

Operators

Field Type

Structures

Query string

Clear

Read Reaction

Read Structure

If you are not sure of the correct text format or syntax to use, see QB Searching Concepts/Examples.


Requirements to Use This Dialog

*	To enter your all-text search query into the Query string text box, you must know the correct text format and syntax. (You can enter your text in upper- or lower-case characters.)

*	To include a graphical structure in your all-text search query, you must enter its file name (not the structure). For the ways that you can enter the file name of a graphical structure into the Query string text box, click here.

*	You can only enter a database field into the Query string text box if that field exists in your database.


Text Format

To Enter a Single Query

The correct text format to use for a single query in the Query string text box is as follows:

DATABASE FIELD   SEARCH OPERATOR   DATA (or file name of structure)

To Enter Multiple Queries

You can string many queries together with the AND, OR, or NOT boolean operators. Examples of the text format for entering two queries are as follows:

DATABASE FIELD   SEARCH OPERATOR   DATA   AND

DATABASE FIELD   SEARCH OPERATOR   DATA

DATABASE FIELD   SEARCH OPERATOR   DATA   OR

DATABASE FIELD   SEARCH OPERATOR   DATA

DATABASE FIELD   SEARCH OPERATOR   DATA   NOT

(DATABASE FIELD   SEARCH OPERATOR   DATA)

Note: The NOT operator requires parentheses around the query.

For more complete information, see QB Searching Concepts/Examples.


Syntax

The correct syntax to use in the Query string text box depends on many factors, including the type of information you want to find and the level that it is stored in the database. For example:

*	To conduct an exact match search in the Query string text box, there are times when you need to specify the search operator syntax LIKE instead of =. However, when you specify LIKE, you must also use double quotes around the data that you want to find.

*	To be sure to retrieve all the data that you want, you need to know when to use wildcards.

For complete information on the correct syntax to use, see QB Searching Concepts/Examples.


Entering the File Name of a Structure into the Query String Text Box

*	To enter a structure that is on the form in ISIS/Base into the Query string text box, double-click query in the Structures box.

*	To enter a structure that was saved in the database into the Query string text box, double-click the name of the structure in the Structures box.

*	To enter a molfile into the Query string text box, click Read Structure, enter the name of the structure in the Files text box, click OK, and then double-click the name of the structure in the Structures box. You see the structure in the box at the bottom-right of the Query Builder dialog.

*	To enter a rxnfile into the Query string text box, click Read Reaction, enter the name of the reaction in the Files text box, click OK, and then double-click the name of the reaction in the Structures box. You see the reaction in the box at the bottom-right of the Query Builder dialog.


QB Searching Concepts/Examples

Click any of the following items:

Molecule records: remote database (QB) or local database (QB)

Reaction records: remote database (QB) or local (QB) database

3D Structure records: remote database (QB) or local (QB) database


Database Fields

To enter a database field at the cursor position in the query string within the Query string text box, double-click the database field of your choice in the Database Fields list box.


Operators

To enter a search operator at the cursor position in the query string within the Query string text box, double-click the search operator of your choice in the Operators list box.

The search operators that you use with text or numeric data are different from the search operators that you use with structural data.

Click one of the following:

Search operators for: Text or Numeric Data or Structural Data


Field Type

The field type is the type of database field that you want to search: Text, numeric values, structures, or reactions.


Structures

Structures in this dialog refers to any searchable graphic data, such as molecules, 3D structures, fragments, submodels, atoms, reactions, or specific reaction components.

Do one of the following:

*	To enter a structure that is on the form in ISIS/Base, double-click query (or mquery or rquery) in the Structures box.

*	To enter a structure that was saved in the database, double-click the name of the structure in the Structures box.


Structural Data

Structures in this dialog refers to any searchable graphic data, such as molecules, 3D structures, fragments, submodels, atoms, reactions, or specific reaction components.


Query string

To edit the query string, click the Query string text box, and enter all or a portion of the query. This box displays the query string as you build it.


Read Structure

To enter a molfile into the Query string text box, click Read Structure, enter the name of the structure in the Files text box, click OK (Mac=Open), and then double-click the name of the structure in the Structures box. You see the structure in the box at the bottom-right of the Query Builder dialog.


Read Reaction

To enter a rxnfile into the Query string text box, click Read Reaction, enter the name of the reaction in the Files text box, click OK (Mac=Open), and then double-click the name of the reaction in the Structures box. You see the reaction in the box at the bottom-right of the Query Builder dialog.


Clear

To remove the current query from the Query string box, click Clear.


Query Restore Error

Use this dialog to:

*	Move the entire query into the Query Builder (if your form does not contain all the boxes and/or table columns required to hold your query.)

*	Partially restore as much of the query as your form can accommodate.

Note: Alternatively, you can edit your existing form to accommodate the entire query.

Click either of the following items:

OK

Query Builder


OK

To restore as much of the query as the form can accommodate and continue, click OK.

Note: Alternatively, you can edit your existing form to accommodate the entire query.


Query Restore Options

Use this dialog to:

*	Retrieve a query into your current form. If your form does not contain all the boxes and/or table columns required to hold your query, you can do one of the following: Move the entire query to the Query Builder, partially restore as much of the query as the form can accommodate, or edit your existing form to accommodate the entire query.

Click either of the following items:

Query Builder

Partial

If you are not sure of the correct text format or syntax to use to edit your query in the Query Builder, see QB Searching Concepts/Examples.

If you are not sure of the correct text format or syntax to use to edit your query in the form, see the ISIS/Base SearchSelector or the ISIS/Base Search Types.


Query Builder

To view and edit the entire query in the Query Builder, click Query Builder. You can then:

*	Add additional all-text search queries with the AND, OR, and NOT boolean operators and conduct a single search. (Although the search queries are all text, you can specify graphical structures with their file names.)

*	Edit an existing all-text search query for any search in ISIS.

Note: Because the text format and syntax of the query are so complex, we recommend that you use another, simpler search. If you are not sure of the search that you need to use, see the ISIS/Base SearchSelector or the ISIS/Base Search Types.


Partial

To restore as much of the query as the form can accommodate and continue, click Partial.

Note: Alternatively, you can edit your existing form to accommodate the entire query.


Ruler Settings

Use this dialog to:

*	Specify the appearance and behavior of the ruler in Forms mode.

Click any of the following items:

Show ruler

Snap to ruler

Inches

Centimeters

Divisions

For information on how to use the ruler, click here.


Show ruler

To display the ruler, set [image] Show ruler.


Snap to ruler

To specify that any object that you draw is sized using the increments marked on the current ruler, set [image] Snap to ruler.


Inches

To display the ruler using inches, click [image] Inches.


Centimeters

To display the ruler using centimeters, click [image] Centimeters.


Divisions

To specify the number of divisions displayed on the ruler, click the Divisions box and choose a value.


Save As Text File

Use this dialog to:

*	Save the current database definition as a text file.

Include vocabulary

To save the vocabulary for the database fields in the text file, set [image] Include vocabulary.

Include external name

To save the external name of the database fields in the text file, set [image] Include external name.

Consult your system documentation for information about the other items in this dialog box.


Save As Text File

Use this dialog to:

*	Save the current database definition as a text file.

Include vocabulary

To save the vocabulary for the database fields in the text file, set [image] Include vocabulary.

Include external name

To save the external name of the database fields in the text file, set [image] Include external name.

Consult your system documentation for information about the other items in this dialog box.


Save List

Use this dialog to:

*	Save a list of search results as an object in your database (but not as part of the database). This allows you to open the same list of records without executing the search again. If you save a list in a remote database, anyone who wants to restore the list must restore it through the same remote-access file.

Caution

Note: Alternatively, you can export a list of search results to a file on disk that anyone can then import to any remote-access file and view.

Click any of the following items:

List Name

Description

Save query under the same name

Permanent

Read-Only


List of Search Results

A list of search results is a set of records that you retrieve from the database that you search with your search query. Each record in the list might contain a structure and associated data. (Some records contain solely data.)


Export List

You can also export your search results to a text file on your host computer. Export your search results when you want to exchange search results with users who access the database through a different remote-access file or when you want to exchange search results with MACCS-II and REACCS users.


List Name

To enter a name for the list, click the List Name box, and then enter a name (of eight or less characters). Do not include a file name extension.


Description

To enter a description of the list, click the Description box, and then enter a new description. You can enter a maximum of forty characters.


Save Query Under the Same Name

To save the query with the same name as the list, set [image] Save query under the same name.


Permanent

To save the list as a permanent list, set [image] Permanent. To save the list as a temporary list, set [image] Permanent.


Read-Only

To save the list as a Read-only database object, set [image] Read-only. You will not be able to save any other list with the same name.


Caution

When you save a list of search results in the remote-access file of your database, ISIS creates a file on your host computer that contains important information. Do not delete this file! If you delete this file, you will lose your search results.

Note: You can only save a list of records if your Hview contains a TINFO line. For more information, see your ISIS Administrator.


Save As File Name

Click the Save As File Name box and enter a new file name.


Save Query

Use this dialog to:

*	Save your search query as an object in your database. You can later restore the query and either edit it or use it as part of a new query. If you save a query in a remote database, anyone who wants to restore the query must restore it through the same remote-access file.

Note: Alternatively, you can export your query to a file on disk that anyone can then import to any remote-access file and use.

Click any of the following items:

Name

Description

Permanent

Read-Only

Current Query

Last Executed Query


Export Query

You can export the query as a file: Export a molecule query as a molfile. Export a reaction query (or a reaction component with a reaction arrow) as a rxnfile.

You can share your molfile or rxnfile with ISIS users who access the database through a different remote-access file. Thus, any user who can access your molfile or rxnfile can import the structure into ISIS and use it.

Note: You can also share your query with users of MACCS-II, REACCS, and CPSS or with any other program that accepts files in Connection Table File (CTfile) format.


Name

To enter a name for the query, click the Name box, and then enter a name (of eight or less characters). Do not include a file name extension.


Description

To enter a description of the query, click the Description box, and then enter a new description. You can enter up to forty characters.


Permanent

To specify that the query is permanent (saved in the database and exists after you close ISIS/Base), set [image] Permanent.

To specify that the query is temporary (stored in the database solely for the current ISIS/Base session), set [image] Permanent.


Read-Only

To save the query as a Read-only database object in the database, set [image] Read-only. You will not be able to save any other query with the same name.


Current Query

To save the current query, set [image] Current query.


Last Executed Query

To save the query that was used in the last search that you completed, set [image] Last executed query.


Open Form

Use this dialog to:

*	Open a form that is an object in your database.

*	Set or change the default form that automatically opens when you open the database.

Note: To select a form to open, click the name of the form.

Click any of the following items:

Description

Default

Set Default Form


Description

Displays the description of the form that was entered when the form was created.


Default

Displays the name of the default form in the database that is currently open.


Set Default Form

To set or change the default form, select a form name, then click Set Default.


Select Object

Use this dialog to:

*	Restore the object of your choice from the database.

Click either of the following items:

Name

Description


Name

To restore an object, click an object name, and then click OK.


Description

Displays the description of the object that was entered when the object was created.


Settings -- Atom Maps

Note: The original default settings in this dialog are optimal for searching and viewing reaction records. Thus, we recommend that you do not change any of the original settings.

Use this dialog to:

*	Specify new default settings for how you want atom-atom maps, reacting centers, and/or inversion and retention marks to be displayed in your query or reaction records.

 Requirements to use this dialog

Click any of the following items:

Atom-Atom Maps

Reacting centers

Inversion/Retention

OK, Cancel

Save, Save As, Read

For more information on how to work with ISIS/Base settings, click here.

If you are not sure when to display these items, see Searching Concepts/Examples.


Requirements to Use This Dialog

*	You can only use these settings with a remote database.

*	You can display these settings if you click the Query, Browse, or Update button. (You cannot display these settings if you click the Forms button.)

*	The atom-atom map setting requires that your query be an entire reaction. An entire reaction contains at least one reactant and at least one product.

*	All settings except the atom-atom map setting allow you to use either an entire reaction or a reaction component (with a reaction arrow).


Searching Concepts/Examples

Click any of the following items:

Your query is a reaction component: RSS/Comp or SBF

Your query is a reaction: RSS/Rxn or SBF

If you are not sure of the query that you need to use, see the ISIS/Base SearchSelector.


Atom-Atom Maps

To specify whether atom-atom maps display in a specific mode by default, click the Query, Browse, or Update button, and then choose On or Off.

Note: If you create a query that contains atom-atom maps, your query must be an entire reaction. An entire reaction contains at least one reactant and at least one product. Your query cannot be a reaction component (with a reaction arrow).


Reacting centers

To specify the default display of reacting centers in a specific mode, click the Query, Browse, or Update button, and then choose a display option.


Inversion/Retention

To specify whether inversion and retention marks display in a specific mode by default, click the Query, Browse, or Update button, and then choose On or Off.


Settings -- Border/Pattern

Use this dialog to:

*	Specify the default appearance of box and table borders, fill color, and fill patterns on forms. You see the defaults take affect for each new box, table, line, or text that you create.

Note: Do not use this dialog box to change the appearance of an existing form. For information on how to edit an existing form, click here.

Click any of the following items:

Style Borders

Show

Fill

OK, Cancel

Save, Save As, Read

For more information on how to work with ISIS/Base settings, click here.


Style Borders

Show Borders

Width

Color

Style


Color

To specify the default color for borders, click the box, and then choose a color. To customize a color or to create a color, click the box and choose Other.... You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on using this feature.


Style

To specify the default style for borders, click the box, and then choose a style.


Width

To specify the default width for borders, click the box, and then choose a width.


Show Borders

Top

To show the top border of a box, table, or column by default, set [image] Top.

Left

To show the left border of a box, table, or column by default, set [image] Left.

Bottom

To show the bottom border of a box, table, or column by default, set [image] Bottom.

Right

To show the right border of a box, table, or column by default, set [image] Right.


Show

Column dividers

To display column dividers by default, set [image] Column dividers.

Row dividers

To display row dividers by default, set [image] Row dividers.

Header bar

To display the header bar by default, set [image] Header bar.

Repeating data

To display, by default, data that appears in many fields under a parent field in a hierarchical table, set [image]. It might be easier to read the data in hierarchical tables if you set [image] Repeating data.


Fill

Color

To specify the default fill color for form boxes, click the box and choose a color. To customize a color or to create a color, click the box and choose Other.... You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on using this feature.

Pattern

To specify the default fill pattern for form boxes, click the box and choose a pattern.


Border

Width

To specify the default width of the border, click the box, and then choose a width.


Shading

Color

To change the shading color, click the box, and then choose a color. (You can change the color for boxes, not columns.)

Style

To change the style, click the box, and then choose a style. (You can change the style for boxes, not columns.)


Pattern

Color

To specify the default color for the pattern, click the box, and then choose a color.

Style

To specify the default style for the pattern, click the box, and then choose a style.


Settings -- Chem Display

Use this dialog to:

*	Specify new default settings for how you want queries and retrieved structures to be displayed in your forms. Structures in this dialog refers to any searchable graphic data, such as molecules, 3D structures, fragments, submodels, atoms, reactions, or specific reaction components.

*	Specify new default settings for how you want the query to be highlighted in the records retrieved.

Note: Do not use this dialog box to change the appearance of an existing form. For information on how to edit an existing form, click here.

Click any of the following items:

Structure Display

Residue/Sequence Display

Query highlight

Atom Display

Orient hits to match query

OK, Cancel

Save, Save As, Read

For more information on how to work with ISIS/Base settings, click here.

If you are not sure what settings to use, see the ISIS/Base Search Types.


Structure Display

As drawn

As drawn (scaled)

Defaults

Defaults (scaled)

Bond length

Atom font

Note: The Structure Display option does not affect how a structure is registered. Click here for information  on how structures are registered.


As Drawn

Choose As Drawn to specify that structures display in a box or column exactly as they were drawn (including font, bond length, and color).

If you have a remote database, this option will display the bond length as it was drawn, but the atom font and structure color are set as form properties. (This option was called Structure Scaling: As Drawn in previous versions of ISIS/Base.)


As Drawn (Scaled)

Choose As Drawn (Scaled) to specify that structures display as they were drawn, but are scaled in size to fit the box or column (if necessary).

If you have a remote database, this setting will display the original bond length or scale the bond length in proportion to is original size. The atom font and structure (data) color are set as form properties.(This is a new option in ISIS/Base.)


Defaults

Choose Defaults to specify that structures display using form properties (bond length, atom font, and data color). (This option was called Structure Scaling: Std. Bond in previous versions of ISIS/Base.)


Defaults (Scaled)

Choose Defaults (Scaled) to specify that structures display using form properties (bond length, atom font, and data color) that are scaled to fit the box or column (if necessary). (This option was called Structure Scaling: Fit Box in previous versions of ISIS/Base.)


Bond Length

To specify the default bond length if you have Structure Display set to Defaults, click the box and enter a bond length in inches. If Structure Display is set to As drawn, ISIS/Base ignores the bond length setting.


Atom Font

To specify the default font, size, and style (including sub- and superscript) for atoms if you have Structure Display set to Defaults, click Atom Font. If Structure Display is set to As drawn, ISIS/Base ignores the Atom font settings.


Residue/Sequence Display

Show leaving groups

Expand residues

Show crosslink bonds

Show sequence bonds

Show residue brackets


Show Leaving Groups

To show residue leaving groups by default, set [image] Show leaving groups.


Expand Residues

To show residues that are expanded by default, set [image] Expand residues.


Show Crosslink Bonds

To show the crosslink bonds by default, set [image] Show crosslink bonds.


Show Sequence Bonds

To show sequence bonds by default, set [image] Show sequence bonds.


Show Residue Brackets

To show the residue brackets by default, set [image] Show residue brackets.


Query highlight

When you use a search query to conduct a search in ISIS/Base, you can view the query highlighted in a specific color (such as red or blue) within the resulting structures that are retrieved from the database.

To specify a new default color for the highlighted query, click the Query highlight box and then choose a color.

To create your own color, click the box and choose Other.... You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on using this feature.


Atom Display

Hydrogen labels

Atom numbers


Hydrogen Labels

To specify whether to display implicit hydrogens as drawn, on all atoms, on heteroatoms, or on all heteroatoms and terminal atoms, click the Hydrogen labels box, and then choose an option.

Note: ISIS does not recognize implicit hydrogens in a search query, even if you display them. If you want to create a search query that allows solely hydrogen atoms at specified positions in the structures retrieved, you must draw explicit hydrogens. For information on how to create an explicit hydrogen, click here.

Examples of Implicit and Explicit Hydrogens


Atom Numbers

To specify whether to display atom numbers on a structure, click the Atom Numbers box, and then choose On or Off.


3D Display

Show data from 3D atom fields

Show data from 3D atom-pair fields


Orient Hits to Match Query

To display hits so that they are positioned the same way that the query is positioned by default, set [image] Orient hits to match query.


Show Data From 3D Atom Fields

To show data from 3D atom fields that are specified in the query, set [image].


Show Data From 3D Atom-Pair Fields

To show the data from 3D atom-pair fields that are specified in the query, set [image].


Label

Alignment

To specify the default alignment for labels, click the box, and then choose an option.

Color

To specify the default color for labels, click the box, and then choose a color. To customize a color or to create a color, click the box and choose Other.... You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on using this feature.

Font

To specify the default font, size, and style (including sub- and superscript) for labels, click Font.


Data

Alignment

To specify the default alignment for data, click the box, and then choose an option.

Color

To specify the default color for data, click the box, and then choose a color. To customize a color or to create a color, click the box and choose Other.... You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on using this feature.

Text format

To specify the default format for text data, click the box, and then choose an option.

Decimal places

To specify the default number of decimal places for data display, click the box, and then enter or choose a number.

Scientific notation

To specify that data of type real or range be displayed in scientific notation by default, click [image].

Font

To specify the default font, size, and style (including sub- and superscript) for data, click Font.


Text Tool

Color

To specify the default color of text when you use the Text tool, click the box, and then choose a color. To customize a color or to create a color, click the box and choose Other.... You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on using this feature.

Font

To specify the default font, size, and style (including sub- and superscript) when you use the Text tool, click Font.


Line Tool

Width

To specify the default line width when you use the Line tool, click the box, and then choose a width.

Color

To specify the default line color when you use the Line tool, click the box, and then choose a color. To customize a color or to create a color, click the box and choose Other.... You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on using this feature.

Style

To specify the default line style when you use the Line tool, click the box, and then choose a style.


Settings -- General

Use this dialog to:

*	Specify new default settings for general displays in ISIS/Base.

Click any of the following items:

Automatic transfer to ISIS/Draw

Transfer to ISIS/Draw with auto-scale

Highlight buttons with reverse video

Copy mol/rxnfile to the Clipboard

Show host errors

Clear old data on new record

Activate extreg prompting for registration

Adjust text display to match printed appearance (PC only)

Locate ISIS/Draw for transfer (Mac only)

OK, Cancel

Save, Save As, Read

For more information on how to work with ISIS/Base settings, click here.


Automatic Transfer to ISIS/Draw

To automatically transfer a structure in an ISIS/Base structure box to ISIS/Draw, set [image] Automatic transfer to ISIS/Draw.

To transfer a structure in an ISIS/Base structure box to ISIS/Draw solely when you click [image] or double-click the structure, set [image] Automatic transfer to ISIS/Draw.


Transfer to ISIS/Draw With Auto-Scale

To automatically resize structures so that they fit in the ISIS/Draw transfer window after you transfer them, set [image] Transfer to ISIS/Draw with auto-scale.

To transfer structures to ISIS/Draw without resizing them, set [image] Transfer to ISIS/Draw with auto-scale. You then might have to resize structures manually if they do not fit in the ISIS/Draw transfer window.


Copy Mol/Rxnfile to the Clipboard

To copy structures and reactions to the Clipboard in the Molfile or the Rxnfile format, set [image]. You can then paste the structures or reactions into any application that recognizes these formats. For information on how to paste Molfiles and Rxnfiles into other applications, click here.

To copy molecules or reactions into applications that do not understand the formats, set [image].


To paste molfiles and rxnfiles into other applications

You can paste chemically significant structures and reactions into any application that recognizes MDL's molfile or rxnfile (Chemical Table) file format. Use this procedure to paste a molecule or reaction from ISIS/Base to an opened application that supports the molfile or rxnfile format.

1.	Choose Options > Settings > Session.

2.	Click the General tab.

3.	To paste chemical information to the Clipboard, you require this setting: Copy mol/rxnfile to the clipboard

4.	(Optional) If you are going to be regularly pasting chemical information to the Clipboard, click Save. This saves your modifications to the file ISISBASE.CFG.

5.	Click OK.

6.	Select the structure or reaction that you want to paste into another application.

7.	Choose Edit > Copy.

8.	In the other application, choose Edit > Paste.


Activate Extreg Prompting for Registration

To have ISIS/Base prompt you during registration if it finds a duplicate extreg and/or an extreg that has been automatically generated, set [image] Activate extreg prompting for registration.

Note: This feature works solely for molecule databases.

For complete instructions on registering extregs, see Chapter 6, "Interactive Registration for Remote Databases," in the ISIS/Base Database Maintenance manual.


Show Host Errors

To display error messages from the host when you access remote databases, set [image] Show host errors.

To hide host error messages, set [image].


Clear Old Data on New Record

To specify that any old data be cleared when you create a new record, set [image] Clear old data on new record.

If you prefer to edit older data when you create a new record, set [image] Clear old data on new record.


Adjust Text Display to Match Printed Appearance (PC Only)

To adjust the screen display to match the appearance of the printed text, set [image] Adjust text display to match printed appearance.

The text on the screen is now formatted to the specifications of the current printer in the Print Setup dialog box. This setting might make text difficult to read on the screen.

Note: This setting is available on the PC only.


Locate ISIS/Draw for Transfer (Mac Only)

To specify the location of ISIS/Draw 2.0 so that you can transfer structures from ISIS/Base, first choose Options > Settings > Session. Then, click the General tab and click Locate ISIS/Draw for transfer. Navigate to the ISIS/Draw 2.0 program and then click Open.

Note: You only need to do this once.


Save, Save As, Read

Save

To save changes you made to the current settings, to the currently-opened settings file, click Save.

Save As

To specify a name and location for a new settings file, click Save As.

Read

To read in a user-defined settings file, click Read.


OK, Cancel

OK

To use the dialog box settings for the current ISIS/Base work session, click OK. The settings that you change in the dialog box are not saved in the settings file when you exit ISIS/Base.

To save the current settings, click Save before you exit ISIS/Base.

Cancel

To cancel all modifications to settings, including modifications made by reading in a new settings file and modifications that you made in other Settings tabs, click Cancel. This also closes the Settings dialog.


Settings -- Header/Footer

Use this dialog to:

*	Specify the default text of headers and footers that ISIS/Base prints with your form.

Note: Do not use this dialog box to change the appearance of an existing form. For information on how to edit an existing form, click here.

Click any of the following items:

Apply

Page, Date, Time

Color, Font

OK, Cancel

Save, Save As, Read

For more information on how to work with ISIS/Base settings, click here.


Color

To specify the default color of text in a specific header/footer position, first click the relevant header/footer box. Then, click the Color box and choose a color.

To customize a color or to create a color, click the box and choose Other.... You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on using this feature.


Font

To specify the default font, size, and style of text in a specific header/footer position, first click the relevant header/footer box. Then, click Font.


Similarity Values

Use this dialog to:

*	Conduct an MSim or an RSim search. You need to enter similarity values into the Structure and/or Reacting Centers text boxes and to specify a similarity type.

 Requirements to use this dialog

Click any of the following items:

Similarity Values: Structure and/or Reacting Centers

Similarity Types: Normal or Super or Sub

Hint: The number of records that you retrieve depends on the number of structural features that your query has in common with the stored structures. If you do not retrieve the right number of records, do the search again with different similarity values.

If you are not sure which similarity values to enter or which similarity type to specify, see Searching Concepts/Examples.

If you are not sure of the search that you need to use, see the ISIS/Base SearchSelector.


Searching Concepts/Examples

Click any of the following items:

Molecule records: MSim

Reaction records: Reaction components (MSim) or reactions (RSim)


Requirements to Use This Dialog

MSim Searches

*	You must use a molecule (or a reaction component without a reaction arrow) as your query.

*	Enter your molecule query into the Structure box or table on your ISIS/Base form. Or, enter your reaction component query into a box or table that will hold it. For example, enter a reactant query into the Reactant Structure box.

*	If your query contains any query features or stereochemistry, the search ignores those features and any stereochemistry.

RSim Searches

*	You must use an entire reaction as your query. An entire reaction contains at least one reactant and at least one product (rather than solely a reactant and a reaction arrow or solely a product and a reaction arrow).

*	Enter your reaction query into the Reaction Structure box or table on your ISIS/Base form.

*	If your query contains any query features or stereochemistry, the search ignores those features and any stereochemistry.


Similarity Values

MSim Searches

You can specify the degree of structural similarity between your molecule query and the structures retrieved if you enter a value from 0 and 100 (these are not actual units). The higher the value, the more similarity.

RSim Searches

You can specify the degree of structural similarity between the reaction components in your reaction query and those in the reaction components retrieved if you enter a value from 0 and 100 (these are not actual units). The higher the value, the more similarity.

In addition, you can specify the degree of transformational similarity between the reacting centers in your transformation (reaction) query and those in the reactions retrieved if you enter a value from 0 and 100. The higher the value, the more similarity.


Similarity Types

If you specify a value for structural similarity, you can also specify that the structures retrieved contain:

*	More structural complexity than your query. (Your query is a substructure of the structures retrieved.) Example

*	Less structural complexity than your query. (Your query is a superstructure of the structures retrieved.) Example

*	The same structural complexity as your query. (Your query is neither a substructure nor a superstructure of the structures retrieved.) Example


Example


Example


Example


Structure

To specify the degree of structural similarity between your query and the structures retrieved, click the Structure box and enter a value from 0 and 100 (these are not actual units). The higher the value, the more similarity.

Note: If you do not retrieve the right number of records, do the search again with different similarity values.


Reacting Centers

The degree of similarity between the reacting centers in your reaction query and those in the structures retrieved is called the transformational similarity (or reacting center similarity).

To specify the degree of transformational similarity between your query and the structures retrieved, click the Reacting Centers box and enter a value from 0 and 100 (these are not actual units). The higher the value, the more similarity.

Note: If you do not retrieve the right number of records, do the search again with different similarity values.


Normal

If you specify a structural similarity value, you can also specify the degree of structural complexity. To retrieve structures that contain the same structural complexity as your query, set [image] Normal.

For example:


Super

If you specify a structural similarity value, you can also specify the degree of structural complexity. To retrieve structures that contain less structural complexity than your query, set [image] Super.

For example:


Sub

If you specify a structural similarity value, you can also specify the degree of structural complexity. To retrieve structures that contain more structural complexity than your query, set [image] Sub.

For example:


TCP/IP Network Information

Use this dialog to:

*	Edit TCP/IP connectivity information when you create a new remote database.

*	Edit TCP/IP connectivity information when you configure an existing remote database.

Click any of the following items:

Hosts

Ports

Internet address

Port


Hosts

To select a node, click the Hosts box, and then click the name of the node. The address for the node that you selected displays in the Internet address box.


Ports

To select a port, click the Ports box, and then click the name of the port. The address for the port that you selected displays in the Port box.


Internet address

To specify an Internet address, click the Internet address box, and then enter the address. Use this box to enter addresses for nodes not listed in the Hosts box.


Port

To specify a port, click the Port box, and then enter the port address. Use this box to enter addresses for ports not listed in the Ports box.


Open List

Use this dialog to:

*	Open a list of search results that is an object that was saved in your database (but that was not saved as part of the database). You can then use this list of records without executing the search again.

Note: To select a list to open, click the name of the list.

Click any of the following items:

Description

Permanent/Temporary

Set search domain to the new list

Set search domain to the entire database


Description

Displays the description of the list that you entered when you created the list.


Permanent/Temporary

Displays whether the list is a permanent list or a temporary list.


Set Search Domain to the New List

To specify that the search domain be set to the selected list, set [image] Set search domain to the new list.


Set Search Domain to the Entire Database

To specify that the search domain be set to the entire currently-open database, set [image] Set search domain to the entire database.


Upgrade Database

Use this dialog to:

*	Upgrade a database created with an earlier version of ISIS/Base to an ISIS/Base 2.0 database.

Note: (1) You will not be able to open an upgraded database with versions of ISIS/Base earlier than 2.0. ISIS/Base automatically saves a copy of the original database with a ".v12" extension. (2) You cannot upgrade a database that contains embedded PL code. See your System Administrator for more information.

Click any of the following items:

Upgrade

Cancel


Upgrade

To upgrade the database, click Upgrade.

*	Lists and queries that you saved as database objects are automatically upgraded.

*	Lists that you saved as external files can be imported into an upgraded database and used.

*	Forms that you saved as database objects in ISIS/Base versions 1.2 or later are automatically upgraded.

*	Forms that you saved as external files in ISIS/Base version 1.2 or later are automatically upgraded when you import them into an upgraded database.

*	Forms that you created in ISIS/Base 1.0, 1.01, or 1.1 and either saved as database objects or saved as external files: You see the Form Upgrade dialog, where you specify which forms to upgrade and how to upgrade them.

Note: (1) You will not be able to open an upgraded database with versions of ISIS/Base earlier than 2.0. (2) You cannot upgrade a database that contains embedded PL code. See your System Administrator for more information.


Cancel

To close the dialog box without upgrading the database, click Cancel.


Conversion Required

You cannot open a database that was created with a pre-2.0 version of ISIS/Base. To open the database, you must first convert it, and then upgrade it. You only need to perform these steps one time to convert and upgrade a database created with a pre-2.0 version of ISIS/Base.

We recommend that you print these instructions before starting the conversion. To do so, choose File > Print.

Note: (1) You will not be able to open an upgraded database with versions of ISIS/Base earlier than 2.0. (2) You cannot upgrade a database that contains embedded PL code. See your System Administrator for more information.

To convert a database that was created with a pre-2.0 version of ISIS/Base, do the following:

1.	Choose File > Quit to exit ISIS/Base.

2.	Double-click the BaseDBConverter icon.

3.	Choose File > Convert Database.

4.	Navigate to the disk and folder that contains the database created with a pre-2.0 version of ISIS/Base that you want to convert.

5.	Highlight the name of the ISIS/Base database.

6.	Click Open. After the conversion is finished, you see a message confirming that the conversion is complete.

7.	Click OK.

8.	Choose File > Quit to exit BaseDBConverter.

To upgrade the converted database so that you can use it with ISIS/Base 2.0, do the following:

1.	Double-click the ISIS/Base 2.0 icon to start ISIS/Base.

2.	Choose File > Open Database.

3.	Navigate to the disk and folder that contains the database that you converted.

4.	You will see two versions of the database, one with the original name and one with _V12 appended to the name. Highlight the name of the ISIS/Base database with the original name.

5.	Click OK.

For information on how upgrading affects existing forms, lists, and queries, click here.


Upgrading existing forms, lists, and queries

*	Forms that you saved as database objects in ISIS/Base versions 1.2 or later are automatically upgraded.

*	Forms that you saved as external files in ISIS/Base version 1.2 or later are automatically upgraded when you import them into an upgraded database.

*	Forms that you created in ISIS/Base 1.0, 1.01, or 1.1 and either saved as database objects or saved as external files: You see the Form Upgrade dialog, where you specify which forms to upgrade and how to upgrade them.

*	Lists and queries that you saved as database objects  are automatically upgraded.

*	Lists that you saved as external files can be imported into an upgraded database and used.

Note: (1) You will not be able to open an upgraded database with versions of ISIS/Base earlier than 2.0. (2) You cannot upgrade a database that contains embedded PL code. See your System Administrator for more information.


Settings -- Form

Use this dialog to:

*	Specify the default appearance of box and table borders, labels, data, text, and lines on forms. You see the defaults take affect for each new box, table, line, or text that you create.

Note: Do not use this dialog box to change the appearance of an existing form. For information on how to edit an existing form, click here.

Click any of the following items:

Label

Data

Line Tool

Text Tool

OK, Cancel

Save, Save As, Read

For more information on how to work with ISIS/Base settings, click here.


Box Properties -- Border/Pattern

Use this dialog to:

*	Change the width, color, and style of box borders

*	Add or change the fill color and fill pattern inside of a box

 Requirements to use this dialog

Click any of the following items:

Field name

Style Borders

Fill

OK, Cancel, Next, Previous

For complete information on editing forms, click here.


Requirements to Use This Dialog

*	In Forms mode, you can change options on all of the tabs, including Field Name, Border/Pattern, Data/Label, Chem Display, Function, and Floating Boxes.

*	In Query, Browse, and Update modes you can change the options for solely the Border/Pattern, Data/Label, and Chem Display tabs.


Show Borders

Top

To show the top border of a box, set [image] Top.

Left

To show the left border of a box, set [image] Left.

Bottom

To show the bottom border of a box, set [image] Bottom.

Right

To show the right border of a box, set [image] Right.


Style Borders

Show Borders

Width

Color

Style


Width

To specify the width for borders, click the Width box, and then choose a width.


Color

To specify the color for borders, click the Color box, and then choose a color. To customize a color or to create a color, click the box and choose Other.... You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on using this feature.


Style

To specify the line style for borders, click the Style box, and then choose a style.


Fill

Color

To specify the fill color for the box, click the Color box and choose a color. To customize a color or to create a color, click the box and choose Other.... You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on using this feature.

Pattern

To specify the style of the fill pattern for the box, click the Pattern box and choose a pattern.

Note: You must choose a fill pattern to see the fill color. However, you can choose a solid pattern.


Box Properties -- Chem Display

Use this dialog to:

*	Set the chemical display for structures in a form box (Structures include molecules, reactions, 3D molecules, and sequences.)

 Requirements to use this dialog

Click any of the following items:

Field name

Structure Display

Residue/Sequence Display

Query highlight

Atom Display

Orient hits to match query

OK, Cancel, Next, Previous

For complete information on editing forms, click here.


Structure Display

To specify how a structure displays in a box, choose one of the following options:

As drawn

As drawn (scaled)

Defaults

Defaults (scaled)

Bond length

Atom font

Note: The Structure Display option does not affect how a structure is registered. Click here for information on how structures are registered.

See also:

To change the bond length of structures in a box or column

To change the atom font attributes of structures in a box or column

To display a structure as drawn or using box defaults and optionally scale the structure to fit inside of the box


As drawn

Choose As Drawn to specify that structures display in a box exactly as they were drawn (including font, bond length, and color).

If you have a remote database, this option will display the bond length as it was drawn, but the atom font and structure color are set as form properties. (This option was called Structure Scaling: As Drawn in previous versions of ISIS/Base.)


As drawn (scaled)

Choose As Drawn (Scaled) to specify that structures display as they were drawn, but are scaled in size to fit the box (if necessary).

If you have a remote database, this setting will display the original bond length or scale the bond length in proportion to is original size. The atom font and structure (data) color are set as form properties.(This is a new option in ISIS/Base.)


Defaults

Choose Defaults to specify that structures display using form properties (bond length, atom font, and data color). (This option was called Structure Scaling: Std. Bond in previous versions of ISIS/Base.)


Defaults (scaled)

Choose Defaults (Scaled) to specify that structures display using form properties (bond length, atom font, and data color) that are scaled to fit the box (if necessary). (This option was called Structure Scaling: Fit Box in previous versions of ISIS/Base.)


Registration of Structures

The Structure Display option only affects the display of structures. This setting is ignored during the registration of a structure. When you transfer an ISIS/Draw sketch into the form of a local database for registration, the sketch is always registered exactly as it was drawn (unless sketch storage is Off through PL). However, the display of the structure might differ from what is registered if the Box/Column properties has the Structure display option set to Defaults. Defaults will display the structure in the bond length, font, and data color that is set for the box/column properties.

When you import an ISIS/Draw molfile/rxnfile into a local or remote database for registration or you register a sketch into a remote database, the bond length is registered as it was drawn. However, molfiles, rxnfiles, and remote databases do not store other sketch properties (for example, color and font information). If you set the Structure Display option to As Drawn, you see the bond length as drawn, but the color and font display are determined by what is set in the Box/Column properties. If you set the Structure Display to Defaults, the entire structure display is determined by what is set in the Box/Column properties.


Atom Display

Hydrogen labels

To show or hide implicit hydrogens on the structure, click the Hydrogen labels box and choose as drawn, on all atoms, on heteroatoms, or on all heteroatoms and terminal atoms.

ISIS does not recognize implicit hydrogens in a search query, even if you show them. Thus, to retrieve the correct search results, always use explicit hydrogens in your search query. For information about how to create an explicit hydrogen, click here.

Atom numbers

To specify whether or not atom numbers display, click the Atom numbers box, and then choose On or Off.

See also:

To display hydrogens on structures

To display atom numbers on structures


Query highlight

For remote databases only: Use this option to highlight the original query within 2D structures, 3D structures, or reactions that are retrieved in a search. Use this option with the following search types:

*	Substructure (SSS)

*	Reaction Substructure (RSS)

*	3D Substructure: SSS3D, SSS3D/Biopoly, CFS, and CFS/Biopoly

See also:

To highlight the query-structure in color

The ISIS/Base search types


Orient hits to match query

For remote databases only: To orient 2D or 3D structures that are retrieved in a search to the three atoms that best fit the query, set [image] Orient hits to match query. To use this option, you must also set Query Highlighting.

See also:

To orient structures to match the query-structure


Residue/Sequence display

Show leaving groups

To show residue leaving groups, set [image] Show leaving groups.

Expand residues

To show residues that are expanded, set [image] Expand residues.

Show crosslink bonds

To show the crosslink bonds, set [image] Show crosslink bonds.

Show sequence bonds

To show sequence bonds, set [image] Show sequence bonds.

Show residue brackets

To show the residue brackets, set [image] Show residue brackets.

See also:

To show or hide residue brackets or leaving groups

To expand a residue to show the underlying structure

To show or hide sequence bonds or crosslink bonds


Box Properties -- Data/Label

Use this dialog to:

*	Change the color, font, or position of data in a box

*	Change the color, font, or position of labels in a box

*	Change how text or numeric data is displayed in the box

*	Change the box label

 Requirements to use this dialog

Click any of the following items:

Label

Data

OK, Cancel, Next, Previous

For complete information on editing forms, click here.


Label

Label

Alignment

Color

Font


Data

Field name

Field type

Alignment

Color

Text format

Decimal places

Scientific notation

Font


Label

To specify a label that will display in a box to identify the data content, enter a name in the Label box.


Alignment

To specify the label position within a box, click the Alignment box and choose one of the nine positions.


Color

To specify the color of the label, click the Color box and choose a color. To customize a color or to create a color, click the box and choose Other.... You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on using this feature.


Font

To specify the font, size, and style (including sub- and superscript) for the label, click Font.


Alignment

To specify the position of data within a selected box, click the Alignment box and choose one of the nine positions.


Color

To specify the color of the data, click the Color box and choose a color. To customize a color or to create a color, click the box and choose Other.... You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on using this feature.

You can change the color of a structure if you set Structure Display on the Chem Display tab to Defaults or Defaults (scaled).


Text format

To specify how text data displays in a box when it reaches the right border and there is additional text to display, click the Text format box. Then, choose As is, wrapped, or truncated.


Decimal places

To specify the number of decimal places for the display of numeric data, click the Decimal places box, and then enter or choose a number.

If you choose Auto, ISIS/Base uses the number of decimal places as registered in the database.

Decimal places is available when the field type is real or range.


Scientific notation

To specify that the data be displayed in scientific notation, click [image]. For example, you can display temperature data as -1.0E+001 in scientific notation.

Scientific notation is available when the field type is real or range.


Font

To specify the font, size, and style (including sub- and superscript) for the data, click Font.


Box Properties -- Field Name

Use this dialog to:

*	Label a box and/or connect the box to a database field

*	Change the label or database field that is connected to a box

*	Remove a field that is connected to a box

 Requirements to use this dialog

Click any of the following items:

Database fields

Field type

Field name

Label

OK, Cancel, Next, Previous

For complete information on editing forms, click here.


Database fields

To connect a database field to the selected box, click a database field name. The scrolling list displays the fields available in the current database.


Field name

Displays the name of the field that is selected in the Database fields box.


Non-Unique Field Selection

If you enter a field name that is not unique, this dialog box shows a list of all the fields in the database that partially match the field name that you entered. Select a field name from the box.


Box Properties -- Function

Use this dialog to:

*	Display default data (date, calculation, sketch, or text) in a box

*	Attach a PL function to a box

*	Change the sequence ID number of the box

 Requirements to use this dialog

Click any of the following items:

Field name

Field type

Field label

PL function

Box name

Default data

Invisible box

Sequence ID

OK, Cancel, Next, Previous

Note: You can only specify these options for one box in a form at a time.

For complete information on editing forms, click here.


Field name

Displays the name of the field connected to the selected box.


Field type

Displays the type of data stored for the field that is connected to the selected box.


Field label

Displays the label that appears in a box to identify the data content.


PL function

To specify that a PL trigger function be connected to the selected box, enter the name of a PL trigger function.

See also:

To attach a PL program to a box or column


Box name

To name a box for use in a calculation, click the box and enter box(name). For example, box(molweight).


Default data

You can specify that a box display or register default data. To do so, click the Default Data box and choose a type:

Today's date

String

Calculation

Sketch

See also:

To set a box or column to use default data


Sequence ID

To specify the order in which the cursor move from box to box when you press the Tab key, click in the Sequence ID box and enter a number.

See also:

To change the sequence ID number of a box or table


Invisible box

To specify that the selected box, and its data contents, be invisible on the form (except in Forms mode), click [image].


OK, Cancel, Next, Previous

OK

To apply the current settings on all of the tabs to the selected box(es), click OK.

Cancel

To close the dialog box without applying the changes, click Cancel.

Next

To accept the changes to the selected box, and then select the next box in the form, click Next. The changes to box properties are immediately applied to the box, before the next box is selected. If the selected box is the last box in the form, click Next to select the first box in the form.

Previous

To accept the changes to the selected box, and then select the previous box in the form, click Previous. The changes to box properties are immediately applied to the box, before the previous box is selected. If the selected box is the first box in the form, click Previous to select the last box in the form.

Notes: (1) The order in which ISIS/Base moves to the next or previous box in a form is determined by the Sequence ID number, located on the Function tab. Each box and table in a form is assigned a sequence ID number in the order in which it was drawn. (2) In the Chemical Display and Floating Boxes tabs, the Next and Previous buttons select the next and previous box connected to a structure or reaction field. If there is only one structure or reaction box in the form, then Next and Previous are not available.


Box Properties -- Floating Boxes

Use this dialog to:

*	Display reaction data within a reaction. You can display reaction data above or below a reactant, arrow, and/or product in floating boxes. Floating boxes are invisible; so that all you see is the reaction data inside of the box, but not the box borders.

 Requirements to use this dialog

Click any of the following items:

Field name

Above/Below Reactants, Arrow, or Products

Data label

Decimal places

Scientific notation

Font

OK, Cancel, Next, Previous

Note: In the Floating Boxes tab, the Next and Previous buttons select the next and previous box connected to a reaction field. If there is only one reaction box in the form, then Next and Previous are not available.

For complete information on editing forms, click here.


Requirements to Use This Dialog

*	In Forms mode, you can change options on all of the tabs, including Field Name, Border/Pattern, Data/Label, Chem Display, Function, and Floating Boxes.

*	In Query, Browse, and Update modes you can change the options for solely the Border/Pattern, Data/Label, and Chem Display tabs.

*	To view individual data for multiple reactants and/or products within a reaction, set external field names for the reactant and product parent fields.


Above/Below Reactants, Arrow, or Products

To set or change a floating box above or below reactants, products, or the reaction arrow, click the relevant radio button. Then, select a field name from the scrolling list to connect to the floating box. Select No Field to remove a floating box.

Note: Parent fields and sketch fields cannot be used as floating boxes.


Data label

To specify a label for the box that will identify the data content, enter a name.


Table/Column Properties -- Border/Pattern

Use this dialog to:

*	Change the width, color, and style of table borders and dividers

*	Show or hide: table borders, column dividers, row dividers, and table header bar

*	Add or change the fill color and/or fill pattern inside of the selected column(s)

 Requirements to use this dialog

Click any of the following items:

Style Borders

Show Style

Fill

Show column divider(s)

OK, Cancel, Next, Previous

For complete information on editing forms, click here.


Show Borders

Note: These options apply only to tables.

Top

To show the top border of a table set [image] Top.

Left

To show the left border of a table, set [image] Left.

Bottom

To show the bottom border of a table, set [image] Bottom.

Right

To show the right border of a table, set [image] Right.


Style Borders

Show Borders

Width

Color

Style


Width

To specify the width for table borders, click the Width box, and then choose a width.


Color

To specify the color for table borders, click the Color box, and then choose a color. To customize a color or to create a color, click the box and choose Other.... You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on using this feature.


Style

To specify the line style for table borders, click the Style box, and then choose a style.


Show Style

Note: These options apply to styling a table and not individual columns.

Header bar

To display the table header bar, set [image] Header-bar.

Row dividers

To display the row dividers, set [image] Row dividers.

Width

To specify the width of the header bar or row dividers, click the Width box and choose a width in points, or choose Hairline.

Color

To specify the color of the header bar or row dividers, click the Color box and choose a color. To customize a color or to create a color, click the box and choose Other.... You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on using this feature.

Style

To specify the line style of the header bar or row dividers, click the Style box and choose a line style.


Fill

Color

To specify the fill color for the selected column(s) in the table, click the box and choose a color. To customize a color or to create a color, click the Color box and choose Other.... You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on using this feature.

Pattern

To specify the style of the fill pattern for the selected column(s) in the table, click the Pattern box and choose a pattern.

Note: You must choose a fill pattern to see the fill color. However, you can choose a solid pattern.


Show column divider(s)

To display column dividers, set [image] Show column divider(s).


OK, Cancel, Next, Previous

OK

To apply the current settings on all of the tabs to the selected column(s) or to the entire table, click OK.

Cancel

To close the dialog box without applying the changes, click Cancel.

Next (applies only to columns)

To accept the changes to the selected column and select the next column, click Next. The changes to column properties are immediately applied to the column, before the next column is selected. If the selected column is the last column in the form, click Next to select the first column in the form.

Previous (applies only to columns)

To accept the changes to the selected column and select the previous column, click Previous. The changes to column properties are immediately applied to the selected column, before the previous column is selected. If the selected column is the first column in the form, click Previous to select the last column in the form.


Table/Column Properties -- Chem Display

Use this dialog to:

*	Set the chemical display for structures within a table or column. (Structures include molecules, reactions, 3D molecules, and sequences.)

 Requirements to use this dialog

Click any of the following items:

Field name

Structure Display

Residue/Sequence display

Query highlight

Atom Display

Orient hits to match query

OK, Cancel, Next, Previous

Notes: (1) If you selected a table, these settings apply to every column in the table that contains a chemical structure. (2) In the Chemical Display tab, the Next and Previous buttons select the next and previous column connected to a structure field. If there is only one structure column in the form, then Next and Previous are not available.

For complete information on editing forms, click here.


Structure Display

To specify how a structure displays in a column, choose one of the following options:

As drawn

As drawn (scaled)

Defaults

Defaults (scaled)

Bond length

Atom font

Note: The Structure Display option does not affect how a structure is registered. Click here for information on how structures are registered.

See also:

To change the bond length of structures in a box or column

To change the atom font attributes of structures in a box or column

To display a structure as drawn or using box defaults and optionally scale the structure to fit inside of the box


As drawn

Choose As Drawn to specify that structures display in a column exactly as they were drawn (including font, bond length, and color).

If you have a remote database, this option will display the bond length as it was drawn, but the atom font and structure color are set as form properties. (This option was called Structure Scaling: As Drawn in previous versions of ISIS/Base.)


As drawn (scaled)

Choose As Drawn (Scaled) to specify that structures display as they were drawn, but are scaled in size to fit the column (if necessary).

If you have a remote database, this setting will display the original bond length or scale the bond length in proportion to is original size. The atom font and structure (data) color are set as form properties.(This is a new option in ISIS/Base.)


Defaults

Choose Defaults to specify that structures display using form properties (bond length, atom font, and data color). (This option was called Structure Scaling: Std. Bond in previous versions of ISIS/Base.)


Defaults (scaled)

Choose Defaults (Scaled) to specify that structures display using form properties (bond length, atom font, and data color) that are scaled to fit the column (if necessary). (This option was called Structure Scaling: Fit Box in previous versions of ISIS/Base.)


Bond Length

To specify the default bond length if you have Structure Display set to Defaults, click the Bond Length text-entry box and enter a bond length in inches. If Structure Display is set to As drawn or As drawn (scaled), ISIS/Base ignores the bond length setting.


Atom Font

To specify the default font, size, and style (including sub- and superscript) for atoms if you have Structure Display set to Defaults, click Atom Font. If Structure Display is set to As drawn, ISIS/Base ignores the Atom font settings.


Field name

Displays the name of the field connected to the selected column.


Table/Column Properties -- Data/Label

Use this dialog to:

*	Change the color, font, or position of data within a column or table

*	Change the position of labels within a column or table

*	Change how text or numeric data is displayed within columns or a table

*	Change a column heading

 Requirements to use this dialog

Click any of the following items:

Label

Data

OK, Cancel, Next, Previous

For complete information on editing forms, click here.


Label

Label

Alignment

Color

Font


Data

Field name

Field type

Alignment

Color

Text format

Decimal places

Scientific notation

Font


Alignment

To specify the label position within a column, click the Alignment box and choose one of the nine positions.

Note: If you selected a table, this sets the label alignment for all columns in the table.


Color

To specify the color of the label, click the box and choose a color. To customize a color or to create a color, click the Color box and choose Other.... You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on using this feature.

Note: If you selected a table, this sets the label color for all columns in the table.


Font

To specify the font, size, and style (including sub- and superscript) for the label, click Font.

Note: If you selected a table, this sets the font, size, and style for labels in all columns in the table.


Label

Displays the label for the selected column. If you selected a table, this box is blank.


Field name

Displays the name of the field connected to the selected column. If you selected a table, this box is blank.


Field type

Displays the type of data stored for the field that is connected to the selected box.


Alignment

To specify the position of data within a column, click the Alignment box and choose one of the nine positions.

Note: If you selected a table, this sets the data alignment for all columns in the table.


Color

To specify the color of the data, click the Color box and choose a color. To customize a color or to create a color, click the box and choose Other.... You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on using this feature.

You can change the color of structures if you set Structure Display on the Chem Display tab to Defaults or Defaults (scaled).

Note: If you selected a table, this sets the for all columns in the table.


Font

To specify the font, size, and style (including sub- and superscript) for the data, click Font.

Note: If you selected a table, this sets the font, size, and style for the data for all columns in the table.


Text format

This option specifies how text data displays in a column when it reaches the right border and there is additional text to display. Click the Text format box, and choose wrap, truncate, or display as registered.

Note: If you selected a table, this sets the data text format for all columns in the table.


Decimal places

To specify the number of decimal places for the display of numeric data, click the Decimal places box, and then enter or choose a number.

If you choose Auto, ISIS/Base uses the number of decimal places as registered in the database.

Decimal places is available when the field type is real or range.

Note: If you selected a table, this specifies the number of decimal places for the display of numeric data for all columns in the table.


Scientific notation

To specify that the data be displayed in scientific notation, click [image]. For example, you can display temperature data as -1.0E+001 in scientific notation.

Scientific notation is available when the field type is real or range.

Note: If you selected a table, this specifies that numeric data for all columns in the table be displayed in scientific notation.


Table/Column Properties -- Field Name

Use this dialog to:

*	Add, delete, or replace columns in a table.

 Requirements to use this dialog

Click any of the following items:

Database fields

Field type

Columns

Show repeating data

Column label

Add, Replace, Delete

Reorder columns

OK, Cancel, Next, Previous

For complete information on editing forms, click here.


Database fields

To add, replace, or delete a database field connected to the selected table or column, click a database field name. The scrolling list displays the fields available in the database that is currently opened.


Field type

Displays the type of data stored for the field that connected to the selected column or table.


Columns

Displays all fields in the selected table, in alphabetical order. To select a column, click the name of the column.

The type of selected table is displayed next to Columns: The three types of tables are simple, layered, and uncoupled.


Show repeating data

To display repeating data, set [image] Show repeating data. It might be easier to read the data in layered or uncoupled l tables if you set [image].

Note: This option is available only for tables.


Column label

To edit the label of the column selected in the Columns box, click the Column label box, and then edit the label.


Add, Replace, Delete

Add

To add a new column to the table, click the name of a child field in the Database fields box, and then click Add. The new column is added to the Columns box. (Available only for tables.)

To add columns for all child fields under a parent field, click the parent field in the Database fields box, and then click Add. The new columns are added to the Columns list.

Replace

To replace a field connected to a column with a different field, select the field that you want to replace in the Column box. Then select a different field in the Database Fields list box. Click Replace. (Available for columns and tables.)

Delete

To delete a column, select the column from the Columns list, and then click Delete. (Available only for tables.)


Reorder columns

To shift a column to the left, select the column, and then click [image].

To shift a column to the right, select the column, and then click [image].


Table/Column Properties -- Function

Use this dialog to:

*	Display default data (date, calculation, sketch, or text) in a column

*	Attach a PL function to a column

*	Change the sequence ID number of the column

 Requirements to use this dialog

Click any of the following items:

Field name

Field type

PL function

Column name

Default data

Sequence ID

OK, Cancel, Next, Previous

Note: You can only specify these options for one column in a form at a time.

For complete information on editing forms, click here.


Field Label

Displays the label that appears in a column to identify the data content.


PL function

To specify that a PL trigger function be connected to the selected column, enter the name of a PL trigger function.

Note: This setting applies for only one column at a time.

See also:

To attach a PL program to a box or column


Column name

To specify a name for the selected column, enter the name.


Default data

You can specify that a column display or register default data. To do so, click the Default Data box and choose a type:

Today's date

String

Calculation

Sketch

See also:

To set a box or column to use default data


Sequence ID

To specify the order in which the cursor move from a box or table to this table when you press the tab key, click in the Sequence ID box and enter a number.

Note: This setting applies only to tables.

See also:

To change the sequence ID number of a box or table


Table/Column Properties -- Floating Boxes

Use this dialog to:

*	Display reaction data within a reaction. You can display reaction data above or below a reactant, arrow, and/or product within a reaction. Floating boxes are invisible; so that all you see is the data.

 Requirements to use this dialog

Click any of the following items:

Field name

Above/below Reactants, arrow, or Products

Data label

Decimal places

Scientific notation

Font

OK, Cancel, Next, Previous

Note: In the Floating Boxes tab, the Next and Previous buttons select the next and previous column connected to a reaction field. If there is only one reaction column in the form, then Next and Previous are not available.

For complete information on editing forms, click here.


Field name

Displays the name of the field connected to the selected column.


Import SDFile

Use this dialog to:

*	Import a batch of records from an SDfile to register as new records or updates to existing records in the current database.

*	Instruct ISIS/Base how to import a record from the SDfile that contains an ID number or structure that already exists as a record in the database.

 Requirements to use this dialog

Click any of the following items:

Duplicate ID Options

Duplicate Structure Options

Date Format

Year Options

Match on external field names only

For step-by-step instructions on importing SDfiles, see the ISIS/Base Database Maintenance 2.0 manual.


Import RDFile

Use this dialog to:

*	Import a batch of records from an RDfile to register as new records or updates to existing records in the current database.

*	Instruct ISIS/Base how to import a record from the RDfile that contains an ID number or structure that already exists as a record in the database. (Structures include: molecules, reactions, 3D molecules, and sequences.)

 Requirements to use this dialog

Click any of the following items:

Duplicate ID Options

Duplicate Structure Options

Date Format

Year Options

Match on external field names only

For step-by-step instructions on importing RDfiles, see the ISIS/Base Database Maintenance 2.0 manual.


Year Options

Use the following options to specify what ISIS/Base should do with an imported RDFile or SDFile record that contains a 2-digit year. Click here for information on Year-2000 issues.

Click here for more information about how ISIS/Base handles date formats.

Append current century and register record

To append the current century (19 or 20) to the 2-digit date and then register the record, set [image] Append current century and register record.

Leave date field blank and register record

To leave the entire date field blank and then register the record, set [image] Leave date field blank and register record.

Note: For remote databases only, ISIS/Host may put in the current date instead of leaving the date field blank. This depends on how ISIS/Host was configured.


Requirements to Use This Dialog

*	To import 2D or 3D structures, the top-level molstructure or modelstructure field must have an external field name of *structure. You can view and create external field names in the View Definition dialog box. Choose Database > View Definition.

*	You must import data in Update mode.


Requirements to Use This Dialog

*	To import reactions from an RDfile, the top-level reaction field in the database must have an external field name of *rxn (or *reaction). To import molecules or models from an RDfile, the top-level molstructure or modelstructure field must have an external field name of *structure. You can view and create external field names in the View Definition dialog box. Choose Database > View Definition.

*	You must import data in Update mode.


Export Fields

Use this dialog to:

*	Use this dialog box to specify from which fields to export data to an SDfile, RDfile, or a local database. If you are exporting data to a local database, the fields that you specify become the fields in the new database.

 Requirements to use this dialog

Click any of the following items:

Database fields

Exported fields

Add, Remove

For step-by-step instructions on exporting a batch of data to an SDfile or RDfile or exporting data from an existing database to create a new local database, see the ISIS/Base Database Maintenance 2.0 manual.


Requirements to use this dialog

*	You must have a list of records to export.

*	You must be in Browse mode to export data.

*	To export reactions to an RDfile, provide external field names for the top-level reaction field.

*	To export 2D or 3D structures to an SDfile or RDfile, provide an external field names for the top-level 2D or 3D structure field.

*	To export reactions to a local database, provide external field names for the reaction, reactant molstructure, and product molstructure field.


Database fields

To specify fields for export, click the field name in the Database fields list, and then click Add. If you select a parent field and click Add, all child fields below the parent field are selected for export.

If you are exporting data to an RDfile, you see a complete list of the fields in the current database. RDfiles have a hierarchical file-structure and allow you to transfer data from all levels of the database. You must export reactions and data to an RDfile because SDfiles do not support reactions.

If you are exporting data to an SDfile from a local database, you see solely the top-level "<ROOT>" fields in the database. SDfiles have a flat file-structure and allow you to transfer top-level data. If you are exporting data from a remote database, you see fields from all levels of the database. However, if you export lower-level fields the database hierarchy is flattened so that all fields are written to the SDfile as top-level fields. (ISIS/Base allows the export of lower level fields from a remote database to be compatible with the EXPORT command in ISIS/Host CLI.)


Exported fields

Displays the fields that are selected to export data to an SDfile, RDfile, or local database. If you are exporting data to a local database, the fields listed in the Exported fields list box become the fields in the new database.

To remove a field from the Exported fields list, click the field name, and then click Remove. If you select a parent field and click Remove, all child fields underneath the parent field are removed from the Exported field list.


Add, Remove

Add

To export data from a field to an SDfile or RDfile, you must add the field name to the Exported fields list. Click a parent or child field in the Database fields list, and then click Add.

Remove

To remove a database field name from the Exported fields list, click a parent or child field, and then click Remove.


Duplicate Structure Options

The following options instruct ISIS/Base which action to take when it finds that the structure for a record in the RDfile or the SDfile already exists in the database:

Add a new record including a structure

Add new subrecords only to this record

Merge new data

Merge new data and overwrite existing data

Replace all data for this record

Skip data for this record

Prompt


Duplicate ID Options

The following options instruct ISIS/Base which action to take when it finds that the ID for a record in the RDfile or the SDfile already exists in the database:

Add a new record including a structure

Add new subrecords only to this record

Merge new data

Merge new data and overwrite existing data

Replace all data for this record

Skip data for this record

Prompt


Add a new record including a structure

To import all of the data in the RDfile or the SDfile and register it as a new record in the database, set [image] Add a new record including a structure.

Note: This option is not available if a record contains a duplicate structure, and you have a remote database that does not allow duplicate structures.


Add new subrecords only to this record

To import subrecord data from a record in an RDfile into a record that already exists in the database, set [image] Add new subrecords only to this record. ISIS/Base registers the data into fields that are located below the top-level of the database hierarchy. If the RDfile contains top-level data, that data is ignored.

Note: This option is not available for SDfiles because SDfiles store top-level data, but not subrecord data.


Merge new data

To import data from a record in the RDfile or SDfile to matching fields in the database record that are empty, set [image] Merge new data. ISIS/Base does not overwrite existing data in the record, and it creates new subrecords if they do not already exist.


Merge new data and overwrite existing data

To import all of the data from a record in the SDfile or RDfile to matching fields in the database record, set [image] Merge new data and overwrite existing data. ISIS/Base overwrites existing data in the record, and creates new subrecords if they do not already exist. When the database contains a field that is not present in the SDfile or RDfile, ISIS/Base preserves that data.

If you chose this option to resolve a duplicate ID, and the structure in the original database record is different from the one in the SDfile or RDfile, then ISIS/Base overwrites the database structure with the structure in the SDfile or RDfile.


Skip data for this record

To retain the data that exists in the database record, and instruct ISIS/Base to attempt to import the next record in the RDfile or SDfile, set [image] Skip data for this record.


Replace all data for this record

To replace the data in the database record with the data in the RDfile or SDfile, set [image] Replace all data for this record.

Note: This option is available only for local databases because you cannot overwrite the record ID (regno) in a remote database.


Prompt

To choose a duplicate option each time that ISIS/Base finds a duplicate structure or ID, set [image] Prompt.


Date Format

Use the following options to specify which date format the database uses. Then, if ISIS/Base imports a record from an RDfile or SDfile that has a different date format, the program translates the date into the right format.

Click here for more information about how ISIS/Base handles date formats.

Month Day Year

To interpret dates formatted as month/day/year, such as 12/31/1995, set [image] Month Day Year.

Day Month Year

To interpret dates formatted as day/month/year, such as 31/12/1995, set [image] Day Month Year.

Year Month Day

To interpret dates formatted as year/month/day, such as 1995/12/31, set [image] Year Month Day.

Year Day Month

To interpret dates formatted as year/day/month, such as 1995/31/12, set [image] Year Day Month.


Match on external field names only

ISIS/Base imports data for a record in an RDfile or SDfile into a database record when field names match. If the field names do not match, create an external field name for the database field. The external field name is used as an alternative field name to match the field name in the RDfile or SDfile to import data. Choose one of these settings when you import the data:

*	To import data only if the field name in the RDfile or SDfile matches an external field name in the database, set [image] Match on external field names only.

*	To import data if the field name in the RDfile or SDfile matches either the external field name or the actual field name in the database, set [image] Match on external field names only.


Duplicate ID

Use this dialog to:

*	Use this dialog box to instruct ISIS/Base which option to use if a record in the RDfile or the SDfile has an ID that already exists in the database. You can apply the option to solely the current record or to the  current record and to all subsequent duplicate records.

Click any of the following items:

Add a new record including a structure

Add new subrecords only to this record

Merge new data

Merge new data and overwrite existing data

Skip data for this record

Replace all data for this record

Auto, Abort, OK

Note: You see this dialog only if you have set [image] Prompt in the Import RDFile or Import SDFile dialog box and ISIS/Base has found a duplicate ID.


Duplicate Structure

Use this dialog to:

*	Instruct ISIS/Base which option to use if a record in the RDfile or SDfile has a structure that already exists in the database. You can apply the option to solely the current record or to the  current record and to all subsequent duplicate records.

Click any of the following items:

Add a new record including a structure

Add new subrecords only to this record

Merge new data

Merge new data and overwrite existing data

Skip data for this record

Replace all data for this record

Auto, Abort, OK

Note: You see this dialog only if you have set [image] Prompt in the Import RDFile or Import SDFile dialog box and ISIS/Base has found a duplicate structure.


Auto, Abort, OK

Auto

To apply the selected duplicate option to the current record and to all subsequent duplicate records, click Auto.

Abort

To stop the import of any further data from the RDfile or SDfile and close the dialog box, click Abort.

OK

To apply the selected duplicate option to the current record only and close the dialog box, click OK. If ISIS/Base finds another duplicate record, then it will prompt you again.


ISIS/Base

This dialog box appears when the destination database does not have a TINFO field that is defined.

Cancel Import

To cancel the import of the structures and close the dialog box, click Cancel Import.

Continue Import

To import structure without checking for duplicate ID numbers and close the dialog box, click Continue Import.


Create Database

Use this dialog to:

*	Copy fields in an existing database (and modify the fields)  to create a new local database. You must open an existing database before you enter this dialog in order to copy and/or modify the existing database fields.

*	Create a new local database without copying fields in an existing database. You must close all ISIS/Base databases before you enter this dialog to avoid copying fields in an existing database.

Click any of the following items:

Field Information

Add, Edit, Delete

Save, Cancel, Clear All

For step-by-step instructions on creating a new local database, see the ISIS/Base Database Maintenance 2.0 manual.


Field Information

To create a new local database without copying fields from an existing database, enter the field information, and then Add the field. To copy and/or modify fields from a database that is already open, select one field at a time in the database field list. Then, Add, Edit, or Delete each field to create a new local database.

Field name

To create or modify a field name, select a field name in the list box. Then, click in the Field name box and modify the field name.

Type

To specify which type of data the field will store, click the Type box and choose a field type.

Length (fixed-text fields only)

To enter or change the number of characters that a fixed text field can store, click the Length box, and then enter the maximum number of characters for the field.

Parent

To specify the parent field of the new or selected field, click the Parent box and choose a parent field.

Vocabulary

To enter or change text or numeric values that are allowable for the field during data entry, click Vocabulary, and then specify the values.

External name

To enter or change an external field name for the selected field, click the External name box and enter an external name.


External Field Name

An external field name is an alternative name for a field that is used for one of the following  purposes:

*	Interactive registration entering data into an ISIS/Base form

*	Batch registration using an SDfile or RDfile to transfer data between databases

*	Exporting a reaction database to create a local database

*	Viewing reaction-condition data within a reaction


Using External Field Names for Batch Registration

When you export and import records using SDfiles and RDfiles, create external field names for the following reasons:

*	To match field names between databases, provide an external field name in one database to match the field name in the other database. For example, if the source database has a boiling.point field and the destination database has a boil_pt field, create an external field name of boiling.point for the boil_pt field in the destination database.

*	To transfer structures between databases, provide an external field name of *structure for the top-level structure or modelstructure field or *reaction for the top-level reaction field in both the source and destination databases.

*	Local databases only: To assign the next available ID (record) number to a new record that is imported, provide an external field name of *ignore for the ID field in the destination database.

You can create an external field name when you create a new field, or you can add the external field name later. To do so, choose Database > View Definition. Select the field, and then click Modify External Name. Enter the external field name, and click OK.


Using External Field Names for Interactive Registration

Local databases only: When you enter structures and data onto an ISIS/Base form to register in a database, create external field names for the following reasons:

*	To enable duplicate structure checking, provide an external field name of *structure for the top-level structure or modelstructure field or *reaction for the top-level reaction field.

*	To automatically register reactant and product molecules when a reaction is registered, provide *reactant and *product external field names for the reactant and product fields. These fields must be located in different branches of a local database hierarchy.

You can create an external field name when you create a new field, or you can add the external field name later. To do so, choose Database > View Definition. Select the field, and then click Modify External Name. Enter the external field name, and click OK.


Using External Field Names to Export a Reaction Database to a Local Database

When you export a reaction database to create a new local database, provide a *rxn external field name for the rxnstructure field. In addition, provide a *reactant external field name for the reactant field and a *product external field name for the product field.

In the following example you provide the *reactant external field name for the reactant molstructure field:

RXN>REACTANT_LINK>MOL>molstructure

And *product for the product molstructure field:

RXN>PRODUCT_LINK>MOL>molstructure

You can create an external field name when you create a new field, or you can add the external field name later. To do so, choose Database > View Definition. Select the field, and then click Modify External Name. Enter the external field name, and click OK.


Using External Field Names to View Reaction-Conditions Within a Reaction

Local databases only: Provide an external field name of *float for the reactant and product parent fields. The reactant and product molstructure fields must be located in separate hierarchies to view reaction-condition data.

In the following example you would provide the *float external field name for the parent fields <REACTANT_LINK> and <PRODUCT_LINK> because they are the parent fields that start the reactant and product hierarchies down to the corresponding molstructure fields:

RXN>REACTANT_LINK>MOL>molstructure

RXN>PRODUCT_LINK>MOL>molstructure

You can create an external field name when you create a new field, or you can add the external field name later. To do so, choose Database > View Definition. Select the field, and then click Modify External Name. Enter the external field name, and click OK.


Add, Edit, Delete

Add

To add a field to the database definition, select the field name, and then click Add.

Edit

To rename a field or change any of its properties, select the field name, and then click Edit.

Delete

To delete a field from the database definition, select the field name, and then click Delete.


Save, Cancel, Clear All

Save

To create the database definition and close the dialog box, click Save.

Cancel

To close the dialog box without creating the database definition, click Cancel.

Clear All

To delete all the fields from the database definition and close the dialog box, click Clear All.


Edit Database Definition

Use this dialog to:

*	Add, delete, or modify fields in the local database that is currently open.

Click any of the following items:

Field Information

Add, Edit, Delete, Undo

Save

Cancel

For step-by-step instructions on editing a local database definition, see the ISIS/Base Database Maintenance 2.0 manual.


Field Information

To add, modify or delete a field, first select a field name in the list box. You see the field information for the selected field:

Name

To add a new field, edit an existing field name. To edit the name of an existing field,  select the field. Then click the Name box and edit the name.

Type

To specify the type of data that the new field will store, click the Type box and choose a field type. You cannot change the field type for an existing field.

Vocabulary

To enter or change text or numeric values that are allowable for the field during data entry, click Vocabulary, and then specify the values.

Length (fixed-text fields only)

To enter or change the number of characters that a fixed-text field can store, click the Length box, and then enter the maximum number of characters allowed for the field. You cannot change the length for an existing fixed-text field.

Parent

To specify which parent field the new field belongs to, click the Parent box and choose a parent. You cannot change the parent field of an existing field.

External name

To add or change the external field name, click the External name box and enter an external field name. An external field name allows you to match the field name in the database with a field name in an SDfile or RDfile that you import.


Add (+), Edit (|), Delete(-), Undo

Add(+)

To add a new field to the database definition, enter the field information and then click Add(+).

Edit(|)

To finalize a change in name, external field name, or vocabulary for an existing field, click Edit(|). To finalize changes for a new field already added to the database, click Edit(|).

Delete(-)

To delete the selected field from the database definition, click Delete(-).

Undo

To undo the last change that you made, immediately click Undo.


Save

To save all changes to the database definition and close the dialog box, click Save.


Cancel

To cancel all the additions, deletions, and changes to the database definition and close the dialog box, click Cancel.


Text Field Vocabulary

Use this dialog to:

*	Add, delete, or modify vocabulary (text entries) that are allowable for data entry into a variable or fixed-text field.

If vocabulary is defined for a field, you see the value(s) during data entry when you click in the box or column that is connected to the field. You choose the appropriate value from a list box.

Allowed values

The Allowed values list box, shows the acceptable data-entry values that have been entered for the field. To modify an existing entry, select the entry in the Allowed values box, and then edit the entry in the text box below. To add a new entry, type it into the box below the Allowed values list box, and then click Add.

Allow vocabulary override

To allow override of the data entry values so that you can enter any value for the field during data entry, set [image] Allow vocabulary override.

Read From File

To read vocabulary values that are defined in a text file, click Read From File. Navigate to the text file, and then click OK. The text file must contain one value per line of the file.

Add

To add the values in the text box to the Allowed values box, click Add.

Delete

To delete the vocabulary value that is currently selected in the Allowed values box, click Delete.

For complete instructions on creating and editing database fields in a local database, see the ISIS/Base Database Maintenance 2.0 manual.


Field Vocabulary

Use this dialog to:

*	Add, delete, or modify vocabulary that is allowable for data entry into a numeric, integer, real, range, or date field.

If vocabulary is defined for a field, you see the value(s) during data entry when you click in the box or column that is connected to the field. You choose the appropriate value from a list box.

Minimum value

Enter the minimum value that is allowable for data entry into the selected field.

Maximum value

Enter the maximum value that is allowable for data entry into the selected field.

Allow vocabulary override

To allow override of the data entry values so that you can enter any values for the field during data entry, set [image] Allow vocabulary override.

For complete instructions on creating and editing database fields in a local database, see the ISIS/Base Database Maintenance 2.0 manual.


Modifying the Database Definition

Use this dialog to:

*	Respond to a message that warns you that you have changed or deleted fields in the database definition. As a result, any database objects that were connected to these fields should also be modified.

After you delete or rename fields in a database, open the database objects (forms, queries, and sorting instructions) to see if they contain references to field names that are no longer present in the database. If you try to restore sorting instructions or queries that have missing field connections, a message will warn you. If you open a form with missing field connections, you will see an empty box or column where the field name used to appear (Forms mode only). You can edit the forms to delete the empty boxes or columns or connect them to different fields in the database.

You have the following options:

Continue

To permanently modify the database and close the dialog box, click Continue.

Cancel

To cancel the changes and return to the Edit Definition dialog box where you can either cancel all changes or make further modifications before you save the changes, click Cancel.


View Database Definition

Use this dialog to:

*	View field information for the current local database or remote database.

To view field information, first select the field in the list box at the top of the dialog.

Note: You can also use this dialog to edit vocabulary for fields in local databases, and add or modify external field names in local and remote databases.

Click any of the following items:

Field Information

Field Vocabulary

Save As Text File

Close


Field Information

To view the definition of a database field, select the field name in the list box. You see the following field information:

Type

Displays the type of data that the selected field stores.

Length

Displays the length in characters of text that you can register to a field that has a field type of Fixed Text.

External name

Displays the external field name, if it exists, for the selected field.

Modify External Name

To add or edit the external field name for the selected field, click Modify External Name and enter an external field name.


Field Vocabulary

Minimum

Displays the minimum data-entry values, if any, for the selected field. Minimum displays only if the field type is integer, real, range, or date.

Maximum

Displays the maximum data-entry values, if any, for the selected field. Maximum displays only if the field type is integer, real, range, or date.

Allow override

Displays whether the selected field can contain a value other than that specified in the Vocabulary dialog. Y indicates that you can override the vocabulary value for the selected field when entering data. N indicates that you cannot override the vocabulary value.

Vocabulary

To change the data-entry values that are allowed for the selected field, click Vocabulary.


Save As Text File

Use this option to save a list of all the database fields and their field types as an ASCII (Mac: Text Type) file, click Save As Text File. You can optionally save the vocabulary values and external field names in the text file. To print the file, open it in a word processing program. For better alignment, select the list and then change the font to a fixed-width font, such as Courier. Then print the list.


Close

To close the database definition, click Close.


Vocabulary

Use this dialog to:

*	Correct the data entered into the selected box or column if the value is not allowed in the field definition.

Value

This box shows the data from the field that is not in the vocabulary definition. To edit this data, enter the new data, and then click OK or Override.

Minimum

This area shows the minimum value that you can assign for the specified numeric field.

Maximum

This area shows the maximum value that you can assign for the specified numeric field.

OK

To correct the data in the value box and close the dialog box, enter the correct data in the value box, and then click OK.

Cancel

To clear the invalid data from the box and remove the dialog box, click Cancel.

Override

To accept the data that you entered in the form without modifying the value, click Override. The override button is active if the field definition was set to allow vocabulary override.


Pick Text Item from Vocabulary

Use this dialog to:

*	Select a data value to be registered into the field that is connected to the selected box or column.

Text Vocabulary List

This area shows the list of acceptable values. To edit a value, first double click the item to select it, and then edit the text in the text box that is immediately below the list box. Finally, click other to show the vocabulary dialog box.

Other

To enter a value in the dialog box that is not defined in the vocabulary, click Other.


Configure Local Database

Use this dialog to:

*	Specify whether or not to record a log of database transactions during registration. The log lists new records, changes to existing records, and deleted records.

When you create or edit a record, the log records the record ID number for each transaction, the date and time, and the data that was registered or updated into the fields affecting that record. If a duplicate ID or structure is loaded, the log records this information.

Log database transactions

To save a log of database transactions during manual or batch registration, set [image] Log database transactions. The log lists new records, changes to existing records, and deleted records.

Note: ISIS/Base saves the log file in the same directory or folder as the database with the same filename as the database (PC: ends in the .LOG file extension). The log file is an ASCII (Text-type) file that you can open in a word processor and print.

Delete the transaction log file after you review it. Each time that you register data, the new entries are appended to the existing log. As a result, the log file can rapidly increase in file size, particularly if you are using batch registration.


Configure Remote Database

Use this dialog to:

*	Add or change the host service, node name, or user name.

*	Configure network connectivity and Hview information for the remote-access file.

If you add this information, then you do not need to enter it each time that you open the remote-access file.

Click any of the following items:

Network Connection

Hview name

SQL statement

SQL database access

For more information, see the ISIS/Host Installation & Administration guide.


Network Connection

Service

Node name

User name

Network

Connection Options

You will also see one of the following items depending on the network that you choose:

TCP/IP Config

AppleTalk Config

Network Info

For more information, see the ISIS/Host Installation & Administration guide.


Service

To add or change the host service that is configured for the remote database, click the Service box and enter a name. For OpenVMS the service name is a logical name for the command procedure that is used to start the ISIS/Host program, for example, ISISHOST. For UNIX, the host service name is the name of the executable file for the ISIS/Host program, for example, isishost.

If you enter a Service name, ISIS/Base will no longer prompt you to enter it when you open the remote-access file. See your ISIS Administrator to obtain the appropriate service name.


Node name

To add or change the host node name that is configured for the remote database, click the Node name box and enter a name.

If you enter a Node name, ISIS/Base will no longer prompt you to enter it when you open the remote-access file. See your ISIS Administrator to obtain the appropriate node name.


User name

To add or change the user name that is configured to access the remote database, click the User name box and enter a name.

If you enter your User name, ISIS/Base will no longer prompt you to enter it when you open the remote-access file. If you do not enter a user name, then multiple users can open a remote database from the same remote-access file. Each user will be prompted to enter their user name and password when they open the remote-access file.


Network

To specify the network protocol to use with the remote database, click Network and choose a protocol.

If you specify the network protocol, ISIS/Base will no longer prompt you to choose one when you open the remote-access file. See your ISIS Administrator to obtain the appropriate network protocol.


TCP/IP Config

To specify TCP/IP network information, click TCP/IP Config.

Note: TCP/IP Config is available only if you clicked Network and selected TCP/IP.

Hosts/Internet address

Select the IP host name or enter an IP address of the host computer on which an ISIS/Host TCP/IP Broker is running, as specified in the hosts file on the workstation. This is usually the same computer as the one on which ISIS/Host will run, though it need not be.

Ports/Port

Select the Internet service name or enter the socket port number of the ISIS/Host TCP/IP as specified in the Services file on the workstation.


AppleTalk Config

To specify AppleTalk network information, click AppleTalk Config.

Note: AppleTalk Config is available only if you clicked Network and selected AppleTalk.

AppleTalk Zones

If you see a list of AppleTalk zones, select the one that you want to use. If you have only one AppleTalk zone, it might not appear in the list box.

Select Service

Select the service that is associated with the AppleTalk zone that you selected.


Network Info

If you clicked Network and selected DECnet then you see a Network Info button that is disabled. The remote-access file does not require additional information about DECnet to connect to the host computer.


Hview name

To enter an Hview name, set [image] Hview name, and then enter an Hview name (without a filename extension) in the text-entry box. Do not press Return.

You can type a single Hview name for a database or concatenated databases, or you can type several Hview names separated by the concatenation operator for union (+) or intersection (*). This concatenates the Hviews and creates a hierarchical view of the fields in the databases referenced in the Hviews. This allows users to search a single logical database. See your ISIS Administrator if necessary to obtain the appropriate Hview names.

Alternatively, click Hviews. Enter the relevant host account information, and then select one or more Hview names. This alternative is only available if your ISIS administrator has defined the Hview names in an Hview list file on the host computer.


SQL Statement

You can enter an SQL statement to access a remote relational database as an alternative to providing an Hview name. To enter an SQL statement, set [image] SQL Statement, and then enter the SQL statement in the box. The SQL statement cannot have a semi-colon at the end.

See your ISIS Administrator to obtain an SQL statement to access the appropriate relational database.


SQL database access name

If you are providing an SQL select statement to access a remote relational database (instead of using an Hview), enter the name of the relational table in the SQL DB Access name box. The SQL DB Access name is the same as the Oracle username, and is saved in the remote-access file to prevent the program from prompting you for this information each time that you open the remote database. (This option is not available unless you click [image] SQL statement first.)

Note: If your relational table is password protected, then ISIS/Base will prompt for the password after the connection is made.


Connection Options

Use this dialog to:

*	Set performance tuning parameters for retrieving data from the Host computer to ISIS/Base. The parameters that you specify will depend on the individual database, computer, and network configuration. Click the parameters that are listed below to see ranges and effects.

*	Specify additional connectivity information.

Click any of the following items:

Packet size (bytes)

Buffer size (records)

Local cache size (entries)

Relational Database Options

Public RAF

For more information, see the ISIS/Host Installation & Administration guide.


Packet size (bytes)

To specify the size (in bytes) of the maximum block of application data that can be transferred from the Host in a single message packet, click the Packet size box and enter a number ranging from 512 to 4096.

Note: Any application data that exceeds the packet size will be sent in multiple packets. This increases network message traffic.


Buffer size (records)

ISIS/Base, by default, retrieves data from a remote database on the Host by requesting one record of data at a time. If you increase the buffer size, then you increase the number of records of data retrieved. To increase the buffer size and the number of records per data request, click the Buffer size box and enter a number ranging from 1 to 20.

When you retrieve one record of data, the data retrieval rate is even, but can cause excess network traffic. When multiple records are retrieved, ISIS/Base and Host must spend additional time transferring the data, but it is done with fewer network messages.

Note: Increasing the buffer size is appropriate for flat databases, but might not improve the performance of hierarchical databases. The reason is the Buffer size setting does not effect the buffering of subrecord data.


Local cache size (entries)

The local cache for a remote database stores field values and other responses received from the Host. When ISIS/Base needs to find information from the Host, it first checks the local cache. If ISIS/Base does not find the information, it then sends a message to the Host. The local cache does not provide much benefit for Browsing from the top to the bottom of a list of records in the ISIS/Base Browse mode, but it does improves the performance of browsing if you browse the same records more than one time.

To specify the number of entries that are stored in the local cache, click the Local cache size box and enter a number ranging from 0 to 2000.

Note: The local cache is emptied and disabled when you switch from Browse to Update mode in ISIS/Base.


Relational Database Options

Use this option to increase the ISIS/Base browsing performance for relational databases.

Choose one of the following options:

Set [image] Allow unknown record count to instruct ISIS/Base to not force a record count when you select a box or column that is connected to a list of relational data. In this case, you always see the status bar display 1 of unknown unless you manually force the count when you click [image].

Set [image] Force record count to display the number of records that are retrieved in a search on the status bar when you select a box or column that is connected to a field in a relational table. ISIS/Base might require a long time to establish the initial cursor index, but the performance of browsing the remaining data on the list should be improved. To maximize performance, we recommend that you only use this option to retrieve a count for small lists of data.


Public RAF

To specify the name of the public RAF (remote-access file) given to you by your ISIS Administrator, either click Public RAF and select a file, or enter the name of a file.


Network Connection

Service

Node name

User name

Network

Connection Options

You will also see one of the following items depending on the network that you choose:

TCP/IP Config

AppleTalk Config

Network Info

For more information, see the ISIS/Host Installation & Administration guide.


Flexmatch Parameters

Use this dialog to:

*	Change flexmatch parameters. The default flexmatch parameters retrieve the most restricted exact match of your FLEX query from the database.

 Requirements to use this dialog

Click any of the following items:

Type of Charge Match

Type of Bond Match

Fragments

Hydrogen count

Isotopes

Metal bonds

Radicals

Salt

Stereo bonds

Valences

If you are not sure which search you need to use, see the ISIS/Base SearchSelector.


Default Flexmatch Parameters

When you begin an ISIS/Base session, you see the following default flexmatch parameters that retrieve the most restricted exact match of your FLEX query from the database:

Type of Bond Match: Bond type

Type of Charge Match: Atom charges

Fragments

Hydrogen count

Isotopes

Metal bonds

Radicals

Salt

Stereo bonds

Valences


Requirements to Use This Dialog
Requirements to use the Flexmatch Parameters dialog

To use this dialog:

*	Your molecule query must not contain any query features.

*	You need to understand the flexmatch parameters and how they interact with each other. To obtain the correct search results, you need to know which flexmatch parameters require other flexmatch parameters to function correctly.


Type of Charge Match

Use these settings to specify how closely you want the charges on the structures that you retrieve to match the charges on your query.

Atom charges

To retrieve only structures where the charge on each atom exactly matches the charge on the corresponding atom in your query, set [image] Atom charges.

Note: This setting automatically ensures that the total charge on each fragment must match.

Ion charges

To retrieve only structures where the total charge on each fragment matches the total charge on each fragment in your query, set [image] Ion charges. Example

Both off

To turn off the Atom charges and the Ion charges constraints, set [image] Both off. Example


Type of Bond Match

Use these settings to specify how closely you want the bonds on the structures that you retrieve to match the bonds your query.

Bond type

To retrieve only structures where all the bond types exactly match your query, set [image] Bond type.

Tautomer

To retrieve only structures where tautomer groups contain the same number of hydrogens in the tautomeric region (within a tolerance limit), set [image] Tautomer. Example

Both off

To turn off the Bond type and the Tautomer constraints, set [image] Both off. Example


Fragments

To retrieve structures where solely those fragments that exist in your query are present in the structures retrieved (without any additional fragments), set [image] Fragments.

If one of the fragments in your query is the counterion of a salt, you retrieve the parent molecule of the salt if you set [image] Fragments and also set [image] Salt. Example

To allow additional fragments from those in the query, set [image] Fragments. Example

All fragments that are present in the query must be present in the structures that you retrieve. Example


Hydrogen count

To retrieve solely structures where the number of hydrogens on each atom matches the number of hydrogens in your query, set [image] Hydrogen count.

To retrieve structures where the number of hydrogens on individual atoms can vary, set [image] Hydrogen count. Example


Isotopes

To retrieve only structures where the isotopic labels on each atom match those in your query, (including H, D, and T), set [image] Isotopes.

To retrieve structures that have different isotopic labels, and H, D, and T are equivalent to each other, set [image] Isotopes. Example


Metal bonds

To retrieve only structures where the connectivity of all metals matches your query, set [image] Metal bonds.

To retrieve structures where the connectivity of metals can vary, set [image] Metal bonds. Example


Radicals

To retrieve only structures where the radical value on each atom matches those in your query, set [image] Radicals.

To ignore radical values, set [image] Radicals. Example


Salts
Salt

To retrieve only structures where the counterions match those in your query, set [image] Salt.

To retrieve structures with a specific counterion, set [image] Salt and also set [image] Fragments. Example

To retrieve molecules with different counterions than those in your salt query, set [image] Salt, and also set [image] Fragments. Example

To retrieve solely molecules that are the parent structures of salts, set [image] Salt and also set [image] Fragments. Example


Stereo bonds

To retrieve only structures where the configuration of the stereo centers match those of your query exactly, set [image] Stereo bonds.

Caution: You can only use this feature if you also set Type of Bond Match [image] Bond Type.

To retrieve all stereoisomers of the query in the database, including structures with unspecified stereo centers, set [image] Stereo bonds. Example


Valences

To retrieve only structures where the valence on each atom matches those in your query, set [image] Valences.

Notes: (1) If no valence is specified, an implicit valence is calculated from the structure. A query with an unspecified valence (with a calculated implicit valence) might retrieve a structure that contains the matching explicit valence. Or, a query with an explicit valence might retrieve a structure that does not contain an explicit valence (that contains a calculated implicit valence). (2) Some valences are illegal. For transition metals, a valence is illegal if it is smaller than the number of bonds to the atom. For other real atom types, an illegal valence is ignored in a FLEX search and the query retrieves any valence.


Example

The following example requires that you set Type of Charge Match [image] Ion charges:

Note: This example also requires the following nondefault flexmatch parameter:

*	Hydrogen count.


Example

The following example requires that you set Type of Charge Match [image] Both Off:

Note: This example also requires the following nondefault flexmatch parameters:

*	Type of Bond Match [image] Both Off

*	Metal bonds


Example

The following example requires that you set Type of Bond Match [image] Tautomer:


Example

The following example requires that you set Type of Bond Match [image] Both Off:

Note: This example also requires the following nondefault flexmatch parameters:

*	Type of Charge Match [image] Both Off

*	Metal bonds


Example

The following example requires that you set [image] Fragments:


Example

The following example requires that you set [image] Fragments:


Example

The following example requires that you set [image] Fragments and also set [image] Salt:

Note: This example also requires the following nondefault flexmatch parameters:

*	Type of Charge Match [image] Both Off

*	Hydrogen count


Example

The following example requires that you set [image] Hydrogen count:

Note: This example also requires the following nondefault flexmatch parameter:

*	Type of Charge Match [image] Ion charges


Example

The following example requires that you set [image] Hydrogen count and also set Type of Bond Match [image] Tautomer:

Note: This example also requires the following nondefault flexmatch parameter:

*	Type of Charge Match [image] Ion charges


Example

The following example requires that you set [image] Hydrogen count and also set Type of Bond Match [image] Tautomer:

Note: This example also requires the following nondefault flexmatch parameter:

*	Type of Charge Match [image] Ion charges


Example

The following example requires that you set [image] Metal bonds:

Note: This example also requires the following nondefault flexmatch parameters:

*	Type of Charge Match [image] Both Off

*	Type of Bond Match [image] Both Off


Example

The following example requires that you set [image] Metal bonds and also set [image] Salt:

Note: This example also requires the following nondefault flexmatch parameters:

*	Type of Bond Match [image] Both off

*	Type of Charge Match [image] Both off

*	Fragments


Example

The following example requires that you set [image] Radicals:

Note: This example also requires the following nondefault flexmatch parameters:

*	Type of Bond Match [image] Both Off

*	Metal bonds


Example

The following examples require that you set [image] Stereo bonds:


Example

The following example requires that you set [image] Salt and also set [image] Fragments:

Note: This example also requires the following nondefault flexmatch parameters:

*	Type of Charge Match [image] Both Off

*	Hydrogen count


OK, Cancel

OK

To accept the flexmatch settings and begin the search, click OK.

Cancel

To close the dialog box without changing the flexmatch settings, click Cancel.


Calculated Fields

Use this dialog to:

*	Create new calculated fields in the remote-access file of your database.

*	Delete existing calculated fields in the remote-access file of your database.

 Requirements to use this dialog

Click any of the following items:

Field to calculate on, Field Information

Add, Delete

Save, Cancel

We strongly recommend that you study Calculated Fields: Concepts/Examples before you attempt to create or delete calculated fields.


Requirements to use the Calculated Fields dialog

To create a suitable calculated field, you need to understand the database structure. We strongly recommend that you study Calculated Fields: Concepts/Examples before you attempt to create calculated fields.


Field to calculate on, Field Information

Use these options to enter information on the calculated fields that you want to create in your database. For information on the types of fields that you can use to create calculated fields, see Calculated Fields: Concepts/Examples.

Select the field to calculate on

To choose the child field to calculate on, click the name of the field.

Note: You see a plus (+) sign beside the names of calculated fields that you have added in the current ISIS/Base session. You see a minus (-) sign beside the names of calculated fields that you have deleted in the current ISIS/Base session.

Calculation type

To specify the type of calculation to perform, click the Calculation type box and choose a calculation type. Calculation type is available solely when you have selected a child field on which a calculation can be performed.

Calculated field name

To change the name of the calculated field, click the box and type the new name. Calculated field name is available solely when you have selected a suitable child field to calculate on.


Add (+), Delete (-)

Add (+)

To create a calculated field, click the name of the child field to calculate on, choose the calculation type, change the calculated field name as desired, then click Add. This option is available solely when you have selected a suitable child field to calculate on.

Delete (-)

To delete the currently-selected calculated field, click the name of the field in the list box, then click Delete. This option is available solely when you have highlighted the name of an existing calculated field in the Select field to calculate on box.


Save, Cancel

Save

To accept the changes that you made to calculated fields and store the changes in the database, click Save.

Cancel

To cancel the changes that you made to calculated fields, click Cancel.


Print

Use this dialog to:

*	Print the current form with the names of database fields that are connected to boxes and columns in the form (Forms mode only).

*	Print the current search query with the form (Query mode only).

*	Print all records on the current list of search results (Browse or Update modes only).

*	Print solely the record that is currently displayed from the current list of search results (Browse or Update modes only).

 Requirements to use this dialog

Click any of the following items:

Current record, Current list

Data to be Printed

Page Layout

Header/Footer

Customize...

OK, Cancel

Note: For more information on printing search results from hierarchical databases, study Printing All the Data, and Only the Data, That You Want.


Requirements to use the Print dialog

To use this dialog to print search results (Browse and Update modes only):

*	You must click the box or table that contains the most important data before you choose File > Print. If you choose the wrong box or table, you might print large amounts of irrelevant data or, worse, print incomplete data without knowing that the data is incomplete.

*	You need to understand how the currently-selected box or table (the ending context) affects the amount of data that you print from each branch of the database hierarchy. For more information on printing search results from hierarchical databases, study Printing All the Data, and Only the Data, That You Want.

Note: The currently-selected box or table does not affect what you print in Forms or Query mode.


Current record, Current list

Current record

To print the form and the names of the fields that are associated with each box on the form, set [image] Current record. You must be in Forms mode.

To print the form and the query, set [image]. You must be in Query mode.

To print the form with data from the current record that you see in the form, set [image]. You must be in Browse or Update mode.

Current list

To print the form with data from all records on the current list, set [image] Current list. You must be in Browse or Update mode.


Data to be Printed

The text in this box describes the data that ISIS/Base prints when you click OK. The description that you see changes according to the mode that you were in when you chose File > Print.

For Browse and Update modes, what you print also changes according to the currently-selected box or table (ending context), the starting context, and whether you specified Current record or Current list.

Note: For Browse and Update modes, it is important to understand how the currently-selected box or table (ending context) affects the amount of data that ISIS/Base prints. Also, if you are not sure how to use the starting context, we strongly recommend that you not change the starting context. If you choose the wrong box or table, or choose the wrong starting context, you might print large amounts of irrelevant data or, worse, print incomplete data without knowing that the data is incomplete. For more information on starting and ending context, study Printing All the Data, and Only the Data, That You Want.


Customize

To change the starting context when you print search results, click Customize.

Note: Do not change the starting context unless you want to restrict the number of subrecords that you print. If you are not sure how to use the starting context, we strongly recommend that you not change the starting context. For more information on starting and ending context, study Printing All the Data, and Only the Data, That You Want.

Customize is available solely in Browse and Update modes.


OK, Cancel

OK

To accept the current print options and print the data, click OK.

Cancel

To accept the current print options and cancel printing, click Cancel.

Note: Any changes that you made to print options, page layout, or headers and footers remain in effect until you close the database.


Header/Footer

To specify the contents of headers and footers, click Header/Footer.


Page Layout

To specify the position and size of printed information, click Page Layout.


Sort

Use this dialog to:

*	Create new sorting instructions that specify the data that you want to use for sorting and the order of sorting (low to high or high to low).

*	Save a set of sorting instructions as an object inside the database.

*	Restore a set of sorting instructions that you previously saved as an object inside the database.

*	Modify existing sorting instructions.

*	Sort search results with the current sorting instructions.

*	Undo sorting

 Requirements to use this dialog

Click any of the following items:

Sort each, By, High to low/Low to high

Add, Delete, Replace

Calculated Field

Sorting Instructions, Reorder Instructions, Clear All

Sort, Cancel, Close, Unsort

Save, Save As, Restore

For complete information on sorting, see the information on the search of your choice in ISIS/Base Search Types.


Requirements to use the Sort dialog

To use this dialog, you need to know:

*	What you want to sort, and how to sort it. For more information, see the Sorting Examples.

*	Whether you need to create any calculated fields to use for sorting (remote databases only).


Sorting Examples

Click one of the following:

*	Molecule records: remote database (Molecules: Sorting Examples) or local database (Local Databases: Sorting Examples)

*	Reaction records: remote database (Reactions: Sorting Examples and Reaction Components: Sorting Examples) or local database (Local Databases: Sorting Examples)

*	3D Structure records: remote database (3D Structures: Sorting Examples) or local database (Local Databases: Sorting Examples)


Sorting Instructions, Reorder Instructions, Clear All

Use these options to change the order of individual sorting instructions within the current set of sorting instructions, and to delete the current set of sorting instructions.

Note: The sorting instructions are listed in the order in which ISIS/Base uses them to sort. If you specify more than one sorting instruction for a parent field, you must specify the most important data first.

Reorder instructions

To move a sorting instruction before another instruction, click the instruction, and then click [image].

To move a sorting instruction after another instruction, click the instruction, and then click [image].

Clear All

To delete all sorting instructions in the current set, click Clear All.

Clear All is active when one or more sorting instructions exist in the Sorting instructions box.


Sort each, By, High to low/Low to high

Use these options to define sorting instructions.

Sort each

To select the record or subrecord that you want to sort, click the field name in the box.

By

To select the field that contains the data by which to sort, click the field name in the box.

High to low/Low to high

To sort in ascending sequence, set [image] Low to high.

To sort in descending sequence, set [image] High to low.


Calculated Field

To add, edit, or delete calculated fields, click Calculated Field.

Calculated Field is available solely for remote databases.


Add, Delete, Replace

Use these options to edit the current sorting instructions.

Add

To add a sorting instruction to the current set of sorting instructions, define the sorting instruction and click Add.

Add is inactive when a record or subrecord already has three sorting instructions, or when the field that you choose from the By box is unsuitable for sorting (for example, you cannot sort by a RXNSTRUCTURE, MOLSTRUCTURE, or MODELSTRUCTURE field).

Delete

To delete a sorting instruction from the current set of sorting instructions, choose the sorting instruction from the Sorting Instructions box, and click Delete. Delete is active when one or more sorting instructions exist in the Sorting Instructions box.

Replace

To replace a sorting instruction within the current set of sorting instructions, choose the sorting instruction from the Sorting Instructions box, define the new sorting instruction, and click Replace. This button is inactive when no sorting instructions exist.


Change order

The sorting instructions are listed in the order in which ISIS/Base uses them to sort. If you specify more than one sorting instruction for a parent field, you must specify the most important data first.

To perform a sorting instruction before another instruction, click the instruction, and then click [image].

To perform a sorting instruction after another instruction, click the instruction, and then click [image].


Sort, Cancel, Close, Unsort

Sort

To sort your search results with the current set of sorting instructions and close the dialog box, click Sort. Sort is active solely when one or more sorting instructions exist in the Sorting Instructions box.

Cancel

To cancel the changes to the current sorting instructions and close the dialog box, click Cancel.

Close

To accept the current sorting instructions and close the dialog box without sorting search results, click Close.

Unsort

To undo the effects of sorting, click Unsort. When you undo sorting, ISIS/Base deletes the current sorting instructions and places records in the order in which ISIS/Base retrieved them from the database.


Save, Save As, Restore

These options allow you to manage sets of sorting instructions that you save within the database as database objects.

Save

To save the current sorting instructions within the database, click Save. Save is active when one or more sorting instructions exist in the Sorting instructions box.

Save As

To save the current sorting instructions within the database under a different name, click Save As. Save As is active when one or more sorting instructions exist in the Sorting instructions box.

Restore

To use a set of sorting instructions that you have previously saved, click Restore, choose a set of sorting instructions from the Select Objects dialog, then click OK. The saved sorting instructions become the current sorting instructions.


CFS Options

Use this dialog to:

*	Specify the options for a CFS or CFS/Biopoly search.

*	Specify the CFS options that you need to view the results of a previous CFS search.

*	Reset the CFS options to their default values.

 Requirements to use this dialog

Click any of the following items:

Fitter selection

Fitting at search time

Max. no. of attempted fittings

Rotate bonds between unsat. atoms

Ring flexing, Min/Max ring size

Bump checking

Global relaxation

Calculate for search/sort

Cutoff for search/view

Defaults

OK, Cancel

If you are not sure which search you need to use, see the ISIS/Base SearchSelector.

Caution: The CFS options interact with each other and can produce undesirable results if improperly used. We strongly recommend that you study CFS Searching Concepts/Examples before you attempt CFS searching.


Requirements to use the CFS Options dialog

To use this dialog:

*	Your molecule query must contain at least one 3D geometric constraint or submodel.

*	You need to understand how to use the CFS options. The CFS options interact with each other and can produce undesirable results if improperly used. We strongly recommend that you study CFS Searching Concepts/Examples before you attempt CFS searching.

Note: If you are not sure how to use the CFS options, we strongly recommend that you use the default CFS options.


Bump checking

Use these options to control whether ISIS performs bump checking during a CFS search (search-time bump checking) and/or while viewing your search results (view-time bump checking).

Bump checking at: Search time

To perform bump checking during the CFS search, set Bump checking at: Search time.

Bump checking at: View time

To perform bump checking as you view your CFS search results, set Bump checking at: View time.

Caution: Bump checking can slow search speed significantly. Therefore, we strongly recommend that you conduct the CFS search with Bump checking at: Search time when you are searching a large number of records. Then, perform bump checking either at view time, or in a separate bump-checking CFS search.


Global Relaxation

To perform global relaxation during bump checking, set [image] Global relaxation.

Note: To use global relaxation during a CFS search, you must also set Bump checking at: Search time.

For more information on bump checking, global relaxation, and other CFS options, see CFS Searching Concepts/Examples.


Calculate for search/sort

To calculate any of the following types of derived data during a CFS search, set [image] for the data that you want:

*	Torsional degrees of freedom (TDF) is the number of rotatable bonds on the paths that connect the mapped atoms in the fitted 3D structure (Mapped atoms are the atoms in the 3D structure that correspond to atoms in the query). The higher the TDF, the more flexible the molecule is in the region that matches the query.

*	Van der Waals energy difference is the difference in nonbonded (van der Waals) interaction energy between the fitted 3D structure and the conformation that is stored in the database.

*	RMS deviation measures how closely the 3D structure fits the query (goodness-of-fit). The lower the RMS deviation, the better the 3D structure fits the query. RMS deviation is the sum of the RMS deviations for each type of 3D feature in your query:

Note: If you want to calculate derived data for RMS deviation, or to specify a search cutoff for RMS deviation, you must use the derivative fitter.

For more information on derived data and other CFS options, see CFS Searching Concepts/Examples.


Cutoff for search/view

To use any of the following search cutoffs, set [image] for the cutoff that you want, then click the corresponding box and enter a value:

*	Torsional degrees of freedom (TDF) is the number of rotatable bonds on the paths that connect the mapped atoms in the fitted 3D structure (Mapped atoms are the atoms in the 3D structure that correspond to atoms in the query). The higher the TDF, the more flexible the molecule is in the region that matches the query. The suggested value is 10 rotatable bonds.

*	Van der Waals energy difference is the difference in nonbonded (van der Waals) interaction energy between the fitted 3D structure and the conformation that is stored in the database. The suggested value is 5.0 Kcals.

*	RMS deviation measures how closely the 3D structure fits the query (goodness-of-fit). The lower the RMS deviation, the better the 3D structure fits the query. RMS deviation is the sum of the RMS deviations for each type of 3D feature in your query (RMS deviation appears in Angstrom deviations for distances, lines, planes, and fixed atoms and in cosine deviations for angles and dihedrals):

The suggested value is 0.7 RMS units.

Note: If you want to calculate derived data for RMS deviation, or to specify a search cutoff for RMS deviation, you must use the derivative fitter.

For more information on search cutoffs and other CFS options, see CFS Searching Concepts/Examples.


Rotate bonds between unsat. atoms

To allow single bonds between atoms with any combination of sp3-. sp2-, or sp-hybridzation (for example, biphenyls) to rotate during conformational fitting, set [image] Rotate bonds between unsat. atoms.

To restrict conformational fitting to bonds that contain at least one sp3-hybridized atom (except amides and similar bonds), set [image] Rotate bonds between unsat. atoms.

Note: Amides and similar bonds are never rotated during conformational fitting. Amide bonds are defined as follows:

For more information on rotatable bonds and other CFS options, see CFS Searching Concepts/Examples.


Ring flexing, Min/Max ring size

Use these options to specify which ring bonds can be rotated during conformational fitting.

Ring flexing

To allow single bonds in rings to rotate, set [image] Ring flexing. To rotate solely acyclic single bonds (except amides and similar bonds), set [image] Ring flexing.

Min ring size

To specify the smallest ring size in which you want to allow single bonds to rotate, click the box, and then enter a number from 4 to 24.

Max. ring size

To specify the largest ring size in which you want to allow single bonds to rotate, click the box, and then enter a number from 4 to 24.

For more information on ring flexing and other CFS options, see CFS Searching Concepts/Examples.


Fitter selection

Use these options to specify the algorithm that ISIS uses to fit 3D structures to the constraints of the query (conformational fitting).

Automatic

To allow ISIS to choose the more appropriate fitter for your query, click [image] Automatic.

Simplex

To specify the simplex fitter, click [image] Simplex.

Derivative

To specify the derivative fitter, click [image] Derivative.

Note: You can use the simplex fitter with any 3D query components. However, you can use the derivative fitter solely with the following 3D query components:

*	Atoms

*	Ring centroids

*	Distances that are defined by two atoms or ring centroids

*	Angles that are defined by three atoms or ring centroids.

For more information on fitters and other CFS options, see CFS Searching Concepts/Examples.


Fitting at search time

To specify conformational fitting during a CFS search (search-time fitting), set [image] Fitting at search time. To specify conformational fitting solely when you view your CFS search results (view-time fitting), set [image] Fitting at search time.

For more information on search-time fitting and other CFS options, see CFS Searching Concepts/Examples.


Max. no. of attempted fittings

To specify the number of unique mappings that ISIS attempts to fit a 3D structure to the query, click the box and enter a number from 1 to 1000.

Notes: (1) The default value of 5 is generally satisfactory for most cases. However, if you also set [image] Ring flexing, specify a value of 25 or greater. (2) ISIS generally retrieves very few extra hits when you specify a number greater than 5. Also, a value of 1000 might not ensure that ISIS attempts all possible mappings for each 3D model.

For more information on number of fittings and other CFS options, see CFS Searching Concepts/Examples.


Defaults

To specify the default CFS options, click Defaults.

The default CFS options provide the best balance between search speed and accuracy for most situations. If you are not sure how to use the CFS options, we strongly recommend that you use the default CFS options.

Note: If you specify the default CFS options, ISIS does not perform bump checking during the search (search-time bump checking). Instead, ISIS performs bump checking on individual structures as you view them (view-time bump checking). We strongly recommend that you conduct the CFS search with default options when you are searching a large number of records, because bump checking can slow search speed significantly. You can perform bump checking either at view time, or in a separate bump-checking CFS search.

For more information on CFS options, study CFS Searching Concepts/Examples.


OK, Cancel

OK

To use the dialog box settings for the current CFS search and close the dialog box, click OK.

Cancel

To cancel changes to the CFS options and close the dialog box, click Cancel.


Settings -- Search

Use this dialog to:

*	Specify new default settings for how you want to view your records after a search.

*	Specify fixed-atom tolerances for 3D searching and registration.

Click any of the following items:

Search by form logic at deepest common parent

Go to Browse after query execution

Return to Browse mode with context set to <Root>

Filter search results

Generate temporary lists automatically

3D Searching

OK, Cancel

Save, Save As, Read

For more information on how to work with ISIS/Base settings, click here.

If you are not sure when to use these items, see the ISIS/Base Search Types.


Search By Form Logic at Deepest Common Parent

For single SBF searches with multiple queries in ISIS 2.0, the results of a search are the same whether the queries are in boxes or in the same line of a table. For these queries, ISIS now retrieves only records in which all queries must match within the same subrecord. The deepest common parent field defines the subrecords within which all search conditions must match.

In versions of ISIS before ISIS 2.0, only multiple queries in boxes retrieve records in which all queries must match within the same subrecord. Multiple queries in tables retrieve records in which all queries must match, but not necessarily within the same subrecord.

To retrieve only records for which all conditions in boxes, or in the same line of a table, must match within the subrecord defined by the deepest common parent, set [image] Search by form logic level at deepest common parent.

To obtain the same search results as earlier versions of ISIS, set [image] Search by form logic level at deepest common parent.

For more information on multiple queries in SBF, see SBF Searching Concepts/Examples.


Go to Browse After Query Execution

To switch to Browse mode automatically after executing a query, set [image] Go to Browse after query execution.


Return to Browse Mode With Context Set to <Root>

To have the context automatically be reset to the root level when you switch to Browse mode, set [image] Return to Browse mode with context set to <Root>. This makes it easier to view all the hits at the root level.

Note: This option is useful only If you search hierarchical databases and your forms connect to multiple levels.


Filter Search Results

You can filter your search results so that you view only the subrecords that match your query. For example, you might want to find literature references by an author named R. L. Smith in a reaction database. To do this, you can conduct a Search By Form (SBF) with the query LIKE "%R. L. SMITH%" in a box or table that is connected to the field RXN>VARIATION>LITTEXT>littext. Each reaction record can have several variation subrecords, and each variation subrecord can contain multiple literature-reference subrecords. ISIS retrieves all reactions that contain at least one literature reference that match your query. However, these reactions might also contain subrecords that do not match your query. To display only the variations and literature references that match your query, you must filter the search results.

To view only the subrecords that match your query, set [image] Filter search results. To view both subrecords that match your query, and subrecords that do not necessarily match your query, set [image] Filter search results.

For more information on filtering in QB searches, see QB Searching Concepts/Examples.

For more information on filtering in SBF, see SBF Searching Concepts/Examples.


Example

In a reaction database, you might want to find literature references by an author named R. L. Smith. To do this, you can conduct a Search By Form (SBF) with the query LIKE "%R. L. SMITH%" in a box or table that is connected to the field RXN>VARIATION>LITTEXT>littext. Each reaction record can have several variation subrecords, and each variation subrecord can contain multiple literature-reference subrecords. ISIS retrieves all reactions that contain at least one literature reference that match your query. However, these reactions might also contain subrecords that do not match your query. To display only the variations and literature references that match your query, you must filter the search results.


Generate Temporary Lists Automatically

To generate temporary lists automatically, set [image] Generate temporary lists automatically.


3D Searching

Sprout hydrogens and lone pairs

Max. atomic displacement

Max. RMS deviation


Sprout Hydrogens and Lone Pairs

3D structures in a molecule database generally do not contain explicit representations of hydrogen atoms. You can, however, sprout explicit hydrogen atoms on the 3D structures that you retrieve. In a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, you can also sprout lone pairs on 3D structures at sites where the query contains lone pairs.

To sprout hydrogens and lone pairs, click the box, and then choose the types of atoms where you want to sprout hydrogens.

Off

Prevents sprouting of hydrogens and lone pairs on retrieved 3D structures, even at sites where hydrogens and lone pairs appear on the query. Use this option when the 3D structures in your database already contain explicit representations of hydrogens and lone pairs.

Query Atoms Only

In a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, sprouts hydrogens and lone pairs on retrieved 3D structures, but solely at sites where hydrogens and lone pairs appear on the query. In a CFS or CFS/Biopoly search, use this option for faster search speeds during the initial CFS search.

All

Sprouts hydrogens at all sites on retrieved 3D structures, and sprouts lone pairs on retrieved structures at sites where lone pairs appear on the query. Use this option when:

*	You want a more realistic representation of 3D structures when you view your search results.

*	You perform bump checking during a CFS or CFS/Biopoly search. Sprouting hydrogens at all sites produces fitted 3D structures that are more realistic.

*	Your 3D database does not contain explicit representations of hydrogen atoms, and you want to export 3D structures to a modeling software program that cannot sprout hydrogens.


Maximum Atomic Displacement

Maximum atomic displacement specifies the allowed deviation (in Angstroms) of individual atoms in a 3D structure from the corresponding atoms in your 3D query. Maximum atomic displacement is one of two fixed-atom tolerances that you use in these searches. You must specify at least one fixed-atom tolerance when:

*	You conduct a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search with a query that contains fixed atoms

*	You conduct a 3DEXACT search in a remote database (ISIS treats all atoms in the query structure like the fixed atoms of a submodel)

*	You register new 3D structures to a database, or update existing 3D structures in a database.

To specify a value for maximum atomic displacement, set [image] Max. atomic displacement. Then, click the box, and enter a value in Angstroms. To inactivate maximum atomic displacement, set [image] Max. atomic displacement.

Caution: Your ISIS Administrator sets default fixed-atom tolerances that your site uses to register 3D structures to the database. If you change these default values for searching, you must restore the default fixed-atom tolerances before you register 3D structures.


Maximum RMS Deviation

Maximum RMS deviation specifies the allowed root-mean-square deviation (in Angstroms) of all atoms in a 3D structure from the corresponding atoms in your 3D query. Maximum RMS deviation is one of two fixed-atom tolerances that you can specify. You must specify at least one fixed-atom tolerance when:

*	You conduct a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search with a query that contains fixed atoms

*	You conduct a 3DEXACT search in a remote database (ISIS treats all atoms in the query structure like the fixed atoms of a submodel)

*	You register new 3D structures to a database, or update existing 3D structures in a database.

To specify maximum RMS deviation, set [image] Max. RMS deviation. Then, click the box, and enter a value in Angstroms. To inactivate maximum RMS deviation, set [image] Max. atomic displacement.

Caution: Your ISIS Administrator sets default fixed-atom tolerances that your site uses to register 3D structures to the database. If you change these default values for searching, you must restore the default fixed-atom tolerances before you register 3D structures.


SBF Searching Concepts/Examples

Click any of the following items:

Molecule records: remote database (SBF) or local database (SBF)

Reaction records: remote database (SBF) or local (SBF) database

3D Structure records: remote database (SBF) or local (SBF) database


Page Layout

Use this dialog to:

*	Adjust the position and size of printed forms on a page.

Note: You see your changes in the Preview box at the right.

Click any of the following items:

Forms Per page

Interform Spacing

Margins

From Edge

Update Preview

Print Setup/Page Setup, Header/Footer, Close, Cancel, Print


Forms Per page

Horizontal

To specify the number of forms that display horizontally on a page, click the box, and then choose a number. Alternatively, choose Auto to specify as many forms as can fit horizontally on the page.

Vertical

To specify the number of forms that display vertically on a page, click the box, and then choose a number. Alternatively, choose Auto to specify as many forms as can fit vertically on the page.

Scale form to fit page

To specify that the form(s) fill up the page, set [image] Scale form to fit page.


Interform Spacing

These options are available only if you specify that more than one form is to be printed on a page.

Horizontal

To specify the horizontal space between forms on a page, click the box and choose or enter a value. Values that you enter must be in .25 inch increments.

Vertical

To specify the vertical space between forms on a page, click the box and choose or enter a value. Values that you enter must be in .25 inch increments.


Margins

Top

To specify the top margin for a page, click the box and choose or enter a value.

Left

To specify the left margin for a page, click the box and choose or enter a value.

Bottom

To specify the bottom margin for a page, click the box and choose or enter a value.

Right

To specify the right margin for a page, click the box and choose or enter a value.


From Edge

Header

To specify the distance between the header and the top edge of the page, click the box and choose or enter a value.

Footer

To specify the distance between the footer and the bottom edge of the page, click the box and choose or enter a value.


Update Preview

To see the results of changes to the page layout, click Update Preview.


Print Setup/Page Setup, Header/Footer, Close, Cancel, Print

Print Setup/Page Setup

To specify the paper size, page orientation, and other printing options, click Print Setup on the PC, Page Setup on the Macintosh.

Header/Footer

To specify the contents of headers and footers, click Header/Footer.

Cancel

To cancel changes and close the Page Layout dialog, click Cancel.

Close

To accept the changes and close the Page Layout dialog, click Close.

Print

To display the Print dialog, where you can specify the data that you want ISIS/Base to print, click Print.


Header/Footer

Use this dialog to:

*	Change the text of headers and footers that ISIS/Base prints with your form. You can type your own text, or use existing header/footer codes to print page numbers, date, time, and other information in the header or footer.

Click any of the following items:

Page, Date, Time

Apply

Color, Font

OK, Cancel


Apply

To insert a header/footer code into a header or footer, click the header or footer section where you want to insert the code, choose the code from the list box, then click Apply.


Page, Date, Time

Use the Page, Date and Time buttons to insert header/footer codes for the page number, date, and time.

Page

To insert the page number in a header or footer, click the header or footer section where you want the page number, then click

Date

To insert the current date in a header or footer, click the header or footer section where you want the date, then click

Time

To insert the current time in a header or footer, click the header or footer section where you want the time, then click


Color, Font

Color

To change the color of text in a header or footer, select the text, click Color, and enter or choose a color from the list.

Font

To change the font, size, or style of text in a header or footer, select the text, click Font, make the changes, and click OK.


OK, Cancel

OK

To accept the current headers and footers, click OK.

Cancel

To cancel changes, click Cancel.


Customized Data Selection

Use this dialog to:

*	Change the starting context when you print search results.

 Requirements to use this dialog

Click any of the following items:

Starting context

OK, Cancel

Note: If you choose the wrong starting context, you might print incomplete data without knowing that the data is incomplete. If you are not sure how to use the starting context, we strongly recommend that you set the starting context to the highest level of the database hierarchy (the default). For more information on printing search results, study Printing All the Data, and Only the Data, That You Want.


Requirements to use the Customized Data Selection dialog

To use this dialog, you need to understand how to use the starting context and ending context to control the amount of data that you print from each record on your list of search results.

If you choose the wrong starting context, you might print incomplete data without knowing that the data is incomplete. If you are not sure how to use the starting context, we strongly recommend that you set the starting context to the highest level of the database hierarchy (the default). For more information on printing search results, study Printing All the Data, and Only the Data, That You Want.


Starting Context

To set the starting context to a different level of the database hierarchy, click the name of the parent field at the level of the hierarchy that you want as the starting context.


OK, Cancel

OK

To accept the current starting context and return to the Print dialog, click OK.

Cancel

To cancel changes, set the starting context to the top level of the database, and return to the Print dialog, click Cancel.


Settings -- Print

Use this dialog to:

*	Specify the default appearance of the printed forms.

Note: Do not use this dialog box to change the appearance of an existing form. For information on how to edit an existing form, click here.

Click any of the following items:

Forms Per Page

Interform Spacing

Margins

From Edge

Print Setup/Page Setup

OK, Cancel

Save, Save As, Read

For more information on how to work with ISIS/Base settings, click here.


Orientation

Portrait

To specify that forms be printed vertically (Portrait mode) by default, click [image].

Landscape

To specify that forms be printed horizontally (Landscape mode) by default, click [image].


Forms Per Page

Horizontal

To specify the default number of forms that display horizontally on a page, click the box, and then choose a number or Auto.

Vertical

To specify the default number of forms that display vertically on a page, click the box, and then choose a number or Auto.

Scale Form to Fit Page

To specify that the form(s) fill up the page, set [image] Scale form to fit page.


Interform Spacing

Horizontal

To specify the default horizontal space between forms on a page, click the box and choose or enter a value.

Vertical

To specify the default vertical space between forms on a page, click the box and choose or enter a value.


Margins

Top

To specify the default top margin for a page, click the box and choose or enter a value.

Left

To specify the default left margin for a page, click the box and choose or enter a value.

Bottom

To specify the default bottom margin for a page, click the box and choose or enter a value.

Right

To specify the default right margin for a page, click the box and choose or enter a value.


From Edge

Header

To specify the default distance between the header and the top edge of the page, click the box and choose or enter a value.

Footer

To specify the default distance between the footer and the bottom edge of the page, click the box and choose or enter a value.


Print Setup/Page Setup

To specify the paper size, page orientation, and other printing options, click Print Setup on the PC, Page Setup on the Macintosh.


Print context markers in forms

To print the marks that indicate the page margins (crop marks), click [image].


Settings -- Ruler Settings

Use this dialog to:

*	Specify the appearance and behavior of the ruler in Forms mode. For information on how to use the ruler, click here.

Click any of the following items:

Show ruler

Snap to ruler

Inches

Centimeters

Divisions

OK, Cancel

Save, Save As, Read

For more information on how to work with ISIS/Base settings, click here.


Hview List

To specify the Hview for the remote database, choose an Hview name and then click OK.


Polymer

Use this dialog to:

*	Conduct any of the following searches: POLY/Sub, POLY/Co, POLY/Both, or POLY/Exact.

 Requirements to use this dialog

Click any of the following items:

Find all polymers that contain this polymer substructure

Find all copolymers that contain this monomer or SRU

Find the monomer or SRU representation of this polymer

Find this exact polymer

Additional Options

For information on drawing polymer structures, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

If you are not sure which search you need to use, click here.


Requirements to use the Polymer dialog

To use this dialog:

*	Your molecule query should contain one or more polymer structures. Optionally, you can specify one or more text/numeric strings in boxes on your form.

*	You need to understand how to draw polymer structures that can retrieve all the polymer structures that you want. If you are not sure whether your polymer query can retrieve all the structures that you want, we strongly recommend that you read Drawing Polymers: MDL Requirements for Database Searching and Registration.


Text/Numeric Strings in Polymer Queries

A text/numeric string in a query for a POLY/Sub, POLY/Co, POLY/Both, or POLY/Exact search is a phrase in a box or cell on the form that specifies the retrieval of data.

Each phrase contains:

*	A search operator that specifies the type of search (such as an equal sign, =, to specify a search that finds solely the exact target text in the query).

*	The text or numeric target value (specific data) that you want to find.

For example, to find structures with a number-average molecular weight greater than 20,000, enter > 20000 in the Molecular Weight box (where > is the search operator and 20000 is the target value).


Find all polymers that contain this polymer substructure

Click POLY/Sub for complete information on:

*	Searching concepts/examples

*	Step-by-step instructions

*	Additional requirements

for this search type.


Find all copolymers that contain this monomer or SRU

Click POLY/Co for complete information on:

*	Searching concepts/examples

*	Step-by-step instructions

*	Additional requirements

for this search type.


Find the monomer or SRU representation of this polymer

Click POLY/Both for complete information on:

*	Searching concepts/examples

*	Step-by-step instructions

*	Additional requirements

for this search type.


Find this exact polymer

Click POLY/Exact for complete information on:

*	Searching concepts/examples

*	Step-by-step instructions

*	Additional requirements

for this search type.


Additional Options

Use these options to specify additional search criteria for the POLY/Exact, POLY/Both, or POLY/Co searches.

Attached data must match

To specify that attached data in the structures that you retrieve must match the search conditions that are specified in the query, set [image]. To ignore the attached data in the query, set [image].

Polymer end groups must match

To specify that polymer end groups in the structures that you retrieve must match the end groups that are specified in the query, set [image]. To ignore the polymer end groups in the query, set [image].


Current Mol

Use this dialog to:

*	Conduct any one of the 5 searches listed below.

 Requirements to use this dialog

Click any of the following items:

Exact match

Isomers

Tautomers

Parent molecule

Flexmatch, [image] (salts, isotopically-labeled compounds, and alternative representations of a structure)

See also:

Flexmatch switches

If you are not sure which search you need to use, see the ISIS/Base SearchSelector


Requirements to use the Current Mol dialog

To use this dialog, your molecule query must not contain any query features.


Exact match

To find structures that are exact duplicates of your query, set [image] Exact match on the dialog.

For complete information on:

*	Searching concepts/examples

*	Step-by-step instructions

*	Additional requirements

click one of the following:

*	Molecule records: MEXACT

*	Reaction records: MEXACT


Tautomers

To find structures that are either exact duplicates or tautomers of your query, set [image] Tautomers on the dialog.

For complete information on:

*	Searching concepts/examples

*	Step-by-step instructions

*	Additional requirements

click one of the following:

*	Molecule records: TAUT

*	Reaction records: TAUT


Isomers

To find structures that are either exact duplicates, optical stereoisomers, and/or geometric stereoisomers of your query, set [image] Isomers on the dialog.

For complete information on:

*	Searching concepts/examples

*	Step-by-step instructions

*	Additional requirements

click one of the following:

*	Molecule records: ISOMER

*	Reaction records: ISOMER


Parent molecule

To find the parent molecule of the salt in your query, set [image] Parent molecule on the dialog.

For complete information on:

*	Searching concepts/examples

*	Step-by-step instructions

*	Additional requirements

click one of the following:

*	Molecule records: PARENT

*	Reaction records: PARENT


Flexmatch

To find structures that match your query exactly, except in ways that you specify, set [image] Flexmatch on the dialog, then click the Flexmatch button to set the Flexmatch Parameters.

For complete information on:

*	Searching concepts/examples

*	Step-by-step instructions

*	Additional requirements

*	Setting flexmatch parameters

click one of the following:

*	Molecule records: FLEX

*	Reaction records: FLEX


Example

This example requires that you set [image] Isotopes:


Alternative Representations of Ferrocene

Historically, the structure of ferrocene has been represented in radically different ways. This has caused great difficulty in searching for ferrocene in a database. This example shows how FLEX search can find different representations of ferrocene:


OK, Cancel

OK

To start the search and close the dialog box, click OK.

Cancel

To close the dialog box without starting the search, click Cancel.


Flexmatch switches

To enter flexmatch parameters as three-letter codes, set [image] Flexmatch on the dialog, click the Flexmatch switches box, then type the three-letter codes that represent the structural features that must match your query.


How to avoid commmon problems with dates
How ISIS/Base Handles Date Formats

ISIS/Base uses the date format that you specify in the Date tab of the Regional Settings control panel (Windows), or in the Date and Time control panel (Macintosh).

*	ISIS/Base will not translate dates that include non-numeric characters, such as Jan31995. Choose a date setting that contains only numeric characters.

*	ISIS/Base will not translate dates that do not include all three date components (Month, Day, Year). Choose a date setting that contains all 3 components.

*	When you enter records in Update mode, make sure to enter dates using the same format that you specified in the Operating System. For example, if you specified M/D/YYYY, enter dates only in that format. Note that is it especially important that you use the same separator character.


 Information on MDL Databases

MDL is a major supplier of databases that you can search with ISIS. For more information, click one of these:

*	The chemical supplier databases help you find and compare chemical suppliers. You can also use these large databases to build libraries for combinatorial chemistry.

*	The OHS safety series databases give you quick access to MSDSs (Material Safety Data Sheet) from your workstation.

*	The synthetic methodology databases provide the comprehensive information you need to easily find new or better reaction methodologies for combinatorial or discrete syntheses.

*	The biological activity databases help you stay abreast of competitive activity and give you insight into the significance of structural features of your lead compounds.

*	The metabolism databases let you explore the metabolic fate of your lead compounds before you embark on expensive studies.


Chemical Supplier Databases

The Available Chemicals Directory (ACD) family of databases help you reduce the cost of doing business by making it easy to compare costs, quantities, and availability of the compounds you work with. You may also find ways to improve synthetic processes by eliminating steps or by using more effective ingredients.

The ACD family contains supplier information from over 200 catalogs. You can find information on everything from supplier sources and ordering information, to specifics such as product purities and grades, physical forms, quantities, units, and prices.

The databases come in a variety of formats that allow you to use the database with the software best suited to your task:

Click any of the following:

*	ACD

*	ACD-3D

*	ACD-SC

*	Chemical Products Information File (CPI File)


Available Chemicals Directory

Use ACD to compare costs, quantities, and availability of the chemicals you use and to find ingredients to make your syntheses more cost-effective.

ACD contains supplier information from over 200 catalogs. Over two-thirds of the database contents change in a typical year due to additions or modifications to listed products. This degree of turn-over ensures that you have the most timely and accurate information available from any published source of chemical supplier data.

The ACD database is updated twice yearly.


Available Chemicals Directory-3D

Use ACD-3D to build libraries for combinatorial synthesis or to find candidates that meet a pharmacophore hypothesis.

This database has the same information contained in ACD and also includes three dimensional models of each compound.

ACD-3D is updated twice yearly.


Available Chemical Directory-SC

The Available Chemicals Directory - Screening Compounds (ACDSC) is an information system that enables you to search for and view chemically diverse compounds for use in high throughput screening. Once you find the chemicals that you want to order, you can display the contact information for the supplier, and you can create an electronic list of the catalog numbers for the chemicals that you want to order. The ACDSC information system consists of the ACDSC database on your host computer, and the ACDSC Finder on your desktop computer.


The Chemical Products Information File

With the Chemical Products Information File (CPI File), companies can build custom applications for managing their chemical inventory and order management systems that build upon the information provided with ACD.

The CPI File contains all the text data found in ACD, in addition to tools for loading the database into a relational database management system.

The CPI File is updated twice yearly.


The OHS Safety Series Database

The OHS Safety Series provides online MSDSs that list carcinogen status, target effects, persons at increased risk, antidote information, chemical properties, handling requirements, hazards, sampling methods, toxicological and other information for chemical compounds.

Click any of the following:

*	OHS Cornerstone MSDS Database

*	OHS MSDS ON DISC

*	OHS Inventory Match Database

*	OHS Reference Database

*	OHS Right to Distribute Database Service


OHS Cornerstone MSDS Database

The OHS Cornerstone MSDS Database contains over 19,000 MSDSs in a format that enables companies to incorporate safety information into their existing search applications. The safety data is presented in the same industry-standard 16-section government format used internationally for ISO 11014 MSDSs.

The Cornerstone Database helps companies comply with government regulations while providing a valuable reference for a variety of departments such as industrial hygiene, safety, shipping, purchasing, and research. Additional options allow companies to print MSDS summary sheets for quick reference and training, extract safety information for use in labeling, or search and view MSDSs using OHS Seamless Software.

This database is updated quarterly.


OHS MSDS ON DISC

Use the OHS MSDS ON DISC with your Windows, DOS, or Macintosh computer to find safety information for over 19,000 chemicals and to view related information in the Code of Federal Regulations (CFRs).

You can search for a particular MSDS by chemical name, synonym, trade name, CAS Number, revision date, or any text in the MSDS. Additional options with this database allow you to print label information, to produce safety summary sheets, and to create your own MSDSs.

This database is updated quarterly.


OHS Reference Database

The OHS MSDS Reference Database currently contains over 49,000 MSDSs for commonly used commercial chemical products. The database can be used with virtually any hardware.

The Reference Database helps companies comply with government regulations while providing a valuable reference for a variety of departments such as industrial hygiene, safety, shipping, purchasing, and research. In addition to the MSDSs, you can license summary sheets for quick reference and training.

This database is updated quarterly.


OHS Inventory Match Database

The OHS MSDS Inventory Match is a database service that provides MSDSs to match your company's chemical inventory. MDL researches and writes MSDSs as needed to ensure 100% coverage.

With this service, everyone in the company concerned with ensuring OSHA regulatory compliance can be confident that MSDSs are up-to-date, accurate, and complete for all the compounds in a company's inventory. In addition to the MSDSs, you can license summary sheets for quick reference and training.

MDL updates custom databases of MSDSs quarterly.


OHS Right to Distribute
OHS Right to Distribute Database Service

The OHS Right to Distribute Database Service is useful for chemical manufacturers who need a cost-effective way to develop and maintain MSDSs that comply with government regulations.

Customers of this service have the right to distribute MDL OHS MSDSs with their products. If no OHS MSDS exists for a chemical, MDL will research and write one.


Finding reactions on synthetic methodology
Synthetic Methodology Databases

Use the synthetic methodology databases to quickly review thousands of reactions. These databases help you find appropriate methodologies for designing novel compounds.

Click any of the following:

*	The ChemInform Reaction Library

*	Current Synthetic Methodology

*	REACCS-JSM

*	ORGSYN

*	The Reference Library of Synthetic Methodology

*	Comprehensive Heterocyclic Chemistry

*	THEILHEIMER

*	SPORE


The ChemInform Reaction Library

Use the ChemInform Reaction Library Database (ChemInform RXL) to answer questions pertinent to combinatorial and discrete synthesis including the role of steric interactions, substituent effects, structural effects, and functional group compatibility.

In ChemInform RXL, you will find:

*	New reactions, including enzymatic or microbial processes

*	Application of known methods to the synthesis of new compounds

*	Improved synthetic methods and application of new reagents

*	Reactions for the synthesis of natural products

*	Use of novel organo-element compounds and new catalysts

ChemInform RXL is a compilation of the world's synthetic organic chemistry literature. Subscribers receive updates to this database two times a year.


The Reference Library of Synthetic Methodology

Use the Reference Library of Synthetic Methodology (Reference Library) database to research novel reaction methodologies and to view example reactions that best represent each methodology.

The Reference Library is a collection of about 170,000 innovative and significant reactions from the synthetic literature of 1946 to 1991.


Currnet Synthetic Methodology
Current Synthetic Methodology

Use the Current Synthetic Methodology database (CSM) to research new synthetic methodologies.

The reactions in this database emphasize:

*	New reagents or important modifications of known reagents

*	Chemo-, regio-, and stereoselective reactions

*	New synthetic methodology, particularly reactions for general use

Reactions in CSM have been abstracted from the primary chemical and patent literature from 1992 to the present. This database gains approximately 3,500 new reactions with each update. Subscribers receive updates two times a year.


REACCS-JSM

Use REACCS-JSM to find new methods of organic synthesis.

The reactions in this database emphasize:

*	Novel functional group and ring chemistry

*	Protecting group chemistry

*	Heterocyclic chemistry

Reactions in REACCS-JSM have been abstracted from the primary chemical and patent literature from 1980 to the present. This database, which is an electronic version of Derwent Publisher's Journal of Synthetic Methods, gains approximately 3,000 new reactions with each annual update.


Organic Synthesis
ORGSYN

Use ORGSYN to find preparations of common reagents and high-yield synthetic methods.

The reactions in this database have been independently tested and optimized. Data for each reaction provides explicit experimental details and hazard warnings.

This database is updated annually.


Comprehensive Heterocyclic Chemistry

Use Comprehensive Heterocyclic Chemistry (CHC) to explore syntheses that involve heterocyclic chemistry.

The reactions in this database emphasize:

*	Synthesis of heterocycles

*	Reactions of heterocyclic systems

*	Use of heterocycles in the synthesis of non-heterocyclic structures

The information in this database originates in Pergamon Press' popular compendium Comprehensive Heterocyclic Chemistry, which is a retrospective examination of heterocyclic chemistry found in the literature through 1983.


THEILHEIMER

Use THEILHEIMER to find high-yield functional group transformation reactions.

The reactions in this database emphasize new applications of known methods, high-yield functional group transformations, and carbon-skeleton formations.

The information in this database originates in Synthetic Methods of Organic Chemistry, volumes 1-35, 1946-1980 (Karger).


Solid-Phase Organic REactions (SPORE)

Use SPORE to find information on solid-phase reaction data.

SPORE contains extensive data from solid-phase organic chemistry, including polymeric materials, linkers, solid supports, and protecting groups.

SPORE was developed jointly by MDL and FIZ CHEMIE Berlin. SPORE contains over 4,100 reactions, and is updated quarterly.


Finding metabolism information
Metabolism Databases

Use the Metabolite Information System to keep abreast of the published metabolism literature and to store the results of proprietary metabolism studies. With Metabolite, you can save research time, generate valuable information for product design, avoid toxic metabolites, and maximize bioavailability before you begin animal studies.

The Metabolite database contains metabolic schemes of xenobiotic compounds, including medicinal drugs, agricultural chemicals, industrial chemicals, and environmental contaminants. In addition to metabolic schemes, Metabolite includes information on:

*	analytical methodology

*	enzymes

*	conjugation reactions

*	species

*	physiological activity

*	bioavailability

*	route of administration

*	excretion

*	CAS Registry Numbers

*	compound class

*	literature references

The Metabolite database, which is updated twice yearly, is abstracted from 150 scientific journals covering the period from 1991 to the present. Metabolite also includes the complete collection of metabolic schemes found in two compendia edited by S. Pfeifer and H. Borchert: Biotransformation von Arzneimittein and Pharmacokinetics.


Metabolite Information System

The Metabolite information system consists of:

*	The Metabolite database which is a database of the published metabolism literature.

*	Metabolite Registrar, which is software used to manage and store information in your corporate metabolism databases.

*	Metabolite Browser, which is software used to search the Metabolite and the corporate metabolism databases.


Finding biologically active compounds
Biological Activity Databases

Use the following databases to help you discover and refine pharmacophores.

Click any of the following:

*	MDL Drug Data Report

*	Comprehensive Medicinal Chemistry

*	National Cancer Institute


MDL Drug Data Report

Use MDL Drug Data Report (MDDR) to stay current with competitive discoveries and to generate ideas for discovery research projects.

The MDDR database contains structures and biological activity information for new drug candidates. The MDDR-3D database contains the same information and adds 3D models of the structures. In addition to structures, the database includes:

*	Common names

*	Descriptions of biological activity

*	Patent information

*	Full bibliographic references

Subscribers to MDDR and MDDR-3D receive monthly updates of recently disclosed biologically active compounds. These updates track a compound's progress from development through clinical trials. The information in MDDR comes from patents, conferences, journals, and company communications.

MDDR contains material copyrighted by J.R. Prous, S.A.


Comprehensive Medicinal Chemistry 3D
Comprehensive Medicinal Chemistry

Use Comprehensive Medicinal Chemistry (CMC-3D) to ask questions about possible structure-activity relationships using well-tested drugs as your source. Gain good baseline information that you can use to explore other commercial databases or your proprietary databases.

The CMC-3D database contains chemical structures, 3D models, and properties of currently marketed drugs. Data include: generic name, CAS Registry Number, drug class, originating company, log P, and pKa.

The database, which is updated yearly, was developed in cooperation with Pergamon Press from the drug compendium in Pergamon's six-volume work Comprehensive Medicinal Chemistry.


National Cancer Institute 3D
National Cancer Institute Database

Use the National Cancer Institute database (NCI-3D) to find information on non-proprietary compounds that have been submitted to the National Cancer Institute for anticancer activity testing.

MDL has enhanced the public domain version of this database by improving the quality of the chemical structures, deleting problematic structures, creating 3D models of the structures, and adding a fast-search index. The NCI-3D database from MDL also contains CAS Registry Numbers, NCI numbers, formulas, and molecular weights.

MDL provides NCI-3D to its ISIS/Host customers free of charge.


Search Operators

Use the following search operators with text or numeric data:

Operator	Definition

<	less than

<=	less than or equal to

>	greater than

>=	greater than or equal to

<>	not equal

=	equal

LIKE	text substring

BETWEEN	numeric or text range

EXISTS	numeric or text values for a field that accepts this search operator (or you see an error message)


Search Operators

Use the following search operators with structural data (2D structures, 3D structures, or reactions):

Operator	Search Type

=	exact match

SSS	2D substructure

ISOMER	isomer (remote databases)

TAUTOMER	tautomer (remote databases)

PARENT	parent (remote databases)

FLEXMATCH <v1>	Flexmatch (remote databases)

MSIMILAR <type><v1>	molecule similarity (remote databases)

SAMEAS3D <v1> <v2>	3D exact match

SSS3D <v1> <v2> <cfs>	CFS (remote databases)

SSS3D <v1> <v2>	3D substructure searches where the query contains submodel components (remote databases)

SSS	3D substructure where the query does not contain submodel components (remote databases)

RSS	reaction substructure

SUBSET	reaction subset (remote databases)

RSIMILAR <v1><v2>	reaction similarity (remote)

For FLEXMATCH, <v1> is a three-letter code that tells ISIS which flexmatch parameters are switched off and on.

For MSIMILAR, <type> is a text string that specifies the amount of similarity to your query (normal, SUB, or SUPER), and <v1> is the similarity value.

For RSIMILAR, <v1> is the transformational similarity value and <v2> is the structural similarity value.

For SAMEAS3D and SSS3D, <v1> is the value of the maximum atomic displacement and <v2> is the value of the maximum RMS deviation. Both <v1> and <v2> are required.

For SSS3D, <cfs> specifies a CFS search and CFS options. The <cfs> value is optional.

For RSIMILAR, <v1> is the transformational similarity value and <v2> is the structural similarity value.


Reacting Center Similarity

Transformational similarity (also called reacting center similarity) is the physical resemblance solely to the reacting centers in your transformation (reaction) query.


Structural Similarity

Structural similarity is the physical resemblance to the substrate molecules in your query.


Field Name

Enter a unique name for the field up to 30 characters long. It makes no difference if field names are entered in uppercase, lowercase, or initial capitals. You can use the following characters in field names:

*	Alphabetic characters. For example, A ... Z and a   z.

*	Numeric characters except for the first character of the name. For example, 0,1,...9.

*	Other characters such as _ (underscore), , (comma), . (period), / (forward slash), # (pound sign), $ (dollar sign), * (asterisk), and + (plus sign).

Field names cannot have spaces or these characters:

!  @  %  ^  &  (  )  -  =  \  |  {  }  [  ]  <  >  ?  ;  :  '  "  ~


Field Type

The field type determines the type of data the field can store:

Fixed Text

Variable Text

Integer

Real

Range

Date

Sketch

Structure

Reaction

Parent


Fixed Text

Text of a specified number of alphanumeric characters. A fixed-text field can store any number of characters up to the maximum number specified in its definition. However, no fixed-text field can store more than 80 characters.


Variable Text

Alphanumeric text of any length that is limited solely by computer memory.


Integer

A whole number, such as 1 or 2. For PC and Macintosh systems, the value of an integer may range from -2147483648 to +2147483648.


Real Number

A real number contains decimals, such as 1.50. The decimal-place precision of the number varies with computer systems.


Range

A range of real number values. The decimal-place precision of the number varies with computer systems.


Date

The date format (such as day/month/year) specified in your windowing software configuration file(s).


Sketch

Stores an ISIS/Draw sketch.


Structure

A molecule (including a reactant, product, 3D structure, or sequence). You can have multiple structure fields in your database, but each must contain a unique field name.


Reaction

A chemical reaction. You can have multiple reaction fields in your database, but each must contain a unique field name.


Parent

A parent field does not store data. Instead, a parent field branches to one or more fields that store related data. For this reason, the parent field name should be representative of the types of data that the lower-level fields will store. For example, <LITREF> is the parent field for JOURNAL and AUTHOR.

ISIS/Base displays parent field names in brackets to distinguish them from other fields.


Counterions

A counterion is any fragment or single atom in the SALTS.DAT file. Your ISIS Administrator can add or delete fragments from this file. The default SALTS.DAT file contains the following:


Parent Molecule

The parent molecule of a salt is the portion of the molecule that remains after removing counterions and neutralizing charges:

A counterion is any fragment or single atom in the SALTS.DAT file. Your ISIS Administrator can add or delete fragments from this file. The default SALTS.DAT file contains the following:


Explicit and Implicit Valence

Each atom type has a standard (default) valence, called the implicit valence. To change this, assign an explicit valence to the atom. For example, use explicit valence to assign carbon a valence of 5.

If you draw a structure with fewer attachments than the valence, ISIS assumes that hydrogens are present at unfilled valences. These are implicit hydrogens. For transition metals, the implicit valence equals the number of bonds that are attached to non-hydrogen atoms. Consequently, if you want to draw transition-metal hydrides, you need to assign an explicit valence to the metal atom:


Header/Footer Codes

When you print your form, query, or search results, you can insert codes for specific information into the header and/or footer of the form. ISIS uses the following header/footer codes:

Note: Codes for starting and ending context apply solely to search results that you print in the Browse mode. For more information on printing search results, see Printing All the Data, and Only the Data, That You Want.


Flexmatch Parameters

In a Flexible Match (FLEX) search, flexmatch parameters define the features of retrieved molecules that must match the query molecule. Changing the default flexmatch parameters allows you to find structures that match your query, but might be represented differently in the database. For example, the structure of ferrocene can be represented in many different ways:

Note: Flexmatch parameters are interactive: To obtain the correct search results, you need to know which flexmatch parameters require other flexmatch parameters to function correctly. To learn these requirements and to see some searching examples, click FLEX Searching Examples.


Similarity

There are two types of similarity that you can specify between your query and the structures retrieved:

*	Structural Similarity -- physical resemblance to the substrate molecules in your query

*	Transformational Similarity -- similar reacting centers if your query is a reaction


Structurally Similar

In an RSim search, you can define the degree of similarity that you want to exist between the reaction substrate molecules in your query and the reaction substrate molecules in the retrieved reactions.

(Reactions retrieved by similarity do not necessarily have specific substructures in common.)

ISIS/Base compares the structural features in common with the total number of structural features present.


Similar Reacting Centers

Reactions that are stored in the database often contain reacting center markings that indicate the type of transformation that occurred. In an RSim search, you can define the degree of similarity that you want to exist between the reacting centers in your query and the reacting centers in the retrieved reactions. ISIS/Base compares the reacting center features in common with the total number of reacting center features present.


Remote Search

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to obtain network access information.


Remote Search
Local Search

A local search is a search over a database that typically exists on your hard disk. To do a local search on your hard disk, you do not need to access network information.

Note: To do a local search that is accessed from a shared network, you need to access network information.


Query

A query is your defined request to retrieve a specific set of records from your search domain. Your request can be in a graphical or a text/numeric (search string) format.


Structural Similarity Value

You assign a structural similarity value between 0 and 100 (these are not actual units) that defines the degree of structural similarity between your query and the structures retrieved. The higher the value, the more similarity.


Transformational Similarity Value

You assign a transformational similarity value between 0 and 100 (these are not actual units) that defines the degree of similarity in the reacting centers between the reaction in your query and the reactions retrieved. This value is also called the reacting center similarity value.


Search Query

A search query is a question in the form of a structure and/or data that searches your database.


ISIS Atom-Query Feature

The ISIS Query-Atom Features

An ISIS atom-query feature is a restriction on an atom in a query that specifies the retrieval of certain types of structures and/or data. For example, you can specify that a chain of atoms be present at a specific position in the molecules retrieved (query feature: Ch).


ISIS Bond-Query Feature

The ISIS Query-Bond Features

An ISIS bond-query feature is a restriction on an bond in a query that specifies the retrieval of certain types of structures and/or data. For example, you can specify that solely aromatic bonds be present at a specific position in the molecules retrieved (query feature: An aromatic bond at a specific position).


Submodel

A submodel is a three-dimensional (3D) representation of a portion of a molecule. The structures that you retrieve with a submodel query have atoms in the same spatial arrangement as those specified in your submodel query, within allowed deviations of the individual and overall atoms. To construct a submodel query, you eliminate parts of a 3D structure until you have the submodel that you want to find in other models. Then, you fix (F) the positions of the atoms that you want to maintain in a fixed spatial relationship. For example:


Current List

A list of search results is a set of records that you retrieve from the database that you search with your search query. Each record in the list might contain a structure and associated data. (Some records contain solely data.)

A current list is the set of records that you see immediately after you search the database.


Searchable Data

Searchable data can be structures or text/numeric data that is retrievable from a search.

An example of data that is not searchable is text that you superimpose on an atom for display purposes (an atom alias).


Searchable Keys

If your database contains the database field MOLSKEYS, you can use numbered keys to retrieve specific substructures or chemical representations. These numbered keys are called searchable keys. Each key corresponds to a substructure or a chemical representation that is written in a special format (called query language).

For more information on searchable keys and query language, see:

Molecule records: SBF or QB a remote database


Reactant

In an MDL reaction database, a reactant is a molecule that contributes at least one carbon atom to the product. By contrast, a reagent/catalyst is a molecule that does not contribute any carbon atoms to the product.

Typically, there are database fields for reactants and reagent/catalysts.


Reagent/Catalyst

In an MDL reaction database, a reagent/catalyst is a molecule that does not contribute any carbon atoms to the product. By contrast, a reactant is a molecule that contributes at least one carbon atom to the product.

Typically, there are database fields for reactants and reagent/catalysts.


Catalyst

In an MDL database, a catalyst (or reagent/catalyst) is a molecule that contributes no carbon atoms to the product.


Database Objects

In ISIS, you can save the following objects in your database: A search query, a list of search results, a form, sorting instructions, and a PL program (Procedural Language).

Note: These objects are in addition to, and separate from, the records in your database.

You cannot save a database object from the File menu. Thus, you cannot see the file name of a database object in your file listing. Instead, to use a database object that you saved in the database, you must restore the object. (Exceptions: You open either an ISIS/Base form or a list of search results.)

Note: Alternatively, you can export a database object from the File menu to a file on disk. (You can see the file name of the object.) Anyone with a different database can then import the object and use it.


Aromaticity

For remote and local databases: A bond is aromatic if it is in a six-membered ring with alternating double and single bonds, such as benzene.

For remote databases: A bond is aromatic if it is in a six-membered ring with alternating double and single bonds, is a perimeter bond of azulene, or is in a five-membered ring such as one of the structures shown below:

For example:


Pharmacophores

A pharmacophore is a 3D arrangement of atoms, bonds, and groups that are thought to cause a desired biological activity in a molecule.


Residue Templates

A residue template is a chemical structure that represents either a residue or a leaving group that you can store in a Residue Template file and use as many times as you want. For example, you can store the following amino acid template for the residue Alanine:

A(l)--Ala--B(r)

Where Ala represents the amino acid residue Alanine; the first letter of the leaving-group designator (A or B) refers to the leaving group ID in the Residue Map file; and the letter in parentheses indicates a left (l), right (r), or a crosslink (x) attachment of the leaving group within the sequence.


Stereochemistry

Molecules in the database might contain the following types of stereochemistry:

*	An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si.

*	Double bonds in the cis or trans stereoconfiguration.

*	A chiral flag to designate that the molecule is the absolute stereoconfiguration.


Aromatic Bonds

When you conduct a substructure search in a remote database, an Aromatic query bond retrieves the following types of ring systems:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:


Aromatic Bonds

When you conduct a substructure search in a local database, an Aromatic query bond retrieves solely six-membered rings with alternating double and single bonds. For example:


Aromatic Bonds

For local databases: A bond is aromatic if it is in a six-membered ring with alternating double and single bonds, such as benzene.

For remote databases: A bond is aromatic if it is in a six-membered ring with alternating double and single bonds, is a perimeter bond of azulene, or is in a five-membered ring such as one of the structures shown below:

For example:


ISIS Atom-Query Feature

An ISIS atom-query feature is a restriction on an atom in a search query that allows you to retrieve solely those molecules from the database that adhere to your restriction.


ISIS Bond-Query Feature

An ISIS bond-query feature is a restriction on a bond in a search query that allows you to retrieve solely those molecules from the database that adhere to your restriction.


ISIS Reaction-Query Feature

An ISIS reaction-query feature is a restriction on a reaction in a search query that allows you to retrieve solely those reactions from the database that adhere to your restriction.


ISIS 3D-Query Feature

An ISIS 3D-query feature is a restriction (also called a 3D constraint) on atoms, functional groups, and/or on 3D Objects in a search query that allows you to retrieve solely those 3D structures from the database that adhere to your restriction.


Query Features

An query feature is a restriction on an atom or bond in a search query that allows you to retrieve solely those molecules from the database that adhere to your restriction.


Structural Constraint

A structural constraint is a restriction on an atom or a bond in a molecule that allows you to retrieve solely those molecules from the database that adhere to your restriction.


A Reaction Substructure

A reaction substructure is any portion of a reactant and any portion of a product, without regard to its 3D spatial arrangement. For example, the following reaction substructure specifies the retrieval of reactions in which aldehydes are converted to alcohols:


Atom-Atom Map

An atom-atom map is a set of numbered atoms on a reaction that defines the correspondence between the atoms in the reactants and the atoms in the products. With a correspondence between atoms, you can follow the structural changes of the transformation.


Stereochemical Equivalents

The following chemical representations are stereochemically equivalent:

Points A, B, and C define a plane (the screen), and the implicit hydrogen atom projects into the plane.

In addition, stereochemistry is perceived at the small end of the Up or the Down bond (and solely one chiral center is specified):


Atom Numbers

Atom numbers on a reaction that is retrieved from the database are integers that are assigned to each atom in a structure. You can show or hide these numbers. For example, you might want to show the atom numbers on an unusual rearrangement reaction.

These atom numbers are different from the atom numbers on a reaction or on a molecule that are assigned during the drawing process.


Root Structure

A root structure is that portion of the query that must be present in all structures retrieved. This portion of the query contains Rgroup labels (such as R1 and R2) that designate the lists of substituents that can be attached to the root structure at the positions specified. For example:


Rgroup Substituents

Rgroup substituents are functional groups or atoms that you can specify to be attached to the root structure at a particular position in the records retrieved. Each Rgroup substituent contains an attachment point (marked with an arrow and an asterisk) to designate the atom that you want to be attached to the root structure:


Rgroup Conditions

Rgroup conditions are the set of restrictions that you can apply to each Rgroup in your query. With the Rgroup condition:

*	Occurrence, you can specify the number of Rgroup sites that must be occupied in the records retrieved. For example, the occurrence designation R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved.

*	RestH, you can specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site.

*	If/then, you can specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.


Rgroup Conditions

Rgroup conditions are the set of restrictions that you can apply to each Rgroup in your query. With the Rgroup condition:

*	Occurrence, you can specify the number of Rgroup sites that must be occupied in the records retrieved. For example, the occurrence designation R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved.

*	RestH, you can specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site.

*	If/then, you can specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.


Query Features

A query feature on a molecule (including a reaction component) is a restriction on an atom and/or a bond that specifies the retrieval of certain types of records from an ISIS/Base database. For example, you can use the atom query feature (H0) to prohibit the attachment of hydrogens on a specific atom in the records retrieved.

A query feature on a reaction is a restriction on the reaction that specifies the retrieval of certain types of records from an ISIS/Base database. For example, you can specify that a specific bond cleaves in all the reactants retrieved.


Reacting Centers

Reacting centers are bonds that participate in the chemical transformation of a reactant to a product. You can specify with reaction query features that a reacting center bond be formed or broken, that its bond type be changed, or that the bond changes in an unspecified way.

For example, you can use the reaction query feature CHANGE in a specific reactant and product (designated by the addition of / to a bond) to specify that the bond order must change in the reactions retrieved.

Note: If you do not restrict the reacting center bonds in your query, you might retrieve additional, unwanted records.


Reacting Centers

Reacting centers are bonds that participate in the chemical transformation of a reactant to a product. You can specify with reaction query features that a reacting center bond be formed or broken, that its bond type be changed, or that the bond changes in an unspecified way.

For example, you can use the reaction query feature CHANGE in a specific reactant (designated by the addition of / to a bond) to specify that the bond order must change in the reactions retrieved.

Note: If you do not restrict the reacting center bonds in your query, you might retrieve additional, unwanted records.


Molfile

A molfile is a file in CTfile (chemical table files) format that contains either a single molecular structure or disjointed structural fragments.


Rxnfile

A rxnfile is a file in CTfile (chemical table files) format that contains the structural information for the reactants and products of a single reaction.


Automap a Reaction

If you atom-atom map a reaction automatically, you execute the automap process. This process both maps your reaction and adds any relevant reacting centers (and any relevant stereo bond inversion and/or retention marks) to your query automatically.


Fragment

In a biopolymer query, a fragment is the set of residues of your choice, such as the set of amino acid residues FRCAT:

-phenylalanyl-arginyl-cysteinyl-alanyl-threonyl-


PTable

The PTable is a table that contains all the chemically searchable atoms that you can enter into a search query.


Tautomers

A tautomer is a group of atoms with any of the following patterns:

Where	Q = O, N, S, Se, or Te

X = C, O, N, S, Se, or Te

Y = C, I, P, As, Sb, Cl, or Br

You can have multiple tautomeric groups in a single molecule. Example

In addition, any bonds in the tautomeric region can be aromatic. Example


Example of Multiple Tautomeric Groups in a Single Molecule


Example of Aromatic Bonds in the Tautomeric Region


Specifying Tautomers Within Tolerance Limits

The tolerance limit on the tautomer setting in a FLEX search is the sum of the absolute values of charges plus the sum of the number of radicals plus the number of metal bonds. Diradicals count as two radicals. (If you specify this feature with the hydrogen count on, the tolerance limit is zero.)


Specifying the Hydrogen Count Within Tolerance Limits

The tolerance limit on the hydrogen count setting in a FLEX search is the sum of the absolute values of charges plus the sum of the number of radicals plus the number of metal bonds. Diradicals count as two radicals.


Metals

A metal is any atom other than H, D, T, He, B through Ne, Si through Ar, As through Kr, Te, I, Xe, At, and Rn.

Note: Metals might be represented differently in the database. For example, the pi-metal bonds in ferrocene can be represented in different ways.


Atom Alias

Click here for step-by-step instructions

An atom alias is any combination of text or numeric characters that you specify in place of an atom or a set of atoms. The atom alias hides the existing atom. (You can use Greek characters in atom aliases if your system has Greek fonts installed.)

When you add an atom alias to a structure, the alias becomes part of the structure and can be saved with the structure. Atom aliases are ignored when a structure is sent to MACCS-II or REACCS.

Note: You can register a structure into a database that contains an atom alias, but you cannot search for it. You can only search for abbreviated structures.


Atom Alias

An atom alias is any combination of text or numeric characters that you specify in place of an atom or a set of atoms. The atom alias hides the existing atom. (You can use Greek characters in atom aliases if your system has Greek fonts installed.)

When you add an atom alias to a structure, the alias becomes part of the structure and can be saved with the structure. Atom aliases are ignored when a structure is sent to MACCS-II or REACCS.

Note: You can register a structure into a database that contains an atom alias, but you cannot search for it. You can only search for abbreviated structures.


Atom Value

Click here for step-by-step instructions

An atom value is any real number or range of real numbers (including exponential notation) that you attach to an atom. For example:

Note: You can not search for atom values using ISIS/Base.


Atom Value

An atom value is any real number or range of real numbers (including exponential notation) that you attach to an atom. For example:

Note: You can not search for atom values using ISIS/Base.


Atom Numbers

Atom numbers on a structure (a molecule or a reaction) are numbers that are assigned to the atom automatically in ISIS/Draw during the drawing process. These numbers allow you to observe the order in which atoms in the structure were drawn.

Note: These numbers are not the same numbers that are used in IUPAC nomenclature.


Atom Query-Feature

An atom query-feature is a requirement that you place on an atom to specify the retrieval of certain types of molecule or reaction records from a database using ISIS/Base. For complete information on the different types of atom query features, see Specifying atom query features

See also:

Creating Molecule Queries

Creating Reaction Queries


Bond Query-Feature

A bond query-feature is a requirement that you place on a bond to specify the retrieval of certain types of molecule or reaction records from a database using ISIS/Base. For complete information on the different types of bond query features, see Specifying bond query features

See also:

Creating Molecule Queries

Creating Reaction Queries


Rgroup Query

An Rgroup query contains a root structure with defined Rgroup substituents attached to it at any position. You can also specify Rgroup conditions for your Rgroup query.

For example, you can specify that the Rgroup label R1 on the root structure allows a carboxyl group at its position and that R2 allows either a chlorine atom or a sulfonic acid group at its position:

For information on Rgroup searching, see Searching Concepts/Examples


Rgroup

An Rgroup query contains a root structure with defined Rgroup substituents attached to it at any position. An Rgroup consists of the molecule fragments (members) that can attach to the corresponding Rgroup sites on the root. That is, any of the members in the Rgroup R1 can attach to any position with the Rgroup label R1.

For example, you can specify that the Rgroup label R1 on the root structure allows a carboxyl group at its position and that R2 allows either a chlorine atom or a sulfonic acid group at its position:

For information on Rgroup searching, see Searching Concepts/Examples


Fixed-Atom Tolerances

Fixed-atom tolerances specify how closely the spatial arrangement of the atoms in your 3D query must fit the corresponding atoms in the 3D structures that you retrieve. ISIS uses fixed-atom tolerances in the following searches:

*	CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly searches in which the query contains fixed atoms.

*	3DEXACT searches in remote databases (ISIS considers all atoms in the query structure to be fixed.)

You can specify two fixed-atom tolerances: maximum atomic displacement and maximum RMS deviation.

Caution: Your ISIS Administrator sets default fixed-atom tolerances that your site uses to register 3D structures to the database. If you change these default values for searching, you must restore default fixed-atom tolerances before you register 3D structures.


List

A list is a set of records that you retrieve during a search (search results). You can save a list as an object within the database or export the list to a disk file.


Measured Values and Constraint Values

For 3D geometric constraints such as distances, the constraint value and measured value are defined as follows:


Remote Database

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to obtain network access information.


Local Database

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to obtain network access information.

Note: If your local database is accessed through a shared network, you need to obtain network access information.


Storing Binary Data in a Database

To store and view binary data (such as metafiles and bitmaps) in a local database, you must use the ISIS Procedural Language to create a variable-length binary-data field type in the database.

You can view binary data stored in raw datatype fields and long raw datatype fields in an Oracle table using the ISIS Procedural Language.

See the ISIS/Application Development Kit Reference for more information on the DbCreateAddField, GetFieldBinaryBuffer, and SetFieldBinaryBuffer intrinsics.


Boxes

A box is one type of object that you can use to create a form. Create a form with boxes to view data for one record at a time:


Tables

A table is one type of object that you can use to create a form. Create a form with tables to view and compare data for multiple records at the same time:


Column

Every table contains at least one column. A columns displays or registers data for one field.


Search Query

A search query is a graphical or text/numeric request to retrieve a specific set of records from a database or list. You enter the request into a box or column that is connected to the database field that you want to search.


Search Results

Search results are the records that are retrieved in a search and display in a form, as the result of a query. You must have boxes and/or columns connected to database fields to hold the data that you want to view:


Print Search Results

Print the results of a search, to view the records that are retrieved in a search on paper. The form must have boxes and/or columns connected to database fields to hold the data that you want to print:


Register/Update Database Records

Register and update database records into the database with a form. The form must have boxes and/or columns connected to database fields to hold the data that you want to register:


Parent Field

Parent fields do not store data. Instead, parent fields point to one or more fields that store related data. For this reason, the parent field name should be representative of the types of data that the lower-level fields will store. For example, <LITREF> is the parent field for JOURNAL and AUTHOR. ISIS/Base displays parent field names in brackets to distinguish them from other fields.


Flat Database

A flat database stores one-level of data. For example, a flat database might store structures and related-data, such as molecule name, molecular weight, boiling point, melting point.


Hierarchical Database

A hierarchical database stores two or more levels of associated data that are joined by a parent field. For example, a hierarchical database might store stores structures and related-data in the top level, batch data associated with the structures in the second level, and test data associated with the batches in the third level.


Simple Table

A simple table has one or more columns connected to fields that are grouped under the same parent field in the database.


Layered Table

A layered table has its columns connected to fields that are from the same branch of the database hierarchy but from sequential levels of the database.


Uncoupled Table

An uncoupled table has its columns connected to fields that are located in different branches of the database hierarchy.


Database Definition

The database definition lists which fields are in the database, how fields are related to each other, and what type of data each field stores.

A flat database stores one-level of related data, and all of the fields are grouped under one parent field. For example, level one stores structures and structure data:

A hierarchical database stores two or more levels of associated data. For example, level one stores reactions, level two stores variations associated with each reaction, and level three stores literature references associated with each variation. Each level is joined by a parent field:


Hash Center
Hash Centers


Thickened Centers


Color Centers


Today's Date

Today's Date displays or registers your computer's system date in the selected box or column.

The program will only register the date, if the box or column is also connected to a date field.


String

String displays or registers the text string that you enter into the text-entry box that is located below the Default data box.

The program will only register the text string, if the box or column is also connected to a database field and the text string is entered in the correct format for the type of field. For example, you can register a date if the box or column is connected to a date field and the date string is entered in the correct format for your computer. Conversely, you cannot enter 1.5 as a text string if the box or column is connected to an integer field. If you do enter an inappropriate text string, ISIS/Base warns you when you attempt to register the record.


Sketch

Sketch displays an ISIS/Draw sketch in the selected box or column.

Enter the sketch file name in the text-entry box that is located below the Default data box. Enter the full pathname if the ISIS/Draw sketch file does not reside in the ISIS/Base executable directory. The sketch file must end with the .SKC extension (Macintosh: No extension is necessary).


Biopolymer

A biopolymer is a linear chain (a sequence) of connected repeating structures that are called residues. Each sequence contains a set of either amino acid residues to form peptides, proteins, or glycoproteins; or a set of nucleic acid residues to form DNA or RNA. You typically represent residues on the screen with either a 1-letter or a 3-letter residue code. For example, you represent Proline as either the 1-letter code P or the 3-letter code PRO.


Sequence

A biopolymer sequence is a linear chain of residues that are connected by sequence bonds.


Residue

A residue is the smallest unit in a biopolymer sequence of connected structures. Each unit is either an amino acid or a nucleic acid.


Residue Code

A residue code is the name of a structure that is a residue in a biopolymer. You use residue codes to create a chain of residues (called a biopolymer sequence). For example, you can create a chain with the residue codes P, R, and C for the amino acid residues Proline, Arginine, and Cysteine:

P  R  C

You can expand a contracted residue to see the underlying chemical structure of the residue.


Residue Map File

In ISIS, each type of biopolymer residue is defined by name in a Residue Map file that is associated with a Residue Template file. (The Residue Template file contains the structures for each name in the Residue Map file). MDL provides you with Residue Map files for amino acids and nucleic acids (DNA and RNA). With these files, you can represent residues on the screen with a residue code.

For more information, click The Contents of Residue Map Files.


List of Residue Codes

In ISIS, a list of residue codes is a set of residue codes that you can use to create a sequence. Each list of residue codes is defined in a Residue Map file. MDL provides you with Residue Map files for amino acids and nucleic acids (DNA and RNA).


Sequence Bond

A sequence bond is the bond that connects each residue in a linear chain in a biopolymer sequence. For example:

In an amino acid sequence, a sequence bond is formed by the connection of the amino group of an amino acid to the carboxyl group at the C-terminus of the elongating chain to form a peptide bond.

In a nucleic acid sequence, a sequence bond is formed by the connection of the 5'-phosphate of a nucleic acid to the 3'-hydroxyl group at the 3'-OH terminus of the elongating chain to form a phosphodiester bond.

Note: The sequence bonds can be displayed or hidden.


Crosslink Bond

A Crosslink bond is any bond between biopolymer residues other than a sequence bond. You can crosslink residues of the same sequence or residues of different sequences. For example:

If crosslinked residues contain leaving groups, it is the leaving groups that form the crosslink bond. For example, in an amino acid sequence, the SH leaving group on one Cysteine residue forms a disulfide bridge with the SH leaving group on another Cysteine residue. You can crosslink residues in a single sequence or residues in different sequences.


Leaving Group

A leaving group is a specific bonding site on a biopolymer residue. In a sequence, a leaving group can be internal or terminal. For example:


Internal Leaving Groups

An internal leaving group is a bonding site that is not at the end of a biopolymer sequence. In an amino acid sequence, the leaving group SH on the Cysteine residue forms a disulfide bridge with another internal leaving group from residues of the same sequence or residues of different sequences.


Terminal Leaving Groups

A terminal leaving group is a bonding site that is at either end of a biopolymer sequence that connects residues linearly to form the sequence.

In an amino acid sequence, a terminal leaving group is either an amino group (at the N-terminus) or a carboxyl group (at the C-terminus). These terminal leaving groups participate in peptide bond formation.

In a nucleic acid sequence, a terminal leaving group is either a 3'-hydroxyl group (at the 3'-end) or a 5'-phosphate group (at the 5'-end). These terminal leaving groups participate in phosphodiester bond formation.


Chain (Biopolymer)

A (biopolymer) chain is a linear sequence of connected repeating structures.


Block (of Residues)

A block of residues is a discrete subset of the residues in a biopolymer sequence. A sequence is divided into a set of blocks as a visual aid. For example, the following sequence contains 5 residues per block:


Line (of Residues)

A line of residues is a set of residues in a biopolymer sequence that are read like a line of text. For example, the following sequence contains a two lines of residues:


Contracted Residue

A contracted residue is a biopolymer residue that you display on screen with a residue code. Hidden underneath this code is the full chemical structure of the residue. To see the underlying structure, expand the residue.

In the following example, the residue codes for five contracted amino acid residues are F (for phenylalanyl), R (for arginyl), C (for cysteinyl), A (for alanyl), and T (for threonyl):


Expanded Residue

An expanded residue is a biopolymer residue that you choose to display on screen with its full chemical structure instead of as a residue code.


Residue Brackets

Residue brackets are markers on either side of an expanded biopolymer residue in the ISIS/Draw window that you can choose to either display or hide. For example:


Crosslink ID Numbers

You can display crosslink bonds in biopolymers as true bonds, or you can hide the bonds and display only the crosslink ID numbers:


Disulfide Bridge

A crosslink bond is a bond that connects nonadjacent residues of a biopolymer. A crosslink bond in a peptide or a protein forms a disulfide bridge between nonadjacent residues from the same sequence or between residues of different sequences. For example, the internal leaving group on the amino acid Cysteine (SH) forms a disulfide bridge with an identical internal leaving group on another Cysteine within the same sequence.


Peptide Bond

A peptide bond is a type of sequence bond that linearly connects the residues in a peptide or a protein.


Blocking Residue

A blocking residue is a residue without a leaving group ID.

A blocking residue without a leaving group ID on the:

*	C-terminal or 3'-end of a sequence prevents the further addition of residues to the sequence.

*	N-terminal or 5'-end of a residue cannot be added to a sequence.


Active Button or Command

An active button or command is one that is not grayed out or dimmed. You can use any active button or command:


Data, types of

The types of data are the storage characteristics that allow you to store different kinds of data efficiently. You might store specific types of data in single or multiple lines or as fixed- or variable-length characters.


Database Definition

The database definition is the entire set of database fields (by name and type) in the database.


Database Index

The database index is an ASCII file that contains a list of all the fields in the database by name and type.


Database Object

An object in a database can be any item that can be stored in a database: A molecule, a query, a reaction, a list, a form, a set of sorting instructions, and a Procedural Language (PL) program.


Default

The default setting specifies preset conditions. You can change many default settings: Choose Settings or Preferences from the options menu.


Field Definition

In a local database, you can specify type of data that can be placed into a field. The field definition (field vocabulary) contains a list of all the acceptable values for a field.


Field Name

A field name is the name of a database field. The name can contain the entire tree name, such as MOL>MOLSTRUCTURE, or the partial tree name, such as MOLSTRUCTURE.


Field Type

The field type is the type of database field: Text, numeric values, structures, or reactions.


Floating Box

A floating box is a box without borders that you can place above or below reaction components or the reaction arrow in a reaction in the Reaction Structure box. You can enter a reaction condition into a floating box.


Formula Style

The formula style is a format in which all numbers are subscripts.


Hview

An Hview (hierarchical view) is a reference file on the host computer that points to the database that you want to search. For information on using Hviews, see the ISIS/Host Hview Developer's Guide. To obtain the appropriate Hview name, see your ISIS Administrator.


Host

The Host is a mainframe computer. This computer contains databases that you can access from your workstation if you have the correct network information. For more information, see your ISIS Administrator.


Internet Address

An Internet Address is a network address that allows you to connect to a host computer.

For more information, see your ISIS Administrator.


Objects

An object in a database can be any item that can be stored in a database: A molecule, a query, a reaction, a list, a form, a set of sorting instructions, and a Procedural Language (PL) program. In addition, an object in a form can be any item that can be stored in a form: A box or a table or a PL trigger function.


Object Number

An object number (previously called the Sequence ID) is assigned to each box and table automatically as you create a form. The order in which you create boxes and tables determines the order that data is transferred to the form for viewing after a search and the order in which you move from object to object in the form when you press the Tab key.

Use the Style Box/Column -- Border/Pattern menu to change the object number of an object in a form.


Parent Field

A parent field is a database field that contains solely other fields. For example, the parent field DECOMPOSITION contains the child fields PERCENT O2 and NO. OF PEAKS. (Parent fields do not contain data.)


Permanent List

A permanent list is a list that is saved in the database and exists after you close ISIS/Base.


PL Trigger Function

A Procedural Language (PL) trigger function is an object on the form that improves the capabilities of the program in some way. For example, you might have a form that allows you to do an ID search with a single click of the button that contains the PL trigger function embedded in it. For more information on PL trigger functions, see your ISIS Administrator.


Remote-Access File

A remote-access file (RAF) contains all of the information that you need to open a remote database.

Your ISIS Administrator generally provides you with a private remote-access file (private RAF) that you store on your workstation. In your private RAF, you can save objects that you create, such as structures (either molecules or reactions), queries, lists of search results, sorting instructions, customized ISIS/Base forms, and Procedural Language (PL) programs.

Your ISIS Administrator creates a public remote-access file (public RAF) that contains additional information (such as network connectivity information and Hview name) that you require to access the remote database. The public RAF might also contain objects that all users require, such as ISIS/Base forms and PL programs. Each time you open a remote database from your private RAF, ISIS/Base copies these objects from the public RAF into your private RAF.

For information on how to create your own remote-access files, see your ISIS/Host Installation & Administration guide.


Temporary List

A temporary list is a list of search results that is stored in the database solely for the current ISIS/Base session. When you close the database, ISIS deletes all temporary lists in the database.

You can create a temporary list manually by saving the list with the List > Save List command and setting: Permanent.

ISIS can automatically save the current list to a temporary list every time you create a new list. ISIS creates a new list when you perform a search, sort search results, import search results from disk, or open a list of search results that you previously saved as an object in the database. ISIS names automatic temporary lists _t00, where 00 is a two-digit number.

By default, ISIS does not automatically save lists. To change this, choose Options > Settings > Session, click the Search tab, and set [image] Generate temporary lists automatically.

Note: If you save lists automatically, you might notice slow performance in some databases.


Temporary List

A temporary list is a list of search results that is stored in the database solely for the current ISIS/Base session. When you close the database, ISIS deletes all temporary lists in the database.

You can create a temporary list manually by saving the list with the List > Save command and setting: Permanent.

ISIS can automatically save the current list to a temporary list every time you create a new list. You create a new list when you perform a search, sort search results, import search results from disk, or open a list of search results that you previously saved as an object in the database. ISIS names automatic temporary lists _t00, where 00 is a two-digit number.

By default, ISIS does not automatically save lists. To change this, choose Options > Settings > Session, and click the Search tab.

Note: If you save lists automatically, you might observe slow performance for some databases.


Status Bar

The status bar shows you the current search domain, the parent field for the data in the selected box or column, and the number of records at that level in the database hierarchy. The following example shows the results of a search in a reaction database:

The message Search Domain: All shows that you searched over all records in the database. <RXN> 1 of 9 shows that you retrieved 9 records, and that you see the first record on display. The currently-selected box contains data from a field that is attached to the RXN parent field, the highest level of the database hierarchy. Click other boxes and tables that contain different data to see how the message changes. Note


Note

When you set the search domain to the current list or to a list that you import from a file, you see Search Domain: Subset. When you set the search domain to a list that you previously saved within the database, you see Search Domain: <listname>, where <listname> is the name of the list.


Atom-Atom Maps

An atom-atom map on the reaction components in a query specifies exactly which atoms in the reactants correspond to the atoms in the products. You can specify the atoms that must (or must not) change in the transformations that you retrieve.

For example, the following query allows you to see exactly which C-O bond is cleaved to form the product:


Reacting Center Marks

A reacting center is a bond that changes in the reactant and in the product. Markings on the bonds of products and reactants specify exactly which bonds change (or do not change) in the reaction. The markings are:

X	Specifies a bond that must not change.

|	Specifies a bond that changes bond type.

||	Specifies a bond that is either formed or broken.

|||	Specifies a bond that is either formed or broken and changes bond type.

#	Specifies a bond as a nonspecific reacting center. That is, the bond can be formed, broken, or change bond type in the reaction.


Inversion and Retention Marks

Inversion and retention marks specify how the stereochemistry of an asymmetric center in a reactant or product changes (or does not change) in a reaction. The markings are:

.Ret.	Specifies that an asymmetric center retains its stereochemical configuration during the reaction.

.Inv.	Specifies that an asymmetric center inverts its stereochemical configuration during the reaction.


Current Search Domain

A search domain is the set of records that are being searched. You can choose the search domain that you want to search.

Each record in a search domain can originate from a database or from a list of records. Two records from the same domain might originate from different databases, or from different lists of records.

The search domain that you choose is called the current search domain. You can view the current search domain on the status bar in ISIS/Base:

In this example, the current search domain consists of all records in the database.


Search Domain

A search domain is the set of records that are being searched. You can choose the search domain that you want to search.

Each record in a search domain can originate from a database or from a list of records. Two records from the same domain might originate from different databases, or from different lists of records.

The search domain that you choose is called the current search domain. You can view the current search domain on the status bar in ISIS/Base:

In this example, the current search domain consists of all records in the database.


Variation Subrecords

A variation subrecord contains data from a different source than the reaction record on display. For example, the yield for the reaction on display might vary for each method of synthesis of the reaction.

You can view variations in the data for any data field in the boxes or table cells on the form. By default, you see the first variation of the variation subrecords.


Sorting Instruction

A sorting instruction is a sentence that tells ISIS how to sort search results. For example, the following sorting instruction sorts reaction records so that reactions with the highest yields appear first:

Sort each RXN by >VARIATION>PRODUCT>YIELD from high to low

This instruction sorts reaction records (RXN) by yield (the data in the field RXN>VARIATION>PRODUCT>YIELD). Reactions with the highest yields are first on the list (high to low) .

You can create sets of sorting instructions that contain one or more individual sorting instructions. You can save a set of sorting instructions in the database or export it to a text file on hard disk or floppy.

The sorting instructions that you choose to sort your search results are the current sorting instructions. To view the current sorting instructions, choose List > Sort. You see the current sorting instructions in the Sorting Instructions box in the Sort dialog box.


Record Indicator

The record indicator marks an individual record within a table. In Browse and Update modes, you can use the record indicator to track data that is related to the data in the table. In the following example from a reaction database, the catalyst structure in the box is related to the catalyst number and name in the table. The structure in the box changes according to the position of the record indicator in the Catalyst# column:


Calculation Type

To create a calculated field, you must specify the calculation that you want to perform on the data. The following calculations are available:


Child Field

A child field is a database field that is attached to a parent field at a higher level of the database hierarchy. Child fields contain stored data. Parent fields contain no data, but point to a group of fields that store related data.

For example, each reaction record in a reaction database might have several variations, and each variation might have several literature references. In a molecule database, each molecule record might have several batches, and each batch might have several sets of test data.

The parent field name should be representative of the types of data that the lower-level fields will store. For example, <LITREF> is the parent field for JOURNAL and AUTHOR. ISIS/Base displays parent field names in brackets to distinguish them from other fields.


Current Form

The current form is the form that you see on your screen in ISIS/Base.


Default Form

The default form is the form that you see on your screen when you open a search domain in ISIS/Base.


Footer

A footer is the text that appears at the bottom of each page that you print.


Header

A header is the text that appears at the top of each page that you print.


Subrecord

A hierarchical database contains subrecords (subordinate records) that contain separate sets of data within the main record. For example:

*	In a reaction database, each reaction might have several variations associated with it. For example, the yield of a product might vary according to reaction conditions such as reaction temperature, catalyst, and solvent. This information is stored in the variation subrecords within each reaction.

*	In a molecule database, you might have several batches of each compound. Each batch has its own set of associated test results. Information on each batch is stored in the batch subrecords within each molecule record.

Data for each type of subrecord is associated with a specific parent field in the database hierarchy. For example, data within the variation subrecords within each reaction record is associated with the <VARIATION> parent field.


Aggregate Field

An aggregate field is another name for a calculated field.


External Registry Number (Extreg)

An external registry number (extreg) identifies molecules, 3D structures, or reactions:

*	In a molecule database, each 2D or 3D structure can have an extreg associated with it. The extreg is generally the company ID number for the structure. In a 3D database, 2D and 3D structures can have separate extregs.

*	In a reaction database, each molecule or reaction can have an extreg associated with it. In MDL reaction databases, the reaction extreg identifies a set of reactions in a multistep synthesis. For example, the following reactions can have the same reaction extreg: each intermediate step in a multistep sequence, the overall step in a multistep sequence, a supplementary reaction, the preparation of a catalyst, or the preparation of a reagent.

Molecule and reaction databases also contain internal registry numbers (regnos). The regno is a unique identifier for each molecule, reaction, or 3D structure. ISIS automatically assigns the regno when you register the structure.


Chemical Significance

Sketch objects (such as molecules and reactions) that are chemically significant can be used as queries to search databases in ISIS/Base.

Use Chem Inspector to see if ISIS/Draw interprets molecules and reactions as chemically significant. Chem Inspector is invoked automatically when you export a structure to a molfile or rxnfile, or when you transfer a structure to ISIS/Base.

The molecules and reactions that you create for presentation graphics might contain elements that are not necessarily chemically significant. For example, sketch elements such as lines, circles, and boxes are chemically insignificant.

For more information on chemical significance, see ISIS/Draw "Quick Start".


Box/Column/Table Properties

The properties of a box, column, or table on a form control the data that appears within each box or column, how that data is displayed, and the appearance of the box, column, or table. You can also use properties to add functionality such as form calculation or PL functions to your form. To change properties, edit boxes, or columns, or tables


Deepest Common Parent

In Search By Form (SBF) queries that contain more than one condition, the deepest common parent defines the level of the database hierarchy at which all query conditions must be met. In the following example from a reaction database, both SBF conditions must be met within the same record and within the same variation subrecord, because VARIATION is the deepest common parent field:


Similarity

In an MSim or RSim search, similarity is a measure of how closely retrieved molecules or reactions resemble your query. There are two types of similarity that you can specify between your query and the structures or reactions that you retrieve:

*	Structural Similarity -- physical resemblance to the substrate molecules in your query

*	Transformational Similarity -- similar reacting centers (solely if your query is a reaction)


Structural Similarity

In a Reaction Similarity (RSim) search, structural similarity specifies how closely the molecules in the reactions that you retrieve resemble the molecules in your reaction query (reactants and products).

You can sort your search results so that reactions or molecules with the highest (or lowest) structural similarity to the query appear first on the list. You can also display structural similarity data in a form box or table.


Transformational Similarity

In a Reaction Similarity (RSim) search, transformational similarity is the degree of similarity between the reacting center of your query and the reacting center of the reactions that ISIS retrieves during the search. You can sort your search results so that reactions with the highest (or lowest) transformational similarity to the query appear first on the list. You can also display transformational similarity data in a form box or table.

Transformational similarity is also called reacting-center similarity.


Hydrogen-Bond Donors and Acceptors

There are two different conventions for defining hydrogen-bond donors and acceptors. This help file uses the definition of a hydrogen-bond donor that is generally used by medicinal chemists. By this convention, the donor of a hydrogen bond is the group to which the hydrogen atom is attached:

An alternative definition of hydrogen-bond donors and acceptors defines a hydrogen-bond donor as the group that provides the lone-pair electrons (LP) to the hydrogen bond.


Static 3D Substructure Search
Rigid 3D Substructure Search

A rigid 3D substructure search finds 3D structures that contain your query as a substructure wholly within a larger structure. For example:

For more information on rigid 3D substructure search, click here.


Initial CFS Search

You generally conduct a Conformationally Flexible Substructure (CFS) search in two phases: an initial CFS search and a bump-checking CFS search. In the initial CFS search, ISIS ignores nonbonded (van der Waals) interactions when 3D structures are fitted to the query. This produces faster search speeds. However, up to 15% of the fitted structures from the initial CFS search might be invalid because the atoms are too close together (that is, the atoms bump into one another). To eliminate these invalid 3D structures, you set the search domain to the records that you retrieved in the initial CFS search and execute a bump-checking CFS search.


Bump-Checking CFS Search

You generally conduct a Conformationally Flexible Substructure (CFS) search in two phases: an initial CFS search and a bump-checking CFS search. In the initial CFS search, ISIS ignores nonbonded (van der Waals) interactions when 3D structures are fitted to the query. This produces faster search speeds. However, up to 15% of the fitted structures from the initial CFS search might be invalid because they contain atoms that are too close together (that is, atoms that bump into one another). To eliminate these invalid 3D structures, you set the search domain to the records that you retrieved in the initial CFS search and execute a bump-checking CFS search.


Initial and Bump-Checking CFS Searches

You generally conduct a Conformationally Flexible Substructure (CFS) search in two phases: an initial CFS search and a bump-checking CFS search. In the initial CFS search, ISIS ignores nonbonded (van der Waals) interactions when 3D structures are fitted to the query. This produces faster search speeds. However, up to 15% of the fitted structures from the initial CFS search might be invalid because the atoms are too close together (that is, the atoms bump into one another). To eliminate these invalid 3D structures, you set the search domain to the records that you retrieved in the initial CFS search and execute a bump-checking CFS search.


Torsional Fitting

In a Conformationally Flexible Substructure (CFS) search, torsional fitting is the process of rotating single bonds in 3D structures to fit the constraints of the query:

Torsional fitting is also called conformational fitting.

For more information on CFS searching, see CFS Searching Concepts/Examples.


Conformational Fitting

In a Conformationally Flexible Substructure (CFS) search, conformational fitting (torsional fitting) is the process of rotating single bonds in 3D structures to fit the constraints of the query:

For more information on CFS searching, see CFS Searching Concepts/Examples.


Bump Checking

In a CFS search, bump checking eliminates fitted 3D structures that contain unfavorable nonbonded interactions (that is, fitted structures that contain atoms in close contact that bump into one another). You can perform bump checking in two ways:

*	At view time. ISIS performs conformational fitting with bump checking on individual 3D structures as you view them. If a fitted 3D structure contains atoms that are too close together, ISIS displays the conformation that is stored in the database, without overlaying the query.

*	At search time. You conduct a bump-checking CFS search that eliminates all fitted 3D structures with atoms that are too close together.

Note: We strongly recommend that you conduct a bump-checking CFS search when you want to export the fitted 3D structures from a CFS search to a modeling software program. Bump checking produces fitted structures that are more realistic.


Global Relaxation

When you use bump checking in a CFS search, the CFS option global relaxation allows ISIS to rotate single bonds in other regions of the structure. This increases the number of 3D structures that you retrieve and produces fitted 3D structures that are more realistic.

However, global relaxation also produces slower search speeds. Consequently, we recommend that you use global relaxation solely at the following times:

*	When you want to export fitted structures to a modeling software program, use global relaxation to produce more realistic fitted structures.

*	When you are conducting a series of CFS searches to refine a query, use global relaxation in the later stages of query refinement to ensure that you obtain as many structures as possible.

Note: For more information on global relaxation, study CFS Searching Concepts/Examples.


Default CFS Options

In Conformationally Flexible Substructure (CFS) searching, the CFS options control how ISIS fits 3D structures in the database to the constraints of the query. The default CFS options provide the best balance between speed and accuracy for most situations. If you are not sure how to choose CFS options, we strongly recommend that you use the default CFS options.

Note: You generally use the default CFS options for the initial CFS search. The default CFS options perform bump checking as you view each structure (view-time bump checking). If you want to conduct a bump-checking CFS search, use the same options that you used for the initial CFS search, but also specify Bump Checking at: Search Time.

For more information on CFS options, see CFS Searching Concepts/Examples.


CFS Search Cutoffs

In a CFS or CFS/Biopoly search, you can specify from one to three search cutoffs that exclude fitted 3D structures that do not match your criteria:

*	Torsional degrees of freedom (TDF) is the number of rotatable bonds in the part of the 3D structure that matches the query. The higher the TDF, the more flexible is the structure.

*	Van der Waals energy difference is the difference in nonbonded (van der Waals) interaction energy between the fitted conformation and the conformation that is stored in the database.

*	RMS deviation measures how closely a fitted 3D structure matches the query.

Note: The CFS options subtly interact with each other and can produce undesirable results if improperly used. Also, certain search cutoffs might require other CFS options, or restrict the types of query features that you can use. We strongly recommend that you study CFS Searching Concepts/Examples before you attempt a CFS search.


Derived Data

For RSim, MSim, and CFS searches, ISIS calculates specific kinds of data from the reactions or structures that it retrieves during the search. You can display this derived data in a form and use it for sorting, just like data in actual database fields.

Caution: If you sort your search results by derived data, ISIS repeats the search so that it can generate the data, then performs sorting. Therefore, if you want to sort by derived data, we strongly recommend that you define your sorting instructions before the search and sort your search results automatically after the search. You must repeat the search when you want to sort a list of search results that you have previously stored.

For more information on derived data, see the step-by-step instructions for the search of your choice. For a list of searches, click here.


Basis

The basis of a 3D object or constraint is the set of atoms and/or 3D objects that comprise it. For example, the basis of a centroid is the set of reference positions (atoms, points, or other centroids) that comprise the centroid.

You can edit the atoms or objects that comprise a 3D object or constraint. For example, you can add or delete points from the basis of a centroid.

For exclusion spheres, you can specify that other atoms in the query that are not directly connected to the atom at the center of the sphere are allowed within the excluded volume. To do this, you add these atoms to the basis of the exclusion sphere.


Fixed Atoms

You use fixed atoms for submodel searching in 3D databases. A submodel is a three-dimensional (3D) representation of a portion of a 3D structure. You specify the spatial arrangement of atoms in the submodel query by fixing the 3D coordinates of two or more atoms in a 3D structure. The following query contains fixed atoms (F):

A search with a submodel query retrieves all models that contain the same spatial arrangement of atoms as the fixed atoms in your query, within specified deviations of the individual and overall atoms.


Maximum RMS Deviation

Maximum RMS deviation specifies the allowed root-mean-square deviation (in Angstroms) of all atoms in a 3D structure from the corresponding atoms in your 3D query. You specify Maximum RMS Deviation in:

*	CFS, CFS/Biopoly, SSS3D, and SSS3D/Biopoly searches in which the query contains four or more fixed atoms

*	3DEXACT searches in remote databases (ISIS treats all atoms in the query like the fixed atoms of a submodel).

Maximum RMS deviation is one of two fixed-atom tolerances that you can specify. The other fixed-atom tolerance, maximum atomic displacement, specifies the allowed deviation of individual atoms in a 3D structure from the corresponding atoms in your 3D query.

Caution: Your ISIS Administrator sets default fixed-atom tolerances that your site uses to register 3D structures to the database. If you change these default values for searching, you must restore the default fixed-atom tolerances before you register 3D structures.


Maximum Atomic Displacement

Maximum atomic displacement specifies the allowed deviation (in Angstroms) of individual atoms in a 3D structure from the corresponding atoms in your 3D query. You specify maximum atomic displacement in:

*	CFS, CFS/Biopoly, SSS3D, and SSS3D/Biopoly searches in which the query contains two or more fixed atoms

*	3DEXACT searches in remote databases (ISIS treats all atoms in the query structure like the fixed atoms of a submodel)

Maximum atomic displacement is one of two fixed-atom tolerances that you use in these searches. The other fixed-atom tolerance, maximum RMS deviation, specifies the allowed root-mean-square (RMS) deviation of all the atoms in a 3D structure from the atoms in your 3D query.

Caution: Your ISIS Administrator sets default fixed-atom tolerances that your site uses to register 3D structures to the database. If you change these default values for searching, you must restore the default fixed-atom tolerances before you register 3D structures.


CFS Options

Conformationally Flexible Substructure (CFS) searching finds 3D structures that contain the query structure embedded within them and can be made to fit the query by rotating single bonds in the structure:

The CFS options control how ISIS fits structures in the database to your query. For more information on CFS options, study CFS Searching Concepts/Examples.


CFS SDfile

After a Conformationally Flexible Substructure (CFS) search, you can export the 3D structures (models) to a special type of SDfile called a CFS SDfile. This allows you to export the fitted conformations that result from the CFS search so that you can use them in modeling software programs. By contrast, exporting 3D structures to an SDfile or RDfile saves the 3D structures that are stored in the database, not the fitted conformations that result from the CFS search.

In addition to fitted 3D structures, the CFS SDfile contains the 3D query features of the fitted structures, any CFS goodness-of-fit data that is in the form, the 3D substructure portion of the 3D query, and a list of mapped atoms and bonds.

Caution: You can not import a CFS SDfile into a database.

For more information on CFS searching, see CFS Searching Concepts/Examples.


RMS Deviation (3D Constraint)

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, you can specify that a set of reference positions (atoms, centroids, or points) must lie along the same line (linearity constraint), or within the same plane (planarity constraint). To do this, you specify the maximum average distance (RMS deviation) of the reference positions from the best-fit line or plane that is derived from the reference positions. The following shows a linearity constraint of 0.5 Angstroms for all atoms in a trialkene:


RMS Deviation (Fixed-Atom Tolerance)

Maximum RMS deviation is one of two fixed-atom tolerances that you can specify for searching and registration. Fixed-atom tolerances specify how closely the spatial arrangement of the atoms in your query must fit the corresponding atoms in the 3D structures that you retrieve. Maximum RMS deviation specifies the maximum allowed deviation of all fixed atoms in the query from the matching atoms in the structures that you retrieve.

ISIS uses fixed-atom tolerances in:

*	CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly searches in which the query contains four or more fixed atoms.

*	All 3DEXACT searches in remote databases (ISIS treats all atoms in the query structure like fixed atoms.)

Caution: Your ISIS Administrator sets default fixed-atom tolerances that your site uses to register 3D structures to the database. If you change these default values for searching, you need to restore the default fixed-atom tolerances before you register 3D structures.


RMS Deviation (CFS Derived Data)

In a Conformationally Flexible Substructure (CFS) search, RMS deviation measures how closely the 3D structure fits the query (goodness-of-fit). RMS deviation is the sum of the RMS deviations for each type of 3D geometric constraint in your query:

ISIS calculates the RMS deviation for each fitted 3D structure during the CFS search. You can view these values in a form or use them to sort your search results. You can also use RMS deviation as a search cutoff to exclude structures that do not meet your criteria.

For more information on CFS searching, see CFS Searching Concepts/Examples.


Torsional Degrees of Freedom (TDF)

In a Conformationally Flexible Substructure (CFS) search, torsional degrees of freedom (TDF) is the number of rotatable bonds on the paths that connect the mapped atoms in the fitted 3D structure (Mapped atoms are the atoms in the 3D structure that correspond to atoms in the query). The higher the TDF, the more flexible the molecule is in the region that matches the query.

ISIS calculates the TDF for each 3D structure during the CFS search. You can view these values in a form or use them to sort your search results. You can also use TDF as a search cutoff to exclude structures that do not meet your criteria.

For more information on CFS searching, see CFS Searching Concepts/Examples.


Van der Waals Energy Difference

In a Conformationally Flexible Substructure (CFS) search, van der Waals energy difference is the difference in nonbonded (van der Waals) interaction energy between the fitted 3D structure and the conformation that is stored in the database.

ISIS calculates the van der Waals energy difference for each fitted 3D structure during the CFS search. You can view these values in a form or use them to sort your search results. You can also use van der Waals energy difference as a search cutoff to exclude structures that do not meet your criteria.

For more information on CFS searching, see CFS Searching Concepts/Examples.


Rotatable Bond

In Conformationally Flexible Substructure (CFS) searching, ISIS rotates certain types of single bonds when it attempts to fit 3D structures to the constraints of the query. By default, rotatable single bonds must meet the following requirements:

*	At least one atom in the bond must be saturated, that is, sp3-hybridized.

*	The bond can not be an amide or similar bond. Amides include the following bonds:

*	The bond can not be part of a ring.

You can specify CFS options that extend the definition of rotatable bonds to include ring bonds in a specified size range and to bonds between unsaturated centers (such as biphenyls). For more information, see CFS Searching Concepts/Examples.


3D Query Features

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, a 3D query feature is a restriction that specifies the spatial arrangement of atoms in the 3D structures that you retrieve. 3D objects, 3D constraints, and fixed atoms are all 3D query features. In the following example, the distance constraint and the fixed atoms of the submodel specify spatial relationships among atoms:


3D Constraints

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, you apply 3D geometric constraints such as distances, angles, dihedral angles, exclusion spheres, planarity constraints, and linearity constraints to atoms and to other 3D objects:

You can also apply 3D data constraints to atoms and to pairs of atoms:


Geometric Constraints
3D Geometric Constraints

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, you use 3D geometric constraints such as distances, angles, dihedral angles, exclusion spheres, linearity constraints, and planarity constraints:


3D Data Constraints

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, you can apply data constraints to atoms and to pairs of atoms. The following is an example of an atom data constraint that specifies the partial charge on an oxygen atom:

The following is an example of a 3D atom-pair data constraint that specifies ring proton spin-spin couplings of methyl 2-furoate:


3D Objects

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, you can construct 3D objects such as points, lines, planes, centroids, and normal vectors. Lines, planes, and normal vectors actually extend infinitely, but are represented in ISIS as shown below:

You use atoms and 3D objects to create 3D geometric constraints such as distances, angles, dihedral angles, exclusion spheres, linearity constraints, and planarity constraints:


3D Atom Field

In a 3D database, 3D atom fields contain data that is associated with individual atoms on a 3D structure, such as partial charges or quantum-mechanical data. The following example shows the partial charge on a ring oxygen:

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, you can specify atom data constraints on specific pairs of atoms in the 3D structures that you retrieve.


3D Atom-Pair Field

In a 3D database, 3D atom-pair fields contain data that is associated with specific pairs of atoms on a 3D structure. The following example shows calculated values for the ring proton spin-spin couplings of methyl 2-furoate:

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, you can specify atom-pair data constraints on specific atoms in the 3D structures that you retrieve.


Atom Data Constraint

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, you can specify atom data constraints on specific atoms. For example, the following query contains a text-numeric string that specifies a charge range of -0.30 to -0.31 for a ring oxygen:

To specify an atom data constraint, you must specify the 3D atom field with which the data is associated and a query that specifies the type of data you want to find. The query can be either a value, or a text-numeric string.


Atom-Pair Data Constraint

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, you can specify atom-pair data constraints on specific pairs of atoms. For example, the following query specifies values for the ring proton spin-spin couplings of methyl 2-furoate:

To specify an atom-pair data constraint, you must specify the 3D atom-pair field with which the data is associated and a query that specifies the type of data you want to find. The query can be either a value, or a text-numeric string.


Centroid

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, a centroid is a 3D object that defines the geometric center of a set of reference positions (atoms, points, or other centroids). For example, the centroids in the structures below (depicted by the triangles) are the geometric centers of selected atoms. The ring centroid on the left defines the centroid of all six ring atoms. The centroid on the right defines the center of the atoms within the box (the box is used here to indicate atoms that comprise the centroid, and does not appear in the query):


Line

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, a line is a 3D object that defines a path through two or more reference positions (atoms, points, or centroids). For example:

If you use three or more reference positions, ISIS derives a best-fit line. The following is a best-fit line derived from all atoms in a trialkene:


Normal

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, a normal is a 3D object that specifies a line (with an arrowhead) that is perpendicular to a plane and that passes through a reference position (an atom, point, or centroid):

Note: If the point that you use lies in the plane of the normal, the direction of the normal is undefined.


Plane

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, a plane is a 3D object that defines a path through three or more reference positions (points, atoms, or centroids). For example:

If you use four or more reference positions, ISIS derives a best-fit plane. The following is a best-fit plane derived from all atoms in benzaldehyde:


Point

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, you can construct a point to use as a reference position. Specify a point at a defined distance and direction from another reference position. To specify the direction, use either another reference position or a normal.


Best-Fit Line

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, ISIS defines a best-fit line when you use three or more reference positions (atoms, points, or centroids) to define a line. You can specify an optional linearity constraint for the best-fit line. The following is a best-fit line derived from all atoms in the trialkene:


Best-Fit Plane

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, ISIS defines a best-fit plane when you use four or more reference positions (atoms, points, or centroids) to define a plane. You can specify an optional planarity constraint for the best-fit plane. The following is a best-fit plane with planarity constraint for all atoms in benzaldehyde:


Linearity

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, you can define a linearity constraint to specify that three or more reference positions (atoms, points, or centroids) must lie along the same line. To do this, you specify the maximum average distance (RMS deviation) of the reference positions from the best-fit line derived from the reference positions. The following shows a best-fit line with linearity constraint for all atoms in a trialkene:


Planarity

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, you can define a planarity constraint to specify that four or more reference positions (atoms, points, or centroids) must lie along the same plane. To do this, you specify the maximum average distance (RMS deviation) of the reference positions from the best-fit plane derived from the reference positions. The following shows a best-fit plane with planarity constraint for all atoms in benzaldehyde:


Angle

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, you can define an angle constraint that specifies a range of angles. You can specify the angle with three reference positions (atoms, points, or centroids), or with two planes, lines, or normals:


Dihedral

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, you can define a dihedral angle constraint that specifies a range of dihedral angles. You specify the dihedral angle as the intersection of two planes. The dihedral angle is created from the common vertex of reference positions 1 and 2 in one plane and reference positions 3 and 4 in the other plane. Reference positions 2 and 3 form the vertex of the angle. For example:


Distance

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, a distance constraint specifies the range of distances in Angstroms between two reference positions (atoms, centroids, or points). For example, the following query specifies a distance constraint of 2 - 10 Angstroms between the centroid of a phenyl ring and the centroid of a phenol ring:


Exclusion Sphere

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, an exclusion sphere excludes atoms within a sphere surrounding a reference position (atom, point, or centroid). For example, the following query contains two exclusion spheres of 1.5 Angstroms, each surrounding a point. This query retrieves compounds that exclude all atoms from the spherical regions that are specified by the exclusion spheres:


Hydrogen Sprouting

3D structures in a molecule database generally do not contain explicit representations of hydrogen atoms. You can, however, create explicit hydrogen atoms on the structures that you retrieve by sprouting hydrogen atoms on 3D structures. You must sprout hydrogen atoms in the following situations:

*	In a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, sprout hydrogen atoms whenever you want to export 3D structures to modeling software programs that cannot sprout hydrogens.

*	In a CFS search, sprout hydrogen atoms during bump checking. This produces more realistic 3D structures and allows ISIS to correctly calculate data on van der Waals energy difference.

Note: If your query contains lone pairs, sprouting hydrogen atoms also sprouts lone pairs at sites that correspond to lone pairs on the query.


Lone Pair Sprouting

3D structures in a molecule database generally do not contain explicit representations of lone-pair electrons. If your CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search query contains explicit lone pairs, however, you can sprout lone pairs on retrieved structures at sites that match lone pairs in the query.

Note: If your substructure search query contains explicit lone-pair electrons, sprouting lone pairs also sprouts hydrogen atoms at sites that correspond to hydrogen atoms on the query.


Lone Pairs

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, you can specify that lone-pair electrons must appear at specific sites on the structures that you retrieve. To do this, you draw lone pairs on your query. For example:


3D Structures or Substructures

A 3D structure defines the spatial arrangement of atoms in a molecule. A 3D substructure defines a portion of a 3D structure. You can specify the 3D spatial relationships among atoms in the 3D substructure by fixing atoms to create submodel components:


3D Substructure

A 3D substructure defines a portion of a 3D structure. For remote searching only, you can specify the 3D spatial relationships among atoms in the 3D substructure by fixing atoms to create submodel components:


3D Structure

A 3D structure defines the spatial arrangement of all atoms in a molecule. In contrast, a 2D structure of a molecule contains information on number, type, and connectivity of atoms in a molecule, and on the configuration of atoms around chiral centers:


3D Query Features

A 3D query feature is a restriction that specifies the spatial arrangement of atoms in the 3D structures that you retrieve. In the following example, the distance constraint and the fixed atoms in the submodel specify spatial relationships among atoms:


2D Query Features

A 2D query feature is a restriction on an atom and/or bond that does not restrict the 3D spatial relationships between atoms. The following are examples of 2D query features:


Default RMS Deviation Constraint

When you create a best-fit line or best-fit plane for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search query, you can specify a linearity or planarity constraint. You specify the linearity or planarity constraint as the maximum average distance (RMS deviation) of the reference positions (atoms, points or centroids) from the best-fit line or plane. ISIS provides a default linearity or planarity constraint that is calculated from the RMS Deviation value in the 3D tab of ISIS/Draw Settings:

*	If the RMS Deviation value in ISIS/Draw Settings is in Angstroms, the default RMS Deviation is the same as the RMS Deviation value in Settings.

*	If the RMS Deviation value in ISIS/Draw Settings is a percentage, the default RMS Deviation is the specified percentage of the measured RMS deviation. For example, if the RMS Deviation in Settings is 20%, and the measured RMS deviation for the best-fit line in your query is 0.40 Angstroms, then the default RMS Deviation is 0.08 Angstroms.


Default Distance Constraint

When you create a distance constraint for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search query, you specify a range of allowed distances. ISIS provides a default distance constraint that is calculated from the Distances value in the 3D tab of ISIS/Draw Settings:

*	If the Distances value in ISIS/Draw Settings is in Angstroms, the default distance constraint is the measured distance between the two reference positions on your query, plus or minus the Distances value. For example, if the Distances value is 0.5 Angstroms, and the distance between the two reference positions on your query is 3.0 Angstroms, then the default range is 2.5 - 3.5 Angstroms.

*	If the Distances value in ISIS/Draw Settings is a percentage, the default distance constraint is the measured distance between the reference positions, plus or minus the specified percentage of the measured distance. For example, if the Distances value is 20%, and the distance between the two reference positions on your query is 3.0 Angstroms, then the default range is 2.4 - 3.6 Angstroms.


Default Angle Constraint

When you create an angle or dihedral angle for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search query, you specify a range of angles. ISIS provides a default angle constraint that is calculated from the Angles value in the 3D tab of ISIS/Draw Settings:

*	If the Angles value in ISIS/Draw Settings is in degrees, the default angle constraint is the measured value of the angle in your query, plus or minus the Angles value. For example, if the Angles value is 10 degrees, and the angle on your query is 40 degrees, then the default angle constraint is 30 - 50 degrees.

*	If the Angles value in ISIS/Draw Settings is a percentage, the default angle constraint is the measured value of the angle in your query, plus or minus the Angles value expressed in degrees. For example, if the Angles value 20%, and the angle on your query has a measured value of 40 degrees, then the default range is 32 - 48 degrees.


Reference Position

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, you can use atoms, points or centroids as reference positions for drawing 3D objects and 3D constraints. For example, the following query contains a distance constraint that uses two reference positions, an atom and a centroid:


Ending Context

When you print search results from a hierarchical database, the ending context is the level and branch of the database hierarchy from which ISIS prints all data. You choose the ending context by clicking the form box or table that contains the data that you want to print. Generally, the box or table that you choose contains the data that is most important to you. This ensures that ISIS prints all important data.

For example, if your form contains a table of literature references from a reaction database, you click that table when you want to print all literature references for all reactions.

For more information on printing from hierarchical databases, see Printing All the Data, and Only the Data, That You Want.


Starting Context

When you print search results from a hierarchical database, you can use the starting context to restrict the number of subrecords that you print within each record. For example, you might want to print data from only the first variation of each reaction, or the first batch of each compound.

Caution: If you are not sure how to use the starting context, we strongly recommend that you not change the starting context. If you choose the wrong starting context, you might print incomplete data without knowing that the data is incomplete.

By default, the starting context is set to the highest parent field in the database. This ensures that ISIS prints all data from every level of the database for the box or table that you chose. For more information on starting and ending contexts, study Printing All the Data, and Only the Data, That You Want.


Calculated Field

A calculated field calculates a value from a set of data. For example, if your molecule database contains several activity measurements of each compound, you can create a calculated field that contains the average of those measurements. You can display data from a calculated field in a form and/or use it to sort search results, just like the data in any other database field.

To create calculated fields, you need to understand the database structure. We strongly recommend that you study Calculated Fields: Concepts/Examples before you attempt to create calculated fields.

Note: Do not confuse calculated fields with form calculations. A form calculation uses data from different database fields. For example, if your database contains a field for concentration in moles per liter and another field for molecular weight, you can use a form calculation to multiply those values to obtain the concentration in grams per liter. You can display a form calculation on your form, but you cannot use it to sort your search results.


Hit

A hit is a record that you retrieve during a search. A list of search results is sometimes called a hit list.


Hit List

A hit list is the list of records that you retrieve during a search. We also refer to a hit list as a list of search results. The individual records are hits.


Concatenated Databases

Your ISIS Administrator supplies you with a remote-access file (RAF) that you use to access remote databases. Your RAF might specify multiple databases (a maximum of 32). The databases that you open through this RAF are concatenated. (A search over the full set of databases of a specific type, such as the full set of reaction databases, is called a global search.)


Formula Box

A formula box is a form box that is linked to the database field for the molecular formula:

*	For remote databases, the formula field is MOLFORMULA.

*	For local databases, the formula field is *fmla_MOLSTRUCTURE.


Keyboard Equivalents of Browse Tools

Tool	Keyboard Equivalent

PC	Mac

Up arrow key	Up arrow key

Down arrow key	Down arrow key

Control-Home	Control-Home*

Control-End	Control-End*

# key

* Not available on systems without Home and End keys.


Text/Numeric Query Strings in 3D Queries
Text/Numeric Queries in 3D Queries

A text/numeric query in a 3D data constraint is a phrase that specifies the retrieval of data. The phrase contains:

*	A search operator that specifies the type of search (such as an equal sign, =, to specify a search that finds solely the exact target text in the query).

*	The text or numeric target value (specific data) that you want to find.

For example, to find an atom with a partial charge greater than -0.31, enter > -0.31 as the query (where > is the search operator and -0.31 is the target value).

Note: Your text/numeric query is case-sensitive solely when you use a relational database or a UNIX platform.


Attached Data

Attached data is chemically-significant text that you can associate with an atom, a bond, a set of atoms and bonds, or with a bracket. For example, the following copolymer structure contains attached data on the mass percentage of each type of repeating unit (75 mass %, 25 mass %):

For information on using attached data in polymer structures, see Drawing Polymers: MDL Requirements for Database Searching and Registration

For information on using attached data in non-polymer structures, see Drawing Mixtures: MDL Requirements for Database Searching and Registration.


Tag

A tag is a single character that serves as a footnote for attached data. You can use any keyboard character as a tag, provided that the character can be printed. For example:

For information on using attached data in polymer structures, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

For information on using attached data in non-polymer structures, see Drawing Mixtures: MDL Requirements for Database Searching and Registration.


* Atom
*Atom (Star Atom)

*Atoms (star atoms) represent a portion of a structure that is unknown or undefined:

For information on using *atoms in polymer structures, see Drawing Polymers: MDL Requirements for Database Searching and Registration

For information on using *atoms in non-polymer structures, see Drawing Mixtures: MDL Requirements for Database Searching and Registration.


SRU Label

An SRU label is a single alphabetic character that appears on the bracket of a structure-based homopolymer. The default SRU label is n, but you can change it to a different letter to show different multiplicities of polymeric or oligomeric sequences. For example:


Unordered Mixture

An unordered mixture is a mixture where the order in which the components are combined is not important. For example, the following is a reaction product that consists of a mixture of stereoisomers:


Ordered Mixture

An ordered mixture is a mixture where the order in which the components are combined (order of addition) is important. For example, the following structure represents the formulation of an aspirin tablet in which the acetaminophen (c1) must be added before the binder (c2) and other components (c3 and c4):

Note: In MACCS-II, ordered mixtures were called formulations.


Polymer Repeat Pattern

Polymer repeat pattern specifies how the structural repeating units of a polymer are joined together. For example, polystyrene has three possible repeat patterns: head-to-tail, head-to-head, and either/unknown. Examples

The possible repeat patterns for a polymer depend on the number of brackets and the number of crossing bonds in the structure. For more information on polymer repeat pattern, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

Note: In MACCS-II, polymer repeat pattern was called polymer configuration.


Ladder-Type Polymer

To draw ladder-type (double-stranded) polymers, use paired brackets with two crossing bonds per bracket. For example:

For more information on polymer representation, see Drawing Polymers: MDL Requirements for Database Searching and Registration.


Repeat Patterns in Ladder-Type Polymers

For ladder-type polymers with the head-to-tail or head-to-head repeat pattern, you must specify how the two crossing bonds on a single bracket connect to the corresponding bonds of the adjacent SRU. To do this, you specify whether the SRU flips around the polymer backbone when it attaches to the adjacent SRU.

Examples: Head-to-Head or Head-to-Tail

For more information on polymer repeat pattern, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

Note: In MACCS-II, the flip/no flip specification was called polymer correspondence.


Substance Group (Sgroup) Field

A Substance Group (Sgroup) field is a special kind of database field that assigns meaning to attached data that is stored with the structure. The data in Sgroup fields is accessible solely through a graphical search query. For example, you can not attach a form box to an Sgroup field.

For information on using attached data with polymers, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

For information on using attached data with non-polymer structures, see Drawing Mixtures: MDL Requirements for Database Searching and Registration.


Multiple Group

A multiple group is a pair of brackets that represents a fixed number of identical repeating units in condensed form. For example:

Note: To represent an unspecified number of identical repeating units within a polymer, use SRU brackets (n).


Source-Based and Structure-Based Polymer Representation

Polymers can be drawn in two styles: the structure-based or source-based representation. The following example shows both representations of a simple homopolymer:

For more information on polymer representation, see Drawing Polymers: MDL Requirements for Database Searching and Registration.


Polymer Brackets

To draw polymer structures for searching and registration, you generally use a combination of the following polymer brackets:

*	Structural Repeating Unit (SRU) brackets

*	Monomer (mon) brackets

*	Copolymer (co) brackets

Additional polymer types such as mer(mer), crosslink(xl), modification(mod), graft(grf), random(ran), block(blk), and alternating (alt) are also available. For information on how to draw structures that you can register to molecule databases, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

For an SSS/Poly search, we provide an additional polymer bracket type, anypolymer (anyp). A query with anyp brackets matches any of the previous polymer bracket types.


Polymer End Groups

The end groups of polymers are often unknown. Therefore, ISIS automatically changes terminal carbon atoms of polymers that you draw to a special type of atom called a *atom (star atom). You can edit the *atoms to draw the end groups explicitly. For example:


Bracket Style

Bracket style can be either square or curved. The following polymer contains both bracket styles:

Bracket style is stored with the structure in the database. However, bracket style affects solely how brackets are displayed; bracket style does not affect searching.

Note: In the polymer shown here, the subscripts p, q, and r are SRU labels.


Earlier Conventions for Polymer Representation

Your ISIS Administrator might specify conventions for drawing polymers that are different from the conventions that MDL recommends. These conventions might include earlier conventions for polymer representation that were available in MACCS-II. If you are not sure which conventions your corporate database uses, see your ISIS Administrator.

 Caution: To draw polymer structures that you can register to a database or use as search queries, you must follow the conventions that your ISIS Administrator specifies. If you do not follow these conventions, other users might not be able to retrieve the structures that you register.

For information on the polymer representation conventions that MDL recommends, see Drawing Polymers: MDL Requirements for Database Searching and Registration.


Monomer

The IUPAC definition of a monomer is: "A compound consisting of molecules each of which can provide one or more constitutional units" of the macromolecule. [process-based]". (From "Basic Definitions of Terms Relating to Polymers (1974)," Pure Appl. Chem. 1974, 40, 477-491.)

Note: Do not confuse a monomer (represented as a structure without brackets) with the source-based representation of a polymer. For example:


Monomeric Unit

The IUPAC definition of a monomeric unit is: "The largest constitutional unit contributed by a single monomer molecule in a polymerization process. [structure-based]". (From "Basic Definitions of Terms Relating to Polymers (1974)," Pure Appl. Chem. 1974, 40, 477-491.)

For example:


Constitutional Unit

The IUPAC definition of a constitutional unit is: "A species of atom or group of atoms present in a chain of a polymer or oligomer molecule. [structure-based]". (From "Basic Definitions of Terms Relating to Polymers (1974)," Pure Appl. Chem. 1974, 40, 477-491.)

For example:


Constitutional Repeating Unit
Constitutional Repeating Unit (Structural Repeating Unit)

The IUPAC definition of a constitutional repeating unit (also called a structural repeating unit, or SRU) is: "The smallest constitutional unit whose repetition describes a regular polymer. [structure-based]". (From "Basic Definitions of Terms Relating to Polymers (1974)," Pure Appl. Chem. 1974, 40, 477-491.)

For example:


Crossing bond

Crossing bonds are the bonds that cross the brackets of a polymer structure. Crossing bonds show how the repeating units within a polymer connect to each other. For example:


Attaching a Text/Numeric Query

You can attach a text/numeric query to a bracket, or to a set of atoms and bonds in a query for an SSS/Poly search. A structure that contains a text/numeric query retrieves structures in which the attached data meets the conditions that are specified by the text/numeric query. For example:

Note: Your text/numeric query is case-sensitive solely when you use a relational database or a UNIX platform.


Note on Mixture Brackets in Queries

Mixture brackets are not required in search queries for SSS search. For example:


Copolymer

The IUPAC definition of a copolymer is: "A polymer derived from more than one species of monomer [process-based]". The terms bipolymer, terpolymer, and quaterpolymer specify copolymers that are derived from two, three, or four species of monomer, respectively. ((From "Basic Definitions of Terms Relating to Polymers (1974)," Pure Appl. Chem. 1974, 40, 477-491.)

The following example shows a terpolymer:


Polymer

The IUPAC definition of a polymer is: "A substance composed of molecules characterized by the multiple repetition of one or more species of atoms or groups of atoms (constitutional units) linked to each other in amounts sufficient to provide a set of properties that do not vary markedly with the addition or removal of one or a few of the constitutional units [structure-based]". (From "Basic Definitions of Terms Relating to Polymers (1974)," Pure Appl. Chem. 1974, 40, 477-491.)

For example:


Oligomer

The IUPAC definition of an oligomer is: "A substance composed of molecules containing a few of one or more species of atoms or groups of atoms (constitutional units) linked to each other. The physical properties of an oligomer vary with the addition or removal of one or a few of the constitutional units [structure-based]". (From "Basic Definitions of Terms Relating to Polymers (1974)," Pure Appl. Chem. 1974, 40, 477-491.)


Text/Numeric Query

In a Search By Form (SBF), a text/numeric query is a phrase in a box or cell on the form that specifies the retrieval of data. Each phrase contains:

*	A search operator that specifies the type of search (such as an equal sign, =, to specify a search that finds solely the exact target text in the query).

*	The text or numeric target value (specific data) that you want to find.

Note: The target value is case-sensitive solely when you use a relational database or a UNIX platform.

For example, to find structures with a molecular weight greater than 350, enter > 350 in the Molecular Weight box (where > is the search operator and 350 is the target value).

For more information on text/numeric queries, see SBF Searching Concepts/Examples.


Extended PTable

The ISIS periodic table or PTable defines the atom symbols that you can register to your database. The Standard PTable contains the natural elements. The Extended PTable provides the following symbols in addition to the natural elements:

D	Deuterium

T	Tritium

H2	Hydrogen molecule

H+	Hydrogen ion

X	Special atom symbol

R	Special atom symbol

The extended PTable also provides symbols for the 20 amino acids that are found in proteins:

Ala	Leu

Arg	Lys

Asn	Met

Asp	Phe

Cys	Pro

Gln	Ser

Glu	Thr

Gly	Trp

His	Tyr

Ile	Val

X, R, and the 20 amino-acid symbols are pseudoatoms that can be used to represent groups of atoms. A pseudoatom is registered as a no-structure atom symbol that your ISIS Administrator defines in the PTABLE.HST file. Your ISIS Administrator can provide additional pseudoatoms by editing your site's PTABLE.DAT file.

Note: Do not confuse pseudoatoms with abbreviated structures. Abbreviated structures can be expanded to reveal the underlying structure which is chemically significant. By contrast, pseudoatoms cannot be expanded and do not have underlying structure.

The R atom type is not part of a generic search query (Rgroup). Unlike an Rgroup, an R atom can be registered into a database.

Notes: (1) Bonded hydrogen, H-H, cannot be registered. (2) The hydrogen molecule H2 can be registered, but only as a no-structure pseudoatom that represents molecular hydrogen.


Display Rgroups

In SAR Table, display Rgroups, such as R1 or R2, are placeholders on structure that designate where functional groups and atoms can attach.

Unlike the Rgroup labels that include Rgroup member lists, display Rgroups are not interpreted as part of the query.


 Using ISIS/Draw

QUICK START: Drawing Molecules, Reactions, Objects, and Text

What is New in ISIS/Draw?

Using Template Tools and Pages

Drawing With the Keyboard

Manipulating Objects

Working With Abbreviated Structures

Aids for Precision Drawing

Drawing for Journal Publication

Working With Polymers, Biopolymers, and Mixtures

Creating Molecule Queries

Creating Reaction Queries

Creating 3D Queries

Verifying the Chemistry of Sketches

File Basics: Saving, Printing, Importing...

Tools, Menus, Settings


ISIS/Draw "Quick Start"

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

Drawing Molecules

*	Basic Strategy	5.1

*	Drawing Structures with Template tools and template pages	5.2

*	Drawing bonds and chains	5.3

*	Drawing atoms	5.4

*	Selecting and deselecting atoms, bonds, and structures	5.5

*	Deleting atoms, bonds, and structures	5.6

*	Editing atoms, bonds, and structures	5.7

*	Resizing or scaling structures	5.8

*	Moving atoms, bonds, and structures	5.9

*	Drawing with the keyboard	5.10

*	Drawing structures for presentation graphics	5.11

Recovering From Problems	5.12

Changing ISIS/Draw Settings	5.13

Drawing Reactions

*	Basic strategy	5.14

*	Editing a reaction	5.15

Working with Text	5.16

Specifying Query Features for an ISIS/Base Search	5.17

Transferring Queries From ISIS/Draw Back to ISIS/Base	5.18

We recommend that you print this 14-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

This Request-A-Document covers the basic concepts that you need to know to quickly learn ISIS/Draw. For additional information, see the ISIS/Draw Table of Contents, or click Search to use the Help system index.

We assume that you know how to move and scroll windows, select objects, and choose menu commands. We also assume that you know how to use Copy and Paste and how to edit text.

Note: This document does not discuss how to draw ISIS/Base forms. For more information, see Creating and Editing Forms in the ISIS/Base Table of Contents.

Drawing Molecules

5.1 Basic Strategy

To draw molecules, do the following:

1.	Draw the basic framework with template tools, templates from a template page, and drawing tools.

2.	Edit atoms, bonds, and molecules as necessary. All atoms are carbons unless you specify otherwise.

3.	(Optional) Use Chem Inspector to ensure that the molecule's chemistry is correct before you register or use the molecule to search in ISIS/Base. For more information, see Verifying the Chemistry of Sketches in the ISIS/Draw Table of Contents.

4.	(Optional) To ensure that a molecule has uniform bond lengths and angles, select the molecule, and then choose Object > Clean Molecule.

5.2 Drawing structures with template tools and template pages

Templates are pre-saved structural fragments or molecules that you can use as building blocks for your own structures. A template tool allows you to use one specific structure, whereas a template page contains many structures from which to choose.

5.2.1 To use a template tool

1.	Click one of the template-tool icons on the horizontal tool bar:

2.	Do one of the following:

*	To place the template anywhere, click an empty area.

*	To fuse the template to an existing bond, click the bond.

*	To attach the template by a single bond to an existing atom, click the atom.

5.2.2 To use a template from a template page

1.	Choose a template page from the Templates menu. You see the template page in a window.

2.	Find the structural fragment or molecule that you want to add to your sketch.

3.	Click an atom or bond in the structural fragment or molecule. The template page goes behind the sketch window.

4.	Do one of the following:

*	To place the template anywhere, click an empty area.

*	To fuse the template to an existing bond, click the bond.

*	To attach the template by a single bond to an existing atom, click the atom.

For more information, see Using Template Tools and Pages in the ISIS/Draw Table of Contents.

5.3 Drawing bonds and chains

Drawing bonds: To draw bonds, click a bond tool on the vertical tool bar, such as [image] or [image]. Then, click the mouse to add a bond to the drawing area, or drag the mouse from an existing atom.

Default values: Any atoms, bonds, or other objects that you draw use pre-set default values. For information on changing these default values, see 5.13 Changing ISIS/Draw Settings.

Some tool icons have a small triangle in the bottom right corner. For example, the single-bond tool:

This indicates that there are additional tools available. For example, to draw a double bond, first press on the single-bond tool:

Next, drag the mouse onto the double-bond tool:

Finally, release the mouse. You see:

The double-bond tool is now the default tool. The cursor indicates that you can draw double bonds. (Click the mouse to draw a double bond.)

Sprouting: To sprout a bond from an atom, click [image] (or any other bond tool), and then click the atom:

Stereo Bond: (Up/Down/Either): To draw an Up, Down, or Either bond, click the appropriate tool icon. Then, click the mouse over the drawing area to draw the bond. The bond you chose displays on the tool bar, and is now the default bond.

Bond Type: To change the bond type of an existing bond, click a different bond tool and then click the bond. The bond changes to the default bond type shown on the tool bar.

Stereo Bond Direction: To reverse the direction of a stereo bond, click one of the stereo bond tools, then click the middle of the bond.

Bond Rotation: To rotate the position of a single bond, click [image], select the free end of the bond, press the mouse and drag to the desired position and length.

Standard Bond Length: To change the standard bond length, choose Options > Settings, and then click the Chemical Drawing tab. Click the Standard bond/grid length box, and enter or choose a bond length. Then, choose the unit of measure. For more information on changing default values, see 5.13 Changing ISIS/Draw Settings.

Drawing Chains: To draw chains in one direction, click [image] and then press and drag the mouse. To draw continuous bonds that follow the position of your mouse, click [image] and then press and drag the mouse in the desired direction. You can draw rings and other molecules of specific shapes with this tool.

Other Objects: You draw other objects, such as lines, boxes, arrows, and polygons as follows: Click the appropriate tool, and then press and drag the mouse to draw the object.

Help on Tools: To see help information for any of the tools on the horizontal or vertical tool bars, move the cursor over the tool, and then press the mouse. To turn this help on or off, choose Options > Settings, click the General tab, and set Show toolbar help messages. You can also find more information in Tools on the ISIS/Draw Table of Contents.

5.4 Drawing Atoms

Drawing atoms: To draw an atom, click [image] and then click the mouse where you want the atom to appear. You see a text entry field where you can either enter an atom symbol or choose one from a list. Then, click elsewhere. As you type in the atom symbol, you can also type in charges, radicals, or isotopes.

Note: If you enter a standard atom symbol, such as br, ISIS/Draw capitalizes it and treats it as the atom symbol Br. If you enter text that is not an atom symbol, such as bu, ISIS/Draw treats the text as an atom alias that is not chemically significant as a search query. For information on atom aliases and other chemically insignificant text, see 5.11 Drawing structures for presentation graphics.

Repeating atom symbols: To repeat an atom symbol that you just entered, press Ctrl (Mac=Command) and click another atom to replace its current symbol. Or, click in the drawing area to add a new atom of the same value.

Editing atoms: To edit an atom, first click [image] or [image], and then double-click the atom. You see the Edit Atom dialog box where you can edit the atom. For more information, see 5.7 Editing Atoms, bonds, and structures.

Chemically-significant text

Chemically-significant text is any atom symbol (element) or set of atom symbols (elements) that you specify. You can include charges, radicals, and isotopes. You add chemically-significant text to structures and then use the structures as queries to search databases in ISIS/Base.

Specifying charges: To specify a charge, enter a plus (+) or a minus (-) after the appropriate character. For example, N2+.

Specifying radicals: To specify a radical, enter one of the following characters after the atom symbol:

:	(singlet diradical)

.	(doublet monoradical)

^^	(triplet diradical)

Specifying isotopes: To specify an isotope, enter the isotope number before the atom symbol. For example, 16O.

Sprouting explicit hydrogens: An explicit hydrogen is a hydrogen with a bond attached to an atom. An implicit hydrogen is either a hydrogen that you know to be present at a specific position in a structure (implied), but it is not visible or, if the hydrogen is visible, it is drawn without the bond attached to the atom.

To sprout an explicit hydrogen, sprout a single bond, select the atom and then choose Object > Edit Atom. Click the Symbol box and choose H.

Chemically-insignificant text

Chemically-insignificant text is any text that you enter from the keyboard. You cannot use structures that contain chemically-insignificant text as reliable queries to search databases in ISIS/Base. For information on atom aliases and other chemically-insignificant text, see 5.11 Drawing structures for presentation graphics.

5.5 Selecting and deselecting atoms, bonds, and structures

When you move the cursor over an item in the drawing area, ISIS/Draw indicates whether the item is an atom, a bond, or an object:

In the following instructions, if you double-click an atom, bond, structure, or any object instead of single-clicking, you see a dialog box where you can edit the object.

5.5.1 Selecting atoms, bonds, and structures

There are three Select tools that you can use: , [image], and [image]. Which one you use is an individual preference.

*	Use [image] or [image] to select individual atoms or bonds, whole structures, and non-chemical objects. Use [image] if you prefer to select objects within a lasso, or use [image] if you prefer a rectangular frame.

*	Use [image] to select whole molecules or non-chemical objects only. You cannot select individual atoms or bonds using this tool.

To switch between the three Select tools: Click the Select tool that appears on the tool bar, then drag the mouse over to one of the other tools and release the mouse.

To select one atom or bond, first click [image] or [image], and then click the atom or bond.

To select multiple atoms, bonds, or structures, do one of the following:

*	Click [image] or [image], and then click one atom or bond. Press the Shift key and then click additional atoms or bonds.

*	Click [image] or [image] and drag the mouse around the atoms, bonds, or structures that you want to select.

To select one structure, do one of the following:

*	Click [image] and then click the structure.

*	Click [image] or [image], then press the Ctrl (Mac=Command) key and click the structure.

Other Objects: You select other objects, such as lines, boxes, arrows, and polygons as follows: Click [image], [image], or [image], then click one object, or press and drag the mouse around multiple objects.

Windows users only: When you select one or more objects and press the right mouse button, you see a pop-up menu with commands that apply to the objects that you selected.

For example, if you select a structure and press the right mouse button, you see a pop-up menu that includes Cut, Copy, Select All, Duplicate and Edit Molecules. The commands that you see on the menu vary according to the objects that you select.

5.5.2 Deselecting atoms, bonds, and structures

To deselect an item and leave other items selected, press the Shift key and click the item to deselect.

To deselect all the items that you selected, click an empty area.

Other objects: You deselect other objects, such as lines, boxes, arrows, or polygons, as follows: Press the Shift key and click one object to deselect, or click an empty area.

5.6 Deleting atoms, bonds, and structures

Select one or more atoms, bonds, or structures. Then, do one of the following:

*	Press the Delete key.

*	Choose Edit > Cut.

To delete atoms or bonds one at a time, click [image], then click an atom or bond.

Note: When you delete an atom, any bonds attached to that atom are also deleted.

Other objects: You delete other types of objects, such as lines, arrows, boxes, Rgroup labels, and so on, as follows: Click [image] and then click an object; or select the objects and press the Delete key or choose Edit > Cut.

Deleting all objects in the drawing area: To delete all of the objects in the drawing area, first choose Edit > Select All, and then press the Delete key or choose Edit > Cut.

5.7 Editing atoms, bonds, and structures

You can edit an atom, bond, or structure. This can include such things as changing the atom symbols, adding a charge, or changing a bond from a double to a triple bond.

To edit atoms, bonds, or structures, do the following:

1.	Click [image] or [image]. Click [image] if you want to edit an entire structure, not individual atoms or bonds.

2.	Select the atoms, bonds, or structures to edit.

3.	Do one of the following:

*	Double-click one of the selected atoms, bonds, or structures.

*	Choose Object > Edit.

You see the Edit dialog box:

4.	Click the tab that identifies the type of change that you want to make. You see only tabs that apply to the atoms, bonds, or structures that you selected. To find information for an item on a tab, click Help.

Note: The wording of the Object > Edit menu command varies depending on what you select. For example:

*	If you select a bond, the command reads Edit Bond.

*	If you select at least one atom and one bond, the command reads Edit Molecule.

*	If you select different types of objects, such as text, atoms, and a box, the command reads Edit Objects.

Other objects: You edit other types of objects, such as lines, arrows, boxes, Rgroup labels, and so on, as follows: Click [image], [image],or [image]. Then, select the objects to edit, and then choose Object > Edit Objects.

Note: On the PC, If you select an OLE object, the Edit <object> command is not available.

5.8 Resizing or scaling structures

To resize a structure, select it, then drag one of the corner handles:

ISIS/Draw displays the percentage by which you are resizing the structure.

Note: If you drag a non-corner handle, the structure becomes distorted.

To scale a structure, select it, and then choose Object > Scale > Percent. Enter a number - without a % sign - to scale the structure.

Note: If you resize or scale all of the molecules in the drawing area, you see a dialog box where you specify if you want your settings to reflect the resizing or scaling. Click Yes to have the settings modified so that any new molecules that you draw are drawn in the same scale. Click No to leave the settings as they are.

Other objects: You resize or scale other types of objects, such as lines, polygons, boxes, and so on, as follows: Select the object, then drag a corner handle, or choose Object > Scale > Percent.

5.9 Moving atoms, bonds, and structures

To move atoms, bonds, or structures, first select them. Then, press the mouse and drag the items to the new location (the cursor changes to a hand).

Other objects: You move other types of objects, such as lines, polygons, boxes, and so on, as follows: Select the object, press the mouse, then drag the object to the new location.

Note: When the cursor looks like a hand, you can move the atom, bond, or object. When the cursor looks like a double-arrow, move the cursor over the item so that it changes to a hand. Otherwise, you will rescale or distort the object instead of moving it.

5.10 Drawing with the keyboard

To add or edit atom symbols, select one or more atoms. Then, type an atom symbol and press the Return key. ISIS/Draw labels all of the selected atoms with the atom symbol that you entered.

To place an abbreviated structure (all or part of a structure that has been abbreviated to a text label) into a sketch, first choose Options > Settings and click the General tab. You require [image] Abbreviate typed-in templates. Click Save to save any changes that you make to the settings. Then, click the atom from which you want the abbreviated structure to spout, or click another part of the sketch. Type the correct abbreviation and press the Return or Enter key. For a list of the predefined abbreviated structures available in ISIS/Draw and additional information, see Drawing with the Keyboard in the ISIS/Draw Table of Contents.

5.11 Drawing structures for presentation graphics

You can draw structures for use as presentation graphics, and you can draw structures that contain atom aliases.

An atom alias is text that you attach to an atom that is not chemically significant for use as a search query in ISIS/Base. The atom alias hides the existing atom but does not replace it. The chemical significance of the atom underneath does not change in any way. An atom alias can be any text or numerical value. You can register a structure with an atom alias into a database using ISIS, but you cannot search for the atom alias as data.

Creating atom aliases: To create an atom alias do one of the following:

*	To specify an atom alias by itself, click [image] and then click where you want the alias to appear. Enter the atom alias text into the text entry field, then click elsewhere.

*	To add an atom alias to an existing structure, click [image] and then click the atom to which you want to attach the atom alias. Enter the atom alias text into the text entry field, then click elsewhere. Do not use all uppercase letters when you type in the atom symbol.

Note: If you use all uppercase letters when you type in the atom alias, ISIS/Draw might add an abbreviated structure to the sketch instead of the atom alias. In addition, when you create an atom alias, numerical values are automatically subscripted.

To enter letters or numerical values that are superscript, enter \S before and after the letter or number. You must use a capital S.

For example: To specify [image], enter \S32\SPO4.

To enter letters that are subscript, enter \s before and after the letter. You must use a lower case s.

To enter numerical values that are not subscripts, enter \n before and after the number. You must use a lower case n.

Positioning atom charges within an alias: To place a charge at the left of an atom, click [image], click the atom, and then enter the charge and atom alias text. Click elsewhere.

For example, to specify [image], enter \S+\SPO.

Editing or deleting atom aliases: To edit or delete an atom alias, click [image] and then click the atom containing the atom alias. Delete or edit the text in the text entry field, then click elsewhere.

Displaying hydrogen labels: To display hydrogen labels, choose Options > Settings and then click the Chemical Drawing tab. Click the Show hydrogen labels box and choose the types of atoms on which to display hydrogen labels: Off, On Hetero, On Hetero or Terminal, and On All.

Positioning hydrogen attachments: To specify the position of hydrogens on an atom, click [image] or [image] and double-click the atom. Click the Atom tab and then click the Hydrogens box and choose where you want the hydrogens to appear.

5.11.1 To sprout one bond from a typed-in formula (atom alias)

Use this procedure to sprout one bond from a typed-in formula (atom alias). For example, to sprout an explicit hydrogen from a carbon atom that exists as an atom alias:

1.	Click [image] and click in the drawing area.

2.	Enter the formula. Include a caret (^) before the character you want the bond to be attached to. For example, enter CH^CH2 to have the attachment point be at the second carbon.

Note: You can include only one caret for one attachment point.

3.	Click one of the bond tools.

4.	Draw a bond under the text string. The bond attaches itself to the correct site.

5.	Click [image].

6.	Click the end of the bond and enter the atom label H.

Note: When you use this procedure, the numerical values that you enter are automatically subscripted, and the text string and bond are automatically grouped.

5.11.2 To sprout two or more bonds from a typed-in formula (atom alias)

Use this procedure to sprout two or more bonds from a typed-in formula (atom alias). For example, to sprout two or more explicit hydrogens from different carbon atoms that exist as atom aliases:

1.	Click

2.	Enter the formula, such as CHCH2.

3.	(Optional) If the formula contains numerical values that should be subscripted, select the formula and choose Text > Formula.

4.	Click

5.	Draw the bonds. The bonds are the standard bond length.

6.	(Optional) Click [image] and enter any atom labels, such as an explicit H, that you want to be attached to the bonds.

7.	To keep the objects together, select all of the objects and choose Object > Group.

5.11.3 To draw a ring that contains an aromatic designation

Use this procedure to draw a chemically-insignificant ring with an aromatic designation, such as benzene:

Note: This ring cannot be used as a query to search databases in ISIS/Base.

1.	Use a template tool to draw the ring of your choice.

2.	Click

3.	Press the Shift key as you draw a circle that is smaller than the ring.

4.	Select the circle and move it inside the ring.

5.	To keep the objects together, select all of the objects and choose Object > Group.

5.11.4 To draw charged aromatic rings

Use this procedure to draw chemically-insignificant charged aromatic rings, such as the following:

Note: These ring cannot be used as a query to search databases in ISIS/Base.

1.	Use a template tool to draw the ring of your choice.

2.	Click

3.	Press the Shift key as you draw a circle that is smaller than the ring.

4.	Select the circle and move it inside the ring.

5.	Press the Shift key as you draw a smaller circle.

6.	Select the smaller circle and move it inside the larger circle.

7.	Click [image] and type a - (minus).

8.	Select the minus and move it inside the smaller circle.

9.	To keep the objects together, select all of the objects and choose Object > Group.

5.12 Recovering From Problems

To reverse your last action, choose Edit > Undo.

To leave a dialog box without changing anything, click Cancel.

To avoid many problems, save your work often.

If you prefer, you can always close the sketch without saving changes. If you saved your work recently, you will not lose many changes.

5.13 Changing ISIS/Draw Settings

You can modify the settings in ISIS/Draw' to suit your drawing needs. To modify any setting, choose Options > Settings, and then click the tabs to view the program defaults that you can modify.

To save any modifications you made to the settings, click Save, otherwise any changes you make to settings apply only until you exit from ISIS/Draw.

To obtain information on the individual items on a tab, click Help.

For more information, see Settings in the ISIS/Draw Table of Contents.

Drawing Reactions

5.14 Basic strategy

1.	Draw the molecule components of the reaction with template tools, template pages, and/or drawing tools. (See Drawing Molecules for more information.)

2.	Use the [image] tool to add arrows. Use the [image] tool to add a plus, or click [image] and type a plus at the cursor position of your choice.

Note: For presentation graphics, you can use any arrow. To use the reaction in ISIS/Base, you must use one of the arrow types labeled Valid for ISIS/Base Reactions in the toolbar help.

3.	(Optional) To add reaction conditions to the reaction, click [image], enter the conditions, and place them at the position of your choice.

For example, to add [image] above an arrow, click [image] and enter the degree symbol as a lower case, superscripted "o".

Note: Reaction conditions are for display only and cannot be used for searching or exporting purposes.

4.	(Optional) Use Chem Inspector to ensure that the reaction is chemically significant before you use the reaction to search in ISIS/Base. For more information, see Verifying the Chemistry of Sketches in the ISIS/Draw Table of Contents.

Note: For searching and registration into ISIS/Base, you can only use one step of a multi-step reaction at a time.

5.15 Editing a reaction

Add, edit, delete, or move reaction elements as necessary.

To align an entire reaction, including arrow and plus signs, select the reaction and choose Object > Align. Use the Alignment Options dialog to specify how to align the reaction.

To align a reaction by molecular components only, first select one atom from each component. Then, choose Object > Align and specify how to align the reaction.

If you do not like the way the reaction is aligned, choose Edit > Undo.

(Optional) Use Chem Inspector to ensure that the reaction's chemistry is correct before you use the reaction to search in ISIS/Base. For more information, see Verifying the Chemistry of Sketches in the ISIS/Draw Table of Contents.

5.16 Working with Text

To enter text, click [image], and then click where you want the text to appear. Now, enter the text. Alternatively, you can enter text by pasting it in from the Clipboard.

To edit text, click [image], click the text, and then edit it as you would with a word processor.

To reformat text, click [image], click the text, and then drag a non-corner handle:

To change text properties, such as making text bold, select the text and do one of the following:

*	Choose Object > Edit Text.

*	Double-click the text.

*	Choose one of the commands on the Text menu.

To set text defaults, choose Options > Settings, and then click the Font tab. To save any modifications you made to the settings, click Save, otherwise any changes you make to settings apply only until you exit from ISIS/Draw.

*	If this is a new sketch, the new font settings are applied to any new text you enter.

*	If this sketch contains existing text, a dialog asks if you want to apply the new font settings to the existing text.

To enter reaction conditions (text that is above or below reactants, products, or the reaction arrow): Click [image], then click where you want the reaction condition to appear, and then enter the text.

5.17 Specifying query features for an ISIS/Base search

You can use ISIS/Draw to specify query features on bonds, atoms, and reactions. A query feature on a molecule (including a reaction component or a biopolymer) is a restriction on an atom and/or a bond that specifies the retrieval of certain types of records from a database using ISIS/Base.

A query feature on a reaction is a restriction on the reaction that specifies the retrieval of certain types of records from a database using ISIS/Base.

You can include query features solely for specific searches. For more information on the query features that you can use and the searches that you can conduct with them, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen. Then click the search of your choice. You will see the full definition of the search, how to do it, and the query features that you can use with that search.

5.18 Transferring Queries From ISIS/Draw Back to ISIS/Base

To transfer a query that you drew in ISIS/Draw back to ISIS/Base, click [image]. You see your query in the structure box or column on the form.

Note: You see [image] only if you started ISIS/Base first, and then either clicked [image] or double-clicked a structure box or column.

If you are in ISIS/Draw and do not see [image], do the following: Select the query and choose Edit > Copy. Then, switch to ISIS/Base and click the Query button. Click the appropriate structure box or column on the form, then choose Edit > Paste.


What is New in ISIS/Draw?

*	New features in ISIS/Draw 2.3

*	New features in ISIS/Draw 2.2.1

*	New features in ISIS/Draw 2.2

*	New features in ISIS/Draw 2.1.4

*	New features in ISIS/Draw 2.1

*	New features in ISIS/Draw 2.0.2

*	New features in ISIS/Draw 2.0


New Features in ISIS/Draw 2.3

*	Specify a secondary templates folder where ISIS/Draw looks for template pages and template tools, in addition to the primary folder. (PC Only)

*	Use the Beilstein Generic dialog to add Beilstein atom and group generics to your query.

To access this dialog, double-click an atom to display the Edit Atom dialog. Click the Query tab, click the Symbol box, and then choose Beilstein generics.


New Features in ISIS/Draw 2.2.1

There are no new features in ISIS/Draw 2.2.1.


New Features in ISIS/Draw 2.2

There are no new features in ISIS/Draw 2.2.


New Features in ISIS/Draw 2.1.4

*	Chemistry > Calculate Mol Values: Pastes the molecular weight, exact mass, formula, and composition of selected chemical objects into a sketch.

Note: This command was an add-in in previous versions of ISIS/Draw.

*	Chemistry > Disable Rgroup Chem Inspector: Ensures that Chem Inspector does not incorrectly flag display Rgroups queries when you try to transfer them back to ISIS/Base.

Note: This command appears only if you have ISIS/Base and SAR Table installed. It was an add-in in previous versions of ISIS/Draw.


New Features in ISIS/Draw 2.0

*	ISIS/Draw has an improved interface. See the ISIS/Draw "Quick Start" for detailed information on these and other changes:

*	Molecule and sketch tools combined into one tool bar

*	Multiple selection tools combined into one tool

*	Pop-up help for tools (can be turned on and off)

*	A simple method to build reactions

*	New chain and multi-bond tools make it simpler to create long chains

*	Displays percent change when you resize objects

*	Context-sensitive help for dialog boxes

*	A simple method to set default tools

*	All preferences can be set in one dialog box

*	Can double-click objects to edit their properties (the Style menu has been eliminated)

*	New arrow tool with more arrow types

*	Create DNA, RNA, or amino acid sequences and other molecules that are larger than 255 atoms

*	Innovative and completely redesigned online help; see How to use ISIS/Desktop help

*	Superatoms are now called abbreviated structures

*	When you attach a template to a terminal atom, the template now fuses to the atom

*	Atom aliases and atom symbols are created using the same method

*	Use Chem Inspector to verify that you can register molecules and reactions in ISIS/Base, and that you can use the molecules and reactions to search a database using ISIS/Base.

*	Use journal configuration files to format sketches to specific journal standards

*	Use Print Preview to see how your sketch will print out

*	A simple method to customize template tools and the template menu

*	A simple method to apply atom-atom maps to reactions


New Features in ISIS/Draw 2.0.2

*	Windows 3.1/ 95/NT Users only: Select objects, then press the right mouse button to use a pop-up menu with commands that apply to the selected objects.

*	Use the keyboard to create Rgroup attachments


New Features in ISIS/Draw 2.1

*	Use the new Bracket tool to create polymers and mixtures

*	Attach data to bonds or atoms, or to brackets

*	Draw a structure that contains a specific number of identical repeating units as a multiple group.


Specifying Molecule, Reaction, and 3D Queries

You create molecule, reaction, and 3D search queries in ISIS/Draw, enter them into the form in ISIS/Base, and then conduct the search.

Click one of the following:

*	Specifying molecule query features

*	Specifying query features on a reaction

*	Specifying 3D query features


Creating 3D Queries

You use a 3D query to search a database for 3D structures. The 3D query that you use depends entirely on the type of 3D search that you want to conduct. For more information on 3D searching, click one of the following search types:

3D Structure Records (Remote Searches):

3DEXACT    ALL    CFS    CFS/Biopoly    ID    MSim    QB    SBF    SSS3D    SSS3D/Biopoly

3D Structure Records (Local Searches):

3DEXACT    ALL    ID    QB    SBF

New users: If you do not know exactly which search you need, see How To Choose the Best Type of Search -- and How to Do It.

You use 3D query features in the following searches: CFS, CFS/Biopoly, SSS3D, and SSS3D/Biopoly. For more information on 3D query features, click here.


Keyboard Equivalent for Creating 3D Objects

As an alternative to choosing Chemistry > 3D > Create, you can use the following keyboard equivalents:

*	PCI: Control-8

*	Mac: Command-8


Specifying 2D Query Features

A 2D query feature is a restriction on an atom and/or bond that does not restrict the 3D spatial relationships between atoms. Example

For more information on 2D query features, see Searching Concepts/Examples for the search of your choice.

Click one of the following:

*	Specifying atom query features

*	Specifying bond query features

*	Specifying Rgroup query features

See also:

To transfer the query back to ISIS/Base


Example

The following are examples of 2D query features:


3D Query Features

A 3D query feature is a restriction that specifies the spatial arrangement of atoms in the 3D structures that you retrieve from a CFS, CFS/Biopoly, or SSS3D. search. Example

*	Specifying 3D submodel components

*	Specifying 3D geometric constraints

*	Specifying chemical environments

*	Specifying interactions with a receptor

*	Specifying lone pairs

*	Specifying explicit hydrogens

*	Specifying 3D data constraints


Specifying 3D Query Features

A 3D query feature is a restriction that specifies the spatial arrangement of atoms in the 3D structures that you retrieve from a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search. Example

Click one of the following:

*	Specifying submodel components

*	Specifying 3D geometric constraints

*	Specifying chemical environments

*	Specifying interactions with a receptor

*	Specifying lone pairs

*	Specifying explicit hydrogens

*	Specifying 3D data constraints

See also:

To remove 3D query features from a structure

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


Specifying 3D Query Features

A 3D query feature is a restriction that specifies the spatial arrangement of atoms in the 3D structures that you retrieve from a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search. Example

Click one of the following:

*	Specifying 3D geometric constraints

*	Editing submodel components

*	Specifying chemical environments

*	Specifying interactions with a receptor

*	Specifying lone pairs

*	Specifying explicit hydrogens

*	Specifying 3D data constraints

See also:

To remove 3D query features from a structure

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


Example

In the following example, the distance constraint and fixed atoms of the submodel specify spatial relationships among atoms:


Specifying 3D Objects

You can construct 3D objects that you can use to construct 3D geometric constraints on a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search. Example

Click one of the following:

*	To specify a centroid

*	To specify a line

*	To specify a plane

*	To specify a normal vector that is perpendicular to a plane

*	To specify a point as a reference position

See also:

To remove 3D query features from a structure

To rotate a 3D structure or query

To edit the reference positions that comprise a 3D object

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


Specifying 3D Geometric Constraints

Use 3D geometric constraints to specify spatial relationships between atoms on the 3D structures that you retrieve from a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search. You construct 3D geometric constraints from atoms and/or 3D objects. Example

Click one of the following:

*	To exclude atoms within a specified volume (exclusion sphere)

*	To specify a distance constraint

*	To specify an angle constraint

*	To specify a dihedral angle constraint

*	To specify a linearity constraint

*	To specify a planarity constraint

See also:

Specifying 3D objects

To edit 3D geometric constraint values

To remove 3D query features from a structure

To rotate a 3D structure or query

To change default constraint values

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


Example

The following example shows a distance geometric constraint between the nitrogen atom on a five-membered ring and the centroid of a six-membered ring:


Specifying 3D Data Constraints

You can apply 3D data constraints to atoms or to pairs of atoms on the structures that you retrieve from a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search.

Click one of the following:

*	To specify an atom data constraint

*	To specify an atom-pair data constraint

See also:

To edit 3D data constraint values

To remove 3D query features from a structure

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


Editing Submodel Components

A submodel is a three-dimensional (3D) representation of a portion of a 3D structure. A submodel search retrieves all models that contain the same spatial arrangement of atoms as those specified in your submodel query, within specified deviations of the individual and overall atoms. Example

Note: These procedures assume that you have already created submodels in your query. For more information on submodels, see Searching Concepts/Examples for the search of your choice.

Click one of the following:

*	To delete fixed atoms from a submodel

*	To add fixed atoms to a submodel

See also:

To remove 3D query features from a structure

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


Example

You specify the spatial arrangement of atoms in a submodel query by fixing the 3D coordinates of specific atoms in a 3D structure. The following submodel query contains fixed atoms (F):


Specifying Chemical Environments

You can specify chemical environments such as basic nitrogens or acidic centers on the structures that you retrieve from a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search. MDL provides some of these chemical environments as ISIS/Draw sketch files. Use the MDL chemical environments as a starting point for drawing your own queries.

Click one of the following:

*	To specify basic nitrogen

*	To specify an acidic center

*	To specify a hydrogen-bond donor

*	To specify a hydrogen-bond acceptor

See also:

To rotate a 3D structure or query

To transfer the query back to ISIS/Base


Specifying Interactions With a Receptor

You can construct 3D objects that represent regions on the receptor that interacts with the 3D structures that you want to retrieve from a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search. Use the following examples as a starting point for drawing your own queries.

Click one of the following:

*	Specifying a hydrogen-bond donor on the receptor

*	Specifying a hydrogen-bond acceptor on the receptor

*	Specifying pi-pi interactions between ring atoms on the ligand and groups on the receptor

*	Specifying the center of an aromatic ring on the receptor.

See also:

Specifying 3D objects

To remove 3D query features from a structure

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


Searching Concepts/Examples

Click any of the following items:

3D Structure records (remote databases): CFS, CFS/Biopoly, SSS3D, SSS3D/Biopoly


To specify explicit hydrogen atoms on a 3D query

To specify hydrogen atoms at specific positions in the structures that you retrieve, you must draw explicit hydrogens in your search query. Use the following procedure to draw an explicit hydrogen on an existing atom in a 3D query.

1.	Click

2.	Click an existing atom (non-hydrogen) and sprout a single bond.

3.	Click

4.	Choose H.

5.	Click elsewhere.

See also:

To transfer the query back to ISIS/Base


To specify basic nitrogen

Use this procedure to insert into your query an MDL sketch file that contains a definition of basic nitrogen.

Note: These definitions of basic nitrogen use Rgroups. For more information on Rgroups, see Searching Concepts/Examples for the search of your choice.

1.	Choose File > Insert. You see a dialog box.

2.	Change to the appropriate directory (Mac=folder) if necessary.

3.	Do one of the following:

*	Click BSC_N_1.SKC on the list of sketch files.

*	Click BSC_N_2.SKC on the list of sketch files.

4.	Click OK (Mac=Open). You see the definition of basic nitrogen that you chose.

5.	(Optional) Edit the query.

See also:

To transfer the query back to ISIS/Base


To edit a 3D graphical query

Use this procedure to edit an existing 3D graphical query in ISIS/Draw.

1.	Edit the query. If you need help, click:

Moving Rgroup query components.

Drawing the Root Structure or

Specifying the Rgroup labels on the root structure. or

Drawing an Rgroup Substituent or

Specifying Attachment Points or

Specifying the Members of an Rgroup or

Specifying Rgroup Conditions or

Specifying 2D Query Features or

Specifying 3D Geometric Constraints or

Editing Submodel Components or

Specifying Chemical Environments or

Specifying Interactions With a Receptor or

Specifying Lone Pairs or

Specifying Explicit Hydrogens or

Specifying 3D Data Constraints or

Tips for selecting 3D objects and constraints

See also:

To transfer the query back to ISIS/Base


BSC_N_1 Sketch File


BSC_N_2 Sketch File


To specify an acidic center

Use this procedure to insert into your query the MDL sketch file that contains a definition of an acidic center.

Note: The definition of an acidic center uses Rgroups. For more information on Rgroups, see Searching Concepts/Examples for the search of your choice.

1.	Choose File > Insert. You see a dialog box.

2.	Change to the appropriate directory (Mac=folder) if necessary.

3.	Click ACID_CTR.SKC on the list of sketch files.

4.	Click OK (Mac=Open). You see the sketch file that you chose.

5.	(Optional) Edit the query.

See also:

To transfer the query back to ISIS/Base


ACID_CTR Sketch File

The following is a suggested definition for an acidic center. This sketch defines an acidic center as either an oxygen of a carboxylic acid or any nitrogen of an unsubstituted tetrazole:


To specify a hydrogen-bond acceptor

Use this procedure to insert into your query the MDL sketch file that contains a definition of a hydrogen-bond acceptor.

Note: The definition of a hydrogen-bond acceptor uses Rgroups. For more information on Rgroups, see Searching Concepts/Examples for the search of your choice.

1.	Choose File > Insert. You see a dialog box.

2.	Change to the appropriate directory (Mac=folder) if necessary.

3.	Click H_ACCEPT.SKC on the list of sketch files.

4.	Click OK (Mac=Open). You see the sketch file that you chose.

5.	(Optional) Edit the query.

See also:

To transfer the query back to ISIS/Base


H_ACCEPT Sketch File


To specify a hydrogen-bond donor

The following is a suggested definition for a hydrogen-bond donor:

Use the following procedure to draw the hydrogen-bond donor in the example:

1.	Draw an explicit hydrogen.

2.	Draw a list of atoms that allows S, N, and O atoms.

See also:

To transfer the query back to ISIS/Base


To specify pi-pi interactions with a receptor

In the following example, the exclusion spheres eliminate 3D structures with atoms that intrude into the excluded volumes. Consequently, all 3D structures that you retrieve contain phenyl rings that can interact freely with the receptor.


Specifying the Center of an Aromatic Ring on a Receptor

If you want to specify a distance from an aromatic ring on the receptor to another feature, you need to create a point that represents the center of the ring. In the following example, the point that is 3.5 Angstroms from the ring represents the center of the aromatic ring on the receptor. The exclusion spheres ensure that all 3D structures that you retrieve can interact freely with the receptor:


To specify a hydrogen-bond donor on the receptor
Specifying a Hydrogen-Bond Donor on a Receptor

The following example shows how to construct an exclusion sphere that represents a hydrogen-bond donor on the receptor. You construct the exclusion sphere around a point that you construct from two atoms of the complementary hydrogen-bond acceptor on the ligand:


To specify a hydrogen-bond acceptor on the receptor
Specifying a Hydrogen-Bond Acceptor on a Receptor

The following example shows how to construct an exclusion sphere that represents a hydrogen-bond acceptor on the receptor. You construct the exclusion sphere around a point that you construct from two atoms of the complementary hydrogen-bond donor on the ligand:


To specify a centroid

This procedure assumes that you have already drawn the reference positions (atoms, points, or other centroids) that you want to include in the centroid.

1.	Select 2 or more reference positions (atoms, points, or other centroids).

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Centroid (if not already selected).

4.	(Optional) To enter a name for the centroid, click the Name box (if not selected) and enter a name.

5.	Click OK. You see the centroid (depicted by a triangle).

See also:

Specifying 3D objects

To edit 3D objects

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


Specifying a Line

You can specify a line in one of two ways.

Click one of the following:

*	To specify a line between two reference positions.

*	To specify a best-fit line from three or more reference positions.

See also:

Specifying 3D objects

To edit 3D objects

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


To specify a line between two reference positions

This procedure assumes that you have already drawn the reference positions (atoms, points, or centroids) to include in the line.

1.	Select two reference positions (atoms, points, or centroids).

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Line (if not already selected).

4.	(Optional) To enter a name for the line, click the Name box (if not selected) and enter a name.

5.	Click OK. You see the line.

See also:

Specifying 3D objects

To edit 3D objects

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


To specify a best-fit line

This procedure assumes that you have already drawn the reference positions (atoms, points, or centroids) to include in the best-fit line.

1.	Select three or more reference positions (atoms, points, or centroids).

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Line (if not already selected). You see a default linearity constraint in the RMS Deviation box.

4.	Do one of the following:

*	To specify the default linearity constraint, do nothing at this step.

*	To specify a line without a linearity constraint, highlight the value in the RMS Deviation box (if not already highlighted) and delete the value.

*	To change the default linearity constraint, highlight the value in the RMS Deviation box (if not already highlighted) and enter the new value.

5.	(Optional) To enter a name for the line and linearity constraint, click the Name box (if not selected) and enter a name.

6.	Click OK. You see the line.

See also:

Specifying 3D objects

To edit 3D objects

To specify the default linearity constraint

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


To specify a normal

This procedure assumes that you have already specified the reference position (atom, point, or centroid) and plane that you want to use to define the normal vector.

1.	Select a plane and a reference position (atom, point, or centroid).

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Normal (if not already selected).

4.	(Optional) To enter a name for the normal, click the Name box (if not selected) and enter a name.

5.	Click OK. You see the normal (depicted by an arrow).

See also:

Specifying 3D objects

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


To rotate a 3D structure or query

Use this procedure to rotate a 3D structure or query. To rotate sketch objects, or to rotate a 2D structure or query, click here.

Caution

1.	Click

2.	Select the structure that you want to rotate.

3.	Rotate the structure to the desired orientation.

See also:

To restore the original orientation of a 3D structure or query

To transfer the query back to ISIS/Base


Caution

We strongly recommend that you use only the 3D Rotate tool to rotate 3D structures. If you use the 2D Rotate tool with 3D structures, you might change the coordinates of the structure. Changing the coordinates changes the spatial relationship among atoms in the structure. If you change the spatial relationships among atoms in the structure, you can not:

*	Use the 3D structure as a query in a 3DEXACT search in a remote database.

*	Use the 3D structure to create a submodel query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search.


Specifying a Plane

You can specify a plane in one of two ways.

Click one of the following:

*	To specify a plane through three reference positions.

*	To specify a best-fit plane from four or more reference positions.

See also:

Specifying 3D objects

To edit 3D geometric constraint values

To specify default linearity and planarity constraints

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


To specify a plane through three reference positions

This procedure assumes that you have already drawn the reference positions (atoms, points, or centroids) to include in the plane.

1.	Select three reference positions (atoms, points, or centroids).

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Plane (if not already selected).

4.	(Optional) To enter a name for the plane, click the Name box (if not selected) and enter a name.

5.	Click OK. You see the plane (depicted as a rectangle).

See also:

Specifying 3D objects

To edit 3D geometric constraint values

To specify the default linearity constraint

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


To specify a best-fit plane

This procedure assumes that you have already drawn four or more reference positions (atoms, points, or centroids) to include in the best-fit plane.

1.	Select four or more reference positions (atoms, points, or centroids).

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Plane (if not already selected). You see the default planarity constraint in the RMS Deviation box.

4.	Do one of the following:

*	To specify the default planarity constraint, do nothing at this step.

*	To change the default planarity constraint for the line, highlight the value in the RMS Deviation box (if not already highlighted) and enter a new value.

*	To specify a plane without a planarity constraint, highlight the value in the RMS Deviation box (if not already highlighted) and delete the default value.

5.	(Optional) To enter a name for the plane, click the Name box (if not selected) and enter a name.

6.	Click OK. You see the plane (depicted as a rectangle).

See also:

Specifying 3D objects

To edit 3D geometric constraint values

To specify the default planarity constraint

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


Specifying a Point

You can specify a point in one of two ways.

Click one of the following:

*	To specify a point between two reference positions

*	To specify a point in the direction of a normal

See also:

Specifying 3D objects

To edit 3D geometric constraint values

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


To specify a point between two reference positions

This procedure assumes that you have already drawn the reference positions (atoms, points, or centroids) that specify the point.

1.	Select two reference positions (atoms, points, or centroids).

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Point (if not already selected).

4.	Do one of the following:

*	To specify the distance in Angstroms, click the Distance box (if not already selected) and enter a value between -100 and +100.

*	To specify the distance as a percentage of the distance between the points, click the Distance box (if not already selected) and enter a value between -1000% and +1000% (You must include the % sign).

5.	(Optional) To enter a name for the point, click the Name box (if not selected) and enter a name.

6.	Click OK. You see the point (depicted as a triangle).

See also:

Specifying 3D objects

To edit 3D geometric constraint values

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


To specify a point in the direction of a normal

This procedure assumes that you have already drawn the reference position (atom, point, or centroid) and normal that you want to use.

1.	Select a reference position (atom, point, or centroid) and a normal.

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Point (if not already selected).

4.	Click the Distance box (if not already highlighted) and enter a value between -100 and +100.

5.	(Optional) To enter a name for the point, click the Name box (if not selected) and enter a name.

6.	Click OK. You see the point (depicted as a triangle).

See also:

Specifying 3D objects

To edit 3D geometric constraint values

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


To specify a linearity constraint

This procedure assumes that you have already drawn the reference positions (atoms, points, or centroids) that you want to include in the linearity constraint.

1.	Select three or more reference positions (atoms, points, or centroids).

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Line (if not already selected). You see a default linearity constraint in the RMS Deviation box.

4.	Do one of the following:

*	To specify the default linearity constraint, do nothing at this step.

*	To change the default linearity constraint, highlight the value in the RMS Deviation box (if not already highlighted) and enter the new value.

5.	(Optional) To enter a name for the linearity constraint, click the Name box (if not selected) and enter a name.

6.	Click OK.

See also:

Specifying 3D objects

To specify the default linearity constraint

To edit 3D geometric constraint values

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


To specify a planarity constraint

This procedure assumes that you have already drawn the reference positions (atoms, points, or centroids) that you want to use in the planarity constraint.

1.	Select four or more reference positions (atoms, points, or centroids).

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Plane (if not already selected). You see a default planarity constraint in the RMS Deviation box.

4.	Do one of the following:

*	To specify the default planarity constraint, do nothing at this step.

*	To change the default planarity constraint, highlight the value in the RMS Deviation box (if not already highlighted) and enter the new value.

5.	(Optional) To enter a name for the planarity constraint, click the Name box (if not selected) and enter a name.

6.	Click OK. You see the plane (represented by a rectangle) and planarity constraint.

See also:

Specifying 3D objects

To specify the default planarity constraint

To edit 3D geometric constraint values

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


Drawing an Angle

You can specify an angle constraint in one of three ways.

Click one of the following:

*	To specify an angle from three reference positions.

*	To specify an angle between two lines or normals.

*	To specify an angle between two planes.

See also:

Specifying 3D objects

To edit 3D geometric constraint values

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


To specify an angle from three reference positions

This procedure assumes that you have already created the reference positions (atoms, points or centroids) that you want to use to specify the angle constraint.

1.	Select three reference positions (atoms, points, or centroids).

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Angle (if not already selected). You see the default angle constraint in the Range box.

4.	(Optional) To change the default angle constraint, highlight the values in the Range box (if not already highlighted) and enter a range of values between 0 and 180.

5.	(Optional) To enter a name for the angle, click the Name box (if not selected) and enter a name.

6.	Click OK. You see the angle (depicted as an arc between two lines).

See also:

Specifying 3D objects

To edit 3D geometric constraint values

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


To specify an angle between two planes

This procedure assumes that you have already drawn the planes that you want to use to specify the angle constraint.

1.	Select two planes.

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Angle (if not already selected). You see the default angle constraint in the Range box.

4.	(Optional) To change the default angle constraint, highlight the values in the Range box (if not already highlighted) and enter a range of values between 0 and 90.

5.	(Optional) To enter a name for the angle, click the Name box (if not selected) and enter a name.

6.	Click OK. You see the angle (depicted as an arc between two lines).

See also:

Specifying 3D objects

To edit 3D geometric constraint values

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


To specify an angle between two lines
To specify an angle between two lines or normals

This procedure assumes that you have already drawn the lines or normals that you want to use to specify the angle constraint.

1.	Select two lines or normals.

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Angle (if not already selected). You see the default angle constraint in the Range box.

4.	(Optional) To change the default angle constraint, highlight the values in the Range box (if not already highlighted) and enter a range of values between 0 and 90.

5.	(Optional) To enter a name for the angle, click the Name box (if not selected) and enter a name.

6.	Click OK. You see the angle (depicted as an arc between two lines).

See also:

Specifying 3D objects

To edit 3D geometric constraint values

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


To specify an atom data constraint

This procedure assumes that you know the name of the 3D atom field that contains the data that you want. If you are not sure which 3D atom field contains the data that you want, print or view a list of database fields.

1.	Select one atom.

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Atom (if not already selected).

4.	Click the Field box and enter the name of the 3D atom field that is associated with the atom data.

5.	Click the Query box (if not selected) and enter a value or a text/numeric query.

6.	Click OK. You see the atom with the field name and query.

See also:

To rotate a 3D structure or query

To edit 3D data constraints

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


To specify an atom-pair data constraint

This procedure assumes that you know the name of the 3D atom-pair field that contains the data that you want. If you are not sure which 3D atom-pair field contains the data that you want, print or view a list of database fields.

1.	Select two atoms.

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Atom-Pair (if not already selected).

4.	Click the Field box and enter the name of the 3D atom-pair field that is associated with the atom-pair data.

5.	Click the Query box (if not selected) and enter a value or a text/numeric query.

6.	Click OK. You see the two atoms with the field name and query.

See also:

To rotate a 3D structure or query

To edit 3D data constraints

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


Printing or Viewing a List of Your Database Fields

Click here for step-by-step instructions

Print or view a list of database fields to obtain the name of the atom or atom-pair field that you want to use in your query.

It is important that you print or view a list of your database fields to understand the database structure. Do not make assumptions about your database structure based on experience with other MDL programs. For example, a flat database in MACCS-II is hierarchical in ISIS.

We recommend that you print a list of database fields, because it is difficult to see the relationship of fields when scrolling through a list box.


Specifying a Distance Constraint

You can specify a distance constraint in one of three ways.

Click one of the following:

*	To specify a distance between two reference positions

*	To specify a distance from a reference position to a line or normal

*	To specify a distance from a reference position to a plane

See also:

Specifying 3D objects

To edit 3D geometric constraint values

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


To specify a distance between two reference positions

This procedure assumes that you have already drawn the reference positions (atoms, points, or centroids) that you want to use to specify the distance constraint.

1.	Select two reference positions (atoms, points, or centroids).

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Distance (if not already selected). You see the default distance constraint in the Range box.

4.	(Optional) To change the default distance constraint, highlight the values in the Range box (if not already highlighted) and enter a range of values between -100 and +100.

5.	(Optional) To enter a name for the distance constraint, click the Name box (if not selected) and enter a name.

6.	Click OK.

See also:

Specifying 3D objects

To edit 3D geometric constraint values

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


To specify a distance between a reference position and a line or normal

This procedure assumes that you have already drawn the reference position (atom, point, or centroid) and line or normal that you want to use to specify the distance constraint.

1.	Select a reference position (atoms, points, or centroids) and a line or normal.

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Distance (if not already selected). You see the default distance constraint in the Range box.

4.	(Optional) To change the default distance constraint, highlight the values in the Range box (if not already highlighted) and enter a range of values between -100 and +100.

5.	(Optional) To enter a name for the distance constraint, click the Name box (if not selected) and enter a name.

6.	Click OK.

See also:

Specifying 3D objects

To edit 3D geometric constraint values

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


To specify a distance between a reference position and a plane

This procedure assumes that you have already drawn the reference position (atom, point, or centroid) and plane that you want to use to specify the distance constraint.

1.	Select a reference position (atoms, points, or centroids) and a plane.

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Distance (if not already selected). You see the default distance constraint in the Range box.

4.	(Optional) To change the default distance constraint, highlight the values in the Range box (if not already highlighted) and enter a range of values between -100 and +100.

5.	(Optional) To enter a name for the distance constraint, click the Name box (if not selected) and enter a name.

6.	Click OK.

See also:

Specifying 3D objects

To edit 3D geometric constraint values

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


To specify a dihedral angle constraint

This procedure assumes that you have already drawn the reference positions (atoms, points or centroids) that you want to use for the dihedral angle constraint.

1.	Select the four reference positions (atoms, points, or centroids) that specify the dihedral angle.

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Dihedral (if not already selected). You see the default angle constraint.

4.	(Optional) To change the default angle constraint, highlight the values in the Range box (if not already highlighted) and enter a range of values between -180 and +180 degrees.

Note on angle direction

5.	(Optional) To enter a name for the angle, click the Name box (if not selected) and enter a name.

6.	Click OK. You see the angle.

See also:

Specifying 3D objects

To edit 3D geometric constraint values

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


Note on Angle Direction

A positive value defines the angle in a clockwise direction, starting with the plane that contains the points 1, 2, and 3. A negative value defines the angle in a counterclockwise direction.

If you do not specify a plus or minus sign, the direction is undefined.


To specify an exclusion sphere constraint

This procedure assumes that you have already drawn the reference position (atom, point, or centroid) that you want at the center of the exclusion sphere.

1.	Select one reference position (atom, point, or centroid).

2.	Choose Chemistry > 3D > Create. You see a dialog box.

Keyboard Equivalent

3.	Click the Type box and choose Exclusion Sphere (if not already selected).

4.	Click the Radius box (if not already selected) and enter a radius between 0.1 and 20 Angstroms.

5.	(Optional) To enter a name for the exclusion sphere, click the Name box (if not selected) and enter a name.

6.	Do one of the following:

*	To allow unconnected atoms that are not part of the query (for example, the counterions of salts) within the exclusion sphere, you require this setting: Ignore unconnected atoms in exclusion sphere.

*	To exclude unconnected atoms from the exclusion sphere, you require this setting: Ignore unconnected atoms in exclusion sphere.

7.	Click OK. You see the exclusion sphere.

8.	(Optional) Allow other atoms in the query within the exclusion sphere.

See also:

Specifying 3D objects

To edit 3D geometric constraint values

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints

To transfer the query back to ISIS/Base


Allowing Other Atoms in the Query Within the Exclusion Sphere

Click here for step-by-step instructions

By default, an exclusion sphere excludes all atoms except the atom at the center of the sphere. However, you might want to allow specific atoms from the query within the volume of the exclusion sphere. In the following example, a carboxyl group that matches a carboxyl group in the query is located within an exclusion sphere on a retrieved structure (query atoms and bonds are in boldface):


To allow other query atoms within the exclusion sphere

This procedure assumes that you want to edit the basis of an exclusion sphere to allow other atoms in the query within the volume of the exclusion sphere. Example

1.	Select the exclusion sphere.

2.	Choose Chemistry > 3D > Edit Basis. You see the 3D pointer.

3.	Click the atoms that you want to allow within the exclusion sphere.

4.	Choose Chemistry > 3D > Set Basis.

5.	(Optional) To view the additional atom(s) that you specified to be allowed within the exclusion sphere, select the exclusion sphere. Then, choose Chemistry > 3D > Select Basis. The allowed atoms are highlighted.

See also:

To transfer the query back to ISIS/Base


Example

The following example shows a query overlaid on a 3D structure. You see the carboxyl group that corresponds to the carboxyl group on the query within the volume of the exclusion sphere (Atoms and bonds that correspond to atoms and bonds on the query are in boldface):


To specify lone pairs

In a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, you can specify that lone-pair electrons must appear at specific sites on the structures that you retrieve. To do this, you draw lone pairs on your query. For example:

Use this procedure to add lone pairs to your query.

1.	Click

2.	Click the atom at which you want to specify a lone pair. You see a bond sprout at the site.

3.	Type LP and press the Return key. You see LP at the end of the bond that you created in Step 2.

See also:

To transfer the query back to ISIS/Base


To create submodel components

Use this procedure to create the submodel components of a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search.

1.	Transfer to ISIS/Base.

2.	Do one of the following:

*	Retrieve a 3D structure from the database.

*	Import a 3D structure from a molfile.

*	Restore a 3D structure that you previously saved as an object in the database.

3.	Transfer the 3D structure to ISIS/Draw.

4.	Delete the parts of the structure that are not part of the submodel. If you accidentally delete atoms that you want, use Edit > Undo to correct your mistake.

Caution

5.	Select the atoms that you want to spatially maintain in a fixed position.

6.	Choose Chemistry > 3D > Fix Position. You see an (F) at each atom that you selected.

See also:

To add fixed atoms to the submodel query

To delete fixed atoms from the submodel query

To rotate a 3D structure or query

To transfer the query back to ISIS/Base


To add additional fixed atom positions to a submodel query

Use this procedure to add additional fixed-atom positions to a submodel query that already contains fixed atoms.

1.	Select the atoms that you want to maintain in a spatially fixed position.

2.	Choose Chemistry > 3D > Fix Position. You see an (F) at each atom that you selected.

See also:

To rotate a 3D structure or query


To delete fixed atoms from a submodel query

Use this procedure to remove one or more fixed-atoms from a submodel query.

1.	Select the fixed atoms (F) that you want to remove from the submodel query.

2.	Choose Chemistry > 3D > Fix Position.

See also:

To rotate a 3D structure or query


To construct a query using default settings

&&&(Question: This procedure is irrelevant. It is an option within each 3D drawing option?)


To view the basis of a 3D object or geometric constraint

Use this procedure to view all the reference positions (atoms, points, or centroids) and other 3D objects that comprise a 3D object or constraint (called the basis of the 3D object or constraint).

1.	Select the 3D object or constraint.

2.	Choose Chemistry > 3D > Select Basis. The reference positions and 3D objects are highlighted.


To edit 3D geometric constraint values

Use this procedure to edit the value and name of a 3D geometric constraint.

1.	Select the 3D geometric constraint that you want to edit.

2.	Double-click the selected 3D geometric constraint.

3.	Click the 3D tab (if not selected).

4.	Click the box that contains the value or range (if not already selected) and enter the new value.

5.	(Optional) To change the name of the 3D constraint, click the Name box (if not selected) and enter the new description.

6.	(Optional) For exclusion spheres, do one of the following:

*	To allow unconnected atoms that are not part of the query (such as the counterions of salts) within the exclusion sphere, you require this setting: Ignore unconnected atoms in exclusion sphere.

*	To exclude unconnected atoms within the radius of the exclusion sphere, you require this setting: Ignore unconnected atoms in exclusion sphere.

7.	Click OK.

See also:

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints


Specifying Default Values of 3D Geometric Constraints

When you create a 3D geometric constraint, ISIS provides a default value for that constraint. ISIS calculates the default value from values that you specify in ISIS/Draw Settings. To change the default constraint value, change the corresponding value in Settings.

Click one of the following:

*	Specify the default value for distance constraints.

*	Specify the default value for angle and dihedral angle constraints.

*	Specify the RMS Deviation value for linearity and planarity constraints.


To specify the default value for distance constraints

Use this procedure to change the Distances value (in ISIS/Draw Settings) that ISIS uses to calculate the default range for distance constraints. For information on how ISIS calculates default constraints from the Distances value in ISIS/Draw Settings, click here.

1.	Choose Options > Settings.

2.	Click the 3D tab (if not selected).

3.	Click the Distances box and enter a distance.

4.	Click the box that corresponds to the units for Distances and choose a unit.

5.	Click OK.


To specify the default value for angle or dihedral angle constraints

Use this procedure to change the Angles value (in ISIS/Draw Settings) that ISIS uses to calculate the default range for angles and dihedral angles. For information on how ISIS calculates default constraints from the Angles value in ISIS/Draw Settings, click here.

1.	Choose Options > Settings.

2.	Click the 3D tab (if not selected).

3.	Click the Angles, dihedral angles box and enter a distance.

4.	Click the box that corresponds to the units for Angles and choose a unit.

5.	Click OK.


To specify the default value for linearity and planarity constraints

Use this procedure to change the RMS Deviation value in ISIS/Draw Settings, from which ISIS calculates default values for linearity and planarity constraints. For information on how ISIS calculates default constraints from the RMS Deviation value in ISIS/Draw Settings, click here.

1.	Choose Options > Settings.

2.	Click the 3D tab (if not selected).

3.	Click the RMS Deviation box and enter a distance.

4.	Click the box that corresponds to the units for RMS Deviation and choose a unit.

5.	Click OK.


To remove 3D query features

Use this procedure to remove 3D query features (3D objects, 3D constraints, and fixed atoms) from a structure.

1.	Select the 3D query features that you want to delete.

2.	Choose Chemistry > 3D > Clear 3D.

Alternative method for 3D objects and constraints only


Alternative method

Select the 3D objects and constraints that you want to delete, then choose Edit > Clear (or press the Backspace key).

Note: You can not use this method to remove the (F) label from fixed atoms. To remove the label without deleting the fixed atom, select the atom, then choose Chemistry > 3D > Fix Position.


To edit 3D data constraint values

Use this procedure to edit the field and constraint (value or text/numeric query) of a 3D data constraint.

1.	Select the 3D data constraint that you want to edit.

2.	Double-click the selected 3D data constraint.

3.	Click the 3D tab (if not selected).

4.	(Optional) To change the field, click the Field box (if not already selected) and enter the name of the new field.

5.	(Optional) To change the constraint, click the Query box (if not selected) and enter a value or a text/numeric query.

6.	Click OK.


To edit 3D objects

Use this procedure to add or subtract reference positions (atoms, points, or centroids) from 3D objects.

1.	Select the 3D object that you want to edit.

2.	Choose Chemistry > 3D > Edit Basis. The reference positions (atoms, points, or centroids) that comprise the 3D object are highlighted, and you see the 3D pointer.

3.	Do one of the following:

*	To add reference positions to the object, click the reference positions that you want to add. The reference positions highlight.

*	To subtract reference positions from the object, click the highlighted reference positions that you want to subtract. The reference positions are deselected.

4.	Choose Chemistry > 3D > Set Basis.

See also:

To rotate a 3D structure or query

Tips for selecting 3D objects and constraints


Tips for Selecting 3D Objects and Constraints

*	When you select objects, ISIS prefers atoms, points, and centroids over other 3D objects and constraints. This allows you to easily select atoms, points, and centroids when other 3D objects overlap.

*	When you create a 3D object or constraint, ISIS ignores objects that are not valid basis objects, such as bonds, distances, or rectangles. This allows you to select all or part of a structure (including bonds and atoms) to create a 3D object or constraint.

*	Select overlapping objects by cycling through them. To do this, press and hold down the Alt (Mac=Option) key and click the left mouse button as needed.

*	For more information on selecting and deselecting objects, see Section 5.5 of the ISIS/Draw "Quick Start".


To restore the original orientation of a 3D structure or query

This procedure assumes that you have a 3D structure or substructure in the current ISIS/Draw window, and that you have rotated the structure to a different orientation.

1.	Select the 3D structure or substructure that you want to restore to its original orientation.

2.	Choose Chemistry > 3D > Restore Coordinates.


Creating Reaction Queries

A reaction query is a structure (all or part of a reaction, a reaction component, or portions of reaction components) that you use to search a database. To draw a reaction query, you first draw the structure that you want to find, then add the stereochemistry restrictions of your choice, and then add additional restrictions on atoms and/or bonds (called query features). If your reaction query is a reaction, you can add atom-atom maps to define the correspondence between the atoms in the reactants and the atoms in the products.

Note: You create a reaction query in ISIS/Draw, enter it into the form in ISIS/Base, and then conduct the search.

Click one of the following:

*	Drawing a reaction with ISIS/Draw "Quick Start"

*	Specifying stereochemistry on a reaction component

*	Specifying query features on a reaction component

*	Specifying query features on a reaction

*	Specifying atom-atom maps on a reaction


Specifying Query Features on a Reaction Component

A query feature on a reaction component is a restriction on an atom and/or a bond that specifies the retrieval of certain types of reaction records from the database.

Click one of the following:

*	Specifying atom query features

*	Specifying bond query features

*	Specifying Rgroup query features


Specifying Query Features on a Reaction

A query feature on a reaction is a restriction on the reacting centers or on the spatial arrangement of stereo bonds or on atoms that specifies the retrieval of certain types of reaction records from the database.

Note: These query features are solely for searching a remote database and cannot be used to search a local database.

Click one of the following:

*	To specify reacting center query features

*	To specify stereo bond query features

*	To specify exact atom query features


Specifying an Atom-Atom Map on a Reaction

How To Atom-Atom Map: Automatically or Manually

Atom-Atom Mapping Guidelines

For remote searching only: An atom-atom map on the reaction components in a query specifies exactly which atoms in the reactants correspond to the atoms in the products. You can specify the atoms that must (or must not) change. For example, the following query allows you to see exactly which C-O bond is cleaved to form the product:

You can atom-atom map automatically or manually. If you map manually, you choose your own correspondence between the atoms in the reactants and the atoms in the products.


Specifying an Atom-Atom Map on a Reaction

An atom-atom map on the reaction components in a query specifies exactly which atoms in the reactants correspond to the atoms in the products. You can specify the atoms that must (or must not) change. For example, the following query allows you to see exactly which C-O bond is cleaved to form the product:


To atom-atom map manually

Use this procedure to manually map a pair of atoms in ISIS/Draw.

1.	Click

ISIS/Draw checks if the reaction is valid for mapping, and that there is only one reaction present in the sketch. If the reaction is not valid for mapping, or if there are more than one reaction, you see a message that tells you to use Chem Inspector.

2.	Click an atom in a reactant, and then click the corresponding atom in the product. The atom numbers (in the form .1.) display next to the atoms.

3.	(Optional) To map a one-to-many relationship, first click an atom that is marked with an existing atom map. Then, click the corresponding atom.

Note: You cannot map a many-to-many relationship.

See also:

To remove atom-atom mapping

To remap a reaction

To hide atom-atom maps in ISIS/Draw

To display atom-atom maps in ISIS/Draw

To display atom-atom maps in ISIS/Base

To transfer the query back to ISIS/Base


To atom-atom map automatically
To atom-atom map automatically (automap)

Use this procedure to map all atoms in a reaction automatically. (Automatic atom-atom mapping is called automapping.) This procedure assumes that you have a reaction in a box or table cell on the form in ISIS/Base.

1.	Choose Search > AutoMap Rxn. You see the atom-atom maps in the reaction.

2.	Visually inspect the atom-atom map to be certain that the reactants and products are mapped correctly.

Note: If your atom-atom map is incorrect: In ISISI/Draw, remove the atom-atom maps and then manually atom-atom map the atoms surrounding the reacting center bonds (typically two to three atoms per structure). Repeat Steps 1 and 2 to complete the mapping process.

See also:

Atom-Atom Mapping Guidelines

To remove atom-atom mapping

To hide atom-atom maps in ISIS/Draw

To display atom-atom maps in ISIS/Draw

To display atom-atom maps in ISIS/Base

To atom-atom map manually

To transfer the query back to ISIS/Base


To remap the atoms in a reaction

Use this procedure to remap the atoms in a reaction after you have removed the atom-atom map.

1.	In ISIS/Draw, click

2.	Click an atom in the reactant, and then click the corresponding atom in the product. The atom numbers (in the form .1.) display next to the atoms.

3.	Repeat Step 2 on the atoms surrounding the reacting center bonds (typically two to three atoms per structure).

4.	Transfer the query back to ISIS/Base

5.	Choose Search > AutoMap Rxn. You see the mapped atoms in the reaction.

6.	Visually inspect the atom-atom map to be certain that the reactants and products are mapped correctly.

See also:

To remove atom-atom mapping

To hide atom-atom maps

To display atom-atom maps


To remove atom-atom mapping

Use this procedure to delete any existing atom-atom map numbers.

1.	Click [image]. ISIS/Draw displays any existing atom-map numbers, reacting centers, and inversion/retention marks.

2.	(Optional) To remove all atom maps, reacting centers, and inversion/retention marks, select the entire reaction and click it.

3.	Do one of the following:

*	To delete a one-to-one atom map: Click a single atom. Both atom maps are deleted.

*	To delete a one-to-many atom map: Click the one atom on the opposite side of the reaction that contains the many correspondence. All corresponding atom maps are deleted.

Note: Any inversion/retention marks associated with the atom maps are also deleted.

4.	(Optional) To clear a reacting center from a bond, click the bond.


To hide atom-atom maps in ISIS/Draw

Use this procedure to hide any existing atom-atom maps in ISIS/Draw when not using the [image] and [image] tools.

Note: When you use these tools, atom-atom maps are always displayed.

1.	You require Show Atom maps on the Options menu. If you see [image], choose the command, otherwise do nothing at this step.


To display atom-atom maps in ISIS/Draw

Use this procedure to display any existing atom-atom maps in ISIS/Draw when not using the [image] and [image] tools.

Note: When you use these tools, atom-atom maps are always displayed.

1.	You require [image] Show Atom maps on the Options menu. If you see [image], do nothing at this step; otherwise choose the command.


To specify reacting center query features

This procedure is for these remote searches only. Use this procedure to mark the reacting centers on bonds.

1.	Click

ISIS/Draw checks if the reaction is valid for mapping, and that there is only one reaction present in the sketch. If the reaction is not valid for mapping, or if there are more than one reaction, you see a message that tells you to use Chem Inspector.

2.	Click the bond on which to mark a reacting center. Each time you click the bond, you see a different reacting center mark. Keep clicking the bond until you see the desired reacting center mark:

*	X: The bond must not change

*	#: The bond changes unspecifically (can form, break, or change its bond type)

*	|: The bond changes its bond type

*	||: The bond is either formed or broken

*	|||: The bond s either formed or broken and changes its bond type

See also:

Specifying an Atom-Atom Map on a Reaction

To transfer the query back to ISIS/Base


To specify exact atom query features

This procedure is for these remote searches only. Use this procedure to mark all atoms that you want to change exactly as you specify them in the reactants and products.

Note: To use this query feature, your query must be a reaction that contains at least one reactant and at least one product.

1.	You must atom-atom map the reaction.

2.	Select the atoms that you want to mark.

3.	Choose Object > Edit Atom.

4.	Click the Query Atom tab.

5.	To specify that you want the marked atoms to change exactly, you require this setting: Exact change [reaction].

6.	Click OK. The selected atoms are marked with .ext.


Reacting Center

A reacting center is a bond that changes in the reactant and in the product. Markings on the bonds of products and reactants specify exactly which bonds change (or do not change) in the reaction.


To remove reacting centers

Use this procedure to remove reacting centers from bonds.

1.	Click

ISIS/Draw checks if the reaction is valid for mapping, and that there is only one reaction present in the sketch. If the reaction is not valid for mapping, or if there are more than one reaction, you see a message that tells you to use Chem Inspector.

2.	Click the bond that you want to remove the reacting center from.


To specify stereo bond query features

This procedure is for these remote searches only. Use this procedure to specify inversion and retention marks on atoms.

1.	Select the atom(s) that you want to mark.

2.	Choose Object > Edit Atom.

3.	Click the Query Atom tab.

4.	Click the Reaction Stereo box, and then choose Inversion or Retention.

5.	Click OK. The selected atom(s) are marked with .inv. or .ret.

See also:

To remove inversions and retentions

To transfer the query back to ISIS/Base


To remove inversions and retentions

Use this procedure to remove inversion and retention marks from atoms.

1.	Select the atom(s) that you want to remove the inversion or retention marks from.

2.	Choose Object > Edit Atom.

3.	Click the Query Atom tab.

4.	Click the Reaction Stereo box, and then choose Off.

5.	Click OK.


Manipulating Objects

Aligning Objects

To resize objects

To resize to the standard bond length

To rotate an object

To rotate a structure so that a specific bond is horizontal or vertical

To rotate a 3D structure or query

To move objects with the arrow keys

To group objects

To ungroup objects

To flip objects

To crop objects

To uncrop objects


To resize objects

Use this procedure to resize one or more objects so that they keep their aspect (width-to-height) ratio. You can resize objects using any of the three Select tools, and the 2D Rotate tool.

1.	Select the object.

2.	Move the cursor over one of the four corner handles.

Caution: If you select a non-corner handle, the object might become distorted.

3.	Drag the mouse.

4.	If you are resizing the object using either of the Rotate tools, press and hold down the Ctrl (Mac=Command) key. (You can also press the key after you start to move the structure.)

5.	Release the mouse button when the object is the size that you want.

6.	If you resized all molecules in a sketch, you see a dialog box where you specify if you want your settings to reflect the resizing. Do one of the following:

*	To have the settings modified so that any new molecules that you draw are drawn in the same scale, click Yes.

*	To leave your setting as they are, click No.


To resize to the standard bond length

Use this procedure to resize structures to the standard bond length. You need to select every atom and bond in the structure that you want to resize.

1.	Select one or more structures to resize.

2.	Choose Object > Scale > Standard Bond Length. The selected structure(s) resize to the standard bond length specified in the Settings -- Chemical Drawing tab.


To rotate an object

Use this procedure to rotate a 2D object around a pivot point. Rounded boxes, arcs, and text do not rotate about a point. Objects such as boxes and polygons do not rotate as smoothly as structures.

To rotate a 3D structure or query, click here.

1.	Select the object to rotate.

2.	Click [image]. You see crosshairs at the pivot point (the center of the object).

Note: If you selected a chemical group to rotate, the pivot point is placed on the atom that is connected to the chemical group.

3.	(Optional) Drag the pivot point to the place about which you want to rotate the object.

4.	Release the mouse button to fix the pivot point.

5.	Move the pointer over any selection handle.

6.	Drag the mouse in a circular motion. The object rotates around the pivot point.

7.	Release the mouse button when the object looks the way you want.


To rotate a structure so that a specific bond is horizontal or vertical

Use this procedure to rotate an entire 2D structure so that one selected bond is horizontal or vertical. Example

1.	Select one bond that you want to rotate horizontally or vertically.

2.	Do one of the following:

*	To rotate the structure so that the selected bond is horizontal, choose Object > Rotate > Bond to Horizontal.

*	To rotate the structure so that the selected bond is vertical, choose Object > Rotate > Bond to Vertical.

The entire structure attached to the selected bond is rotated so that the bond is horizontal or vertical.


Example


Aligning Objects

To align multiple objects horizontally or vertically

To align multiple objects to a line

To align multiple molecules by individual atoms

Note: You can use any of these procedures to align reactions.

For examples of how to align objects into rows and columns, see Drawing Sketch Tables.


To align multiple objects horizontally or vertically

Use this procedure to align objects, entire reactions, or molecules horizontally or vertically.

1.	Select the objects to align.

2.	Choose Object > Align.

3.	Do one of the following:

*	To align objects horizontally: Click Tops, Top/Bottom Centers, or Bottoms in the Horizontal box. Click None in the Vertical box.

*	To align objects vertically: Click Left Sides, Left/Right Centers, or Right Sides in the Vertical box. Click None in the Horizontal box.

4.	(Optional) To space the selected objects evenly, you require this setting: Space Evenly.

Note: If you specified None in both the Horizontal and Vertical boxes, Space Evenly is not available.

5.	Click OK. The objects are aligned according to your choice.

6.	(Optional) If you do not like the way the objects align, choose Edit > Undo.

For examples of how to align objects into rows and columns, see Drawing Sketch Tables.


To align multiple objects to a line

Use this procedure to align objects, entire reactions, or molecules to a new or existing line. This line can be at any angle.

1.	Select the objects to align.

2.	Choose Object > Align.

3.	Do one of the following:

*	To align the sides of the objects: Click Left Sides, Left/Right Centers, or Right Sides in the Vertical box. Click None in the Horizontal box.

*	To align the tops, bottoms, or centers of the objects: Click Tops, Top/Bottom Centers, or Bottoms in the Horizontal box. Click None in the Vertical box.

4.	To align the selected objects, you require this setting: Align To a Line.

Note: If you specified None in both the Horizontal and Vertical boxes, Align To a Line is not available.

5.	Click OK. Your mouse pointer becomes a special pointer.

6.	Drag the pointer to draw the line. To align objects to an existing line, drag the pointer over the existing line.

7.	Release the mouse button.


To align multiple molecules by individual atoms

Use this procedure to align molecules by selected atoms. When you select one atom from each molecule and align them, the entire molecules are shifted. Example

1.	Select one atom in each molecule that you want to align.

2.	Choose Object > Align.

3.	Do one of the following:

*	To align molecules horizontally: Click Tops, Top/Bottom Centers, or Bottoms in the Horizontal box. Click None in the Vertical box.

*	To align molecules vertically: Click Left Sides, Left/Right Centers, or Right Sides in the Vertical box. Click None in the Horizontal box.

4.	Click OK. The molecules are aligned according to your choice.


Example


To group objects

Use this procedure to group multiple objects. You must select multiple objects to use the Group command.

1.	Select the objects that you want to group.

2.	Choose Object > Group. The objects are combined into one object, and you see one set of selection handles.

Note: (1) If you group solely molecules together, you can select individual bonds and atoms using the Select or Lasso tools. (2) A grouped object that contains solely molecules can be exported to a molfile or registered into a database using ISIS/Base. The object retains its chemical significance. (3) If you group 3D models with other objects, the original model coordinates will be lost.


Group

When you group multiple objects in ISIS/Draw or ISIS/Base, you combine them into one object. You can then apply changes (such as resizing) to all group members at the same time. When you click anywhere in the group, you see eight selection handles that indicate that the entire group is selected.


To ungroup objects

Use this procedure to ungroup objects that have been grouped together.

1.	Select the grouped object.

2.	Choose Object > Ungroup.


Snap

In ISIS/Draw, Snap joins objects together when you draw them. It ensures that objects are accurately joined and not just close to each other. Snap places a handle at a join to indicate when the join is made.


To crop objects

Use this procedure to crop an object. To crop multiple objects, group them first.

1.	Select the object.

2.	Choose Object > Crop. The selection handles are joined by a box-shaped dashed line.

3.	Move the mouse over any handle.

4.	Drag the selection handle inward. The part of the object still within the dashed line is retained. The part outside is cropped.

5.	Click an empty area.


To uncrop objects

Use this procedure to uncrop an object that was previously cropped. This reveals the part of the object that was previously hidden.

1.	Select the cropped object.

2.	Choose Object > Crop. The selection handles are joined by a box-shaped dashed line.

3.	Move the mouse over any handle.

4.	Drag the selection handle outwards. The part of the object that was hidden is now displayed.

5.	Click an empty area.


Crop

In ISIS/Draw, to crop an object is to hide unwanted parts, such as corners or sides. When you print or display the sketch, the hidden parts are not visible. Note that the unwanted parts are not actually deleted.


To flip objects

Use this procedure to flip one or more objects:

1.	Select one or more objects to flip.

2.	Choose Object > Flip > Horizontal or Object > Flip > Vertical. The object(s) flip to a new position horizontal or vertical to the current position.


Flip

In ISIS/Draw, to flip an object is to move it about a vertical or horizontal axis.


ISIS/Draw File Basics

To create a new sketch file

To save a new sketch file

To open an existing sketch file

To save an existing sketch file

To insert the contents of a file into a sketch

To close a sketch file

To print a sketch

To exit ISIS/Draw

To import data into ISIS/Draw

To export data from ISIS/Draw


To create a new sketch file

1.	Choose File > New. You see a new, untitled ISIS/Draw window.


To save a new sketch file

Use this procedure to save a new sketch file for the first time.

1.	Choose File > Save As.

2.	Navigate to the disk and directory or folder where you want to save the new sketch file.

3.	Enter a name for the file. PC Only: The file name must end with the .SKC extension.

4.	(Optional) To save a name and comment with the file, click Save/Name Comments and then enter a name and a comment. Then, click OK.

5.	(Optional) To save the ISIS/Draw file with the current default settings, you require this setting: Save Settings.

6.	Click OK (Mac=Save).


To open an existing sketch file

Use this procedure to open a sketch file that has already been saved on your disk.

1.	Choose File > Open.

2.	Navigate to the disk and directory or folder that contains the sketch file to open.

3.	Highlight the name of the ISIS/Draw sketch file to open.

4.	(Optional) To display any names and comments that might have been saved with the selected ISIS/Draw file, click Read Name/Comments. Then, click OK.

5.	(Optional) To display the selected ISIS/Draw file with the default settings the file had when it was saved, you require this setting: Use Settings.

6.	Click OK (Mac=Open).


To save an existing sketch file

Use this procedure to save a sketch file that you have previously saved. Save your work at regular intervals.

1.	Choose File > Save.

Caution: The Save command overwrites any file with the same name that is in the same directory or folder. If you do not want to do this, choose File > Save As and give the file a different name.


To insert the contents of a file into a sketch

Use this procedure to insert the contents of a selected sketch file directly into the active window.

1.	Choose File > Insert.

2.	Navigate to the disk and directory or folder that contains the sketch file to insert.

3.	Highlight the name of the ISIS/Draw file to insert.

4.	(Optional) To display any names and comments that might have been saved with the selected ISIS/Draw file, click Read Name/Comments. Then, click OK.

5.	(Optional) To display the selected ISIS/Draw file with the default settings the file had when it was saved, you require this setting: Use Settings.

6.	Click OK (Mac=Open).


To print a sketch

Use this procedure to print the contents of the active window. Before you can print, make sure that:

*	The printer is correctly connected to your computer or network.

*	The printer is correctly configured and switched on.

*	Your computer is correctly configured so that it recognizes the printer.

1.	From the active window, choose File > Print Setup on the PC or File > Page Setup on the Macintosh.

2.	Specify the paper size and page orientation required for printing, along with other printing options. Consult your system documentation for information on printing options.

3.	(Optional) To view the page as it will look when printed, use Print Preview.

4.	Choose File > Print.

Note: OSF/Motif users, see your System Administrator for further information on how to print.


To exit ISIS/Draw

1.	Choose File > Exit on the PC or File > Quit on the Macintosh.

2.	If you have an open window that contains work that you have not saved, a dialog asks if you want to save the changes. Do one of the following:

*	If this is a new file and you want to save your work, click Yes. You see the Save As dialog box. Follow the procedure To save a new sketch file, starting at Step 2.

*	If this is an existing file that you have modified and you want to save your work, click Yes.

*	If you do not want to save your work, click No.

*	If you decide that you do not want to exit ISIS/Draw, click Cancel.

ISIS/Draw displays the next open window that contain unsaved work, if one exists.


To close a sketch file

1.	Choose File > Close.

2.	If the open window contain work that you have not saved, a dialog asks if you want to save the changes. Do one of the following:

*	If this is a new file and you want to save your work, click Yes. You see the Save As dialog box. Follow the procedure To save a new sketch file, starting at Step 2.

*	If this is an existing file that you have modified and you want to save your work, click Yes.

*	If you do not want to save your work, click No.

*	If you decide that you do not want to close the sketch, click Cancel.


Drawing With the Keyboard

To draw or sprout a bond

To draw a ring

To add atom symbols

To add isotopes

To add atom charges

To type predefined abbreviated structures


To draw or sprout a bond using the keyboard

1.	Do one of the following

*	Select the atom from which to sprout the new bond.

*	Click an empty area to start a new structure.

2.	Enter + followed by an atom symbol. For example, +N.

3.	Press the Return key. You see a standard-length single bond sprout from the selected atom or from where you clicked in the drawing area.


To draw a ring using the keyboard

Use this procedure to use the keyboard to draw rings that have from 3 to 21 atoms. For information on how to use the keyboard to draw rings that have more than 21 atoms, click here.

Note: You need to perform Steps 1-5 only once.

1.	Choose Options > Settings.

2.	Click the General tab.

3.	You require this setting: Abbreviate typed-in templates.

4.	Click OK.

5.	To save your modifications, click Save.

6.	Click [image] or

7.	Do one of the following:

*	Select one or more atoms where you want to place the ring.

*	Click an empty area where you want to place the ring.

8.	Type ringn, where n is a number from 3 to 21 (not including 17 or 19). For example, type ring7 to place a seven-membered ring on the selected atom(s).

9.	Press the Return key.


To draw a ring using the keyboard

Use this procedure to draw rings with more than 21 atoms.

1.	Click an empty area to start a new ring.

2.	Enter [ followed by a number greater than 3 representing the number of bonds in the ring, followed by r. For example, enter [24r to draw a ring with 24 atoms.

Note: The left bracket is required.

3.	Press the Return key.


To add atom symbols using the keyboard

Use this procedure to add atom symbols using the keyboard. You can add multiple non-hydrogen atoms to a sprouted bond. For example, you can add CN or PO4 or Na+ to a sprouted bond.

Note: If you create a search query in which you enter the symbol H with another, non-hydrogen atom (such as OH), the hydrogen is implicit. To retrieve the correct search results, always use explicit (rather than implicit) hydrogens in your query. To create an explicit hydrogen, click here.

For information on displaying hydrogens, click here.

1.	Select one or more atoms where you want to place the atom symbol.

2.	Enter an atom symbol.

3.	Press the Return key. The atom symbol is placed on the selected atom(s).


To display hydrogens

Use this procedure to display hydrogens for all the terminal carbon atoms and heteroatoms in a structure. These hydrogens are implicit.

Caution: ISIS/Base does not recognize implicit hydrogens in a search query, even if you show them. Thus, to retrieve the correct search results, always use explicit hydrogens in your search query. To create an explicit hydrogen, click here.

Examples of Implicit and Explicit Hydrogens

1.	Choose Options > Settings.

2.	Click the Chemical Drawing tab.

3.	Click the Show hydrogen labels box and choose On All.

4.	(Optional) To save your modifications to the currently-open settings file, click Save.

5.	Click OK.


To add isotopes using the keyboard

Use this procedure to enter isotopes and their atom symbols using the keyboard.

1.	Select one or more atoms where you want to place the isotope.

2.	Enter the isotope number, followed by the atom symbol. For example, to label an atom [image], enter 58Cu.

3.	Press the Return key. The isotope is displayed is superscript on the selected atom(s).

Note: If an atom that you typed is not recognized as an atom, it is added as an atom alias.


To add atom charges using the keyboard

Use this procedure to enter atoms and their charges using the keyboard.

1.	Select one or more atoms where you want to place the atom charge.

2.	Enter the atom symbol, followed by the number of charges, followed by + for a positive charge or - for a negative charge. For example, to label an atom [image], enter Ca2+.

Note: You do not need to enter 1 to specify one charge.

3.	Press the Return key. The atom charge is displayed is superscript on the selected atom(s).

Note: If an atom that you typed is not recognized as an atom, it is added as an atom alias.


To type predefined abbreviated structures using the keyboard

MDL supplies predefined abbreviated structures that you can enter using the keyboard. Predefined abbreviated structures are saved as ISIS/Draw sketch files or molfiles. Note

You can choose whether to have the abbreviated structure appear in your sketch as text or as the full structure. Click here for the procedure to set this default.

1.	Click [image] or

2.	Do one of the following:

*	Select one or more atoms where you want to place the abbreviated structure.

*	Click an empty area.

3.	Type the name of the predefined abbreviated structure. For example, type Pyrim to place the abbreviated structure that is located in either PYRIM.SKC or PYRIM.MOL on the selected atom(s).

Caution: Before you enter an amino acid, click here for more information.

4.	Press the Return key.

5.	(Optional) If you displayed the abbreviated structure as text, you can display the underlying chemistry: Select the name of the abbreviated structure, then choose Chemistry > Residue > Expand.

To see a list of the predefined abbreviated structures that are included with ISIS/Draw 2.1, click here.


Amino Acid Abbreviated Structures

MDL supplies predefined abbreviated structures that represent amino acids. These abbreviated structures use the same three-letter abbreviations as some entries in the extended Periodic Table. The following abbreviated structures have this problem:

ALA	LEU

ARG	LYS

ASN	MET

ASP	PHE

CYS	PRO

GLN	SER

GLU	THR

GLY	TRP

HIS	TYR

IIE	VAL

For these abbreviated structures only, how you enter the three-letter abbreviation determines what ISIS/Draw adds to your sketch.

*	To add the complete structure of the amino acid, enter the name in uppercase letters, such as CYS.

*	To represent the amino acid as a pseudoatom in the extended Periodic Table, enter the name in lowercase or mixed case letters, such as cys or Cys.

Note: The same issue exists when you enter NO. In addition, custom template files created by users might conflict with entries in the standard and extended Periodic Tables.


To specify how predefined abbreviated structures appear

Use this procedure to specify that abbreviated structures appear in your sketch as text, or as the full structure.

1.	Choose Options > Settings.

2.	Click the General tab.

3.	Do one of the following:

*	To be able to type the name of an abbreviated structure and have it appear as a structure, you require this setting: Abbreviate typed-in templates.

*	To be able to type the name of an abbreviated structure and have it appear as text, you require this setting: Abbreviate typed-in templates.

4.	Click OK.

5.	(Optional) To save your modifications, click Save.


To create customized abbreviated structures

MDL supplies predefined abbreviated structures that you can enter using the keyboard. Use this procedure to create you own customized predefined abbreviated structures.

You save predefined abbreviated structures as ISIS/Draw sketch files or molfiles. Note

1.	Choose File > New.

2.	Use the drawing tools, template tools, or template pages to draw the structure that you want to use as a predefined abbreviated structure.

3.	Click the atom on the template that will attach the template to structures that you draw.

4.	Choose Edit > Set Sprout Atom.

5.	Choose File > Save As.

6.	Navigate to the Templates directory or folder. The sketch must be located in this directory or folder, otherwise ISIS/Draw will not recognize the name that you enter as the name of a file that contains an abbreviated structure.

7.	Enter a name for the file. Make sure that the name is meaningful to you so that you can easily enter it into future sketches. PC Only: The file name must end with the .SKC extension.

8.	Click OK (Mac=Save).

To see tips on how to correctly enter predefined abbreviated structures, as well as a list of the predefined abbreviated structures that are included with ISIS/Draw 2.1, click here.


Note

Sketch files or molfiles that you want to use as abbreviated structures must be located in the same directory or folder as your template files.

ISIS/Draw looks first in the Templates directory or folder for a sketch file. If it doesn't find the sketch file, it then looks in the same directory or folder for a .MOL file.

If ISIS/Draw does not recognize an abbreviated structure that you type in, it adds the abbreviated structure as an atom alias.


Abbreviated Structures

An abbreviated structure is all or part of a structure (molecule or reaction component) that has been abbreviated to a text label. Structures that you abbreviate keep their chemical significance, but their underlying structure is hidden.

In this example, the phenyl rings in the 2,5-diphenylfuran are abbreviated to the text string Ph:


To move objects with the arrow keys

Use this procedure to move objects one pixel at a time using the keyboard.

1.	Select the object(s) to move.

2.	Do one of the following:

*	To move the object(s) to the right, press the right arrow key.

*	To move the object(s) to the left, press the left arrow key.

*	To move the object(s) up, press the up arrow key.

*	To move the object(s) down, press the down arrow key.


ISIS/Draw Menus

Chemistry menu

Edit menu

File menu

Object menu

Options menu

Templates menu

Text menu


File Menu

New

Open...

Insert...

Close

Save

Update <application> (PC)

Save As...

Save Copy As (PC)

Import

Export

PL

Print/Page Setup...

Print...

Print Preview

Exit/Quit

Exit and Return to <application>  (PC)


New (File menu)

Opens a new, empty, and untitled ISIS/Draw window.


Open... (File menu)

Displays a dialog box allowing you to open an existing sketch file and display the contents in a new window.

For more information, see:

To open an existing sketch file


Insert... (File menu)

Displays a dialog box allowing you to insert the contents of the selected sketch file directly into the active window.

For more information, see:

To insert the contents of a file into a sketch


Close (File menu)

Closes the active window. If the active window contains work that you have not saved, a dialog asks if you want to save or abandon the changes, or cancel the command.

For more information, see:

To close a sketch file


Save (File menu)

Saves the contents of the active window as a file in the current directory or folder on the disk. If this is the first time that you are saving the file, you must enter a file name. If the file has been saved before, the existing file name (and extension, if present) are used.

Caution: The Save command overwrites any file with the same name that is in the same directory or folder. If you do not want to do this, choose File > Save As and give the file a different name.

For more information, see:

To save a new sketch file

To save an existing sketch file


Update <application> (PC only, File menu)

Updates an embedded object without returning to the non-ISIS application in which the object is embedded.

See your Windows documentation for more information on this feature.

Note: This command temporarily replaces File > Save, and is available solely after you edit the embedded object.


Save As... (File menu)

Displays a dialog box allowing you to save the contents of the active window in a file, with a file name and extension that you provide. The file is saved in the current directory or folder on the current disk (unless you specify otherwise).

For more information, see:

To save a new sketch file


Save Copy As (PC only, File menu)

Saves a copy of the edited embedded object in an ISIS/Draw sketch.

See your Windows documentation for more information on this feature.

Note: This command temporarily replaces File > Save As, and is available solely after you edit the embedded object.


Import (File menu)

Imports the contents of a selected file into the active window.

For more information, see:

Importing data into ISIS/Draw


Export (File menu)

Exports sketches in formats that can be read by ISIS, MACCS-II, REACCS, and CPSS.

For more information, see:

Exporting data from ISIS/Draw


PL (File menu)

Allows you to execute commands in the Procedural Language. This menu item is available only if you have PL installed.

Execute

Displays a dialog box allowing you to specify .EPL files that contain Procedural Language command sequences to execute.

For more information, see The Procedural Language Reference.


Print/Page Setup... (File menu)

Displays a dialog box allowing you to specify the paper size and page orientation required for printing, and other printing options.

Print Setup is the PC command, Page Setup is the Macintosh equivalent.

For more information, see:

To print a sketch


Print Preview (File menu)

When checked, displays a page view of the active window which includes the print borders.

For more information, see:

To view the page as it will look when printed


Print... (File menu)

Displays a dialog box allowing you to specify some printing options, and then print the contents of the active window.

For more information, see:

To print a sketch


Exit/Quit (File menu)

Closes the active window and exits the current ISIS/Draw session. If you have an open window that contains work that you have not saved, a dialog asks if you want to save or abandon the changes, or cancel the command.

Exit is the PC command, Quit is the Macintosh equivalent.

For more information, see:

To exit ISIS/Draw


Exit and Return to <application> (PC only, File menu)

Exits ISIS/Draw after you view or edit an object embedded in another application.

See your Windows documentation for more information on this feature.

Note: This command temporarily replaces File > Exit.


Edit Menu

Undo

Cut

Copy

Paste

Paste Link (PC)

Clear

Links... (PC)

Insert Object... (PC)

Edit <application name> Object (PC)

Select All

Select Chem Group

Duplicate

Set Sprout Atom


Undo (Edit menu)

Reverses the last command that you performed. Undo only works for some commands.


Cut (Edit menu)

Removes one or more selected objects from the active window and places them on the Clipboard. This overwrites the previous contents of the Clipboard (if any). The objects remains on the Clipboard until you perform another Cut or Copy operation.

Note: To recover cut objects, choose Edit > Undo.


Copy (Edit menu)

Copies one or more selected objects from the active window to the Clipboard. This overwrites the previous contents of the Clipboard (if any). The original objects stay on the screen. The objects remains on the Clipboard until you perform another Cut or Copy operation.


Paste (Edit menu)

Takes the last objects placed in the Clipboard (by Cut or Copy) and places them in the active window. If placed in a new window, the objects are placed in approximately the same position as they were in their original location.

You can paste objects an unlimited number of times.

PC only: You can paste an object from the Clipboard as an embedded object. This only works if the application from which the object was copied from supports object embedding.


Paste Link (PC only, Edit menu)

Pastes a link to an object in another application from the Clipboard into the active window. This only works if the application from which the object was copied from supports object linking.

See your Windows documentation for more information on this feature.


Clear (Edit menu)

Deletes one or more selected objects from the active window without placing them on the Clipboard.

Note: To recover cleared objects, choose Edit > Undo.


Links... (PC only, Edit menu)

Displays a dialog box allowing you to specify when to update or cancel an OLE link.

See your Windows documentation for more information on this feature.


Insert Object... (PC only, Edit menu)

Displays a dialog box allowing you to use an application that supports object linking and embedding to create an object and embed it in an ISIS/Draw sketch.

See your Windows documentation for more information on this feature.


Edit <application name> Object (PC only, Edit menu)

Opens the application that created the selected embedded or linked object.

See your Windows documentation for more information on this feature.


Select All (Edit menu)

Selects every object in the active window.


Duplicate (Edit menu)

Makes an exact copy of one or more selected objects, slightly offset from the originals.


Select Chem Group (Edit menu)

Allows you to select your choice of an entire group of contiguous atoms and bonds that are within a larger structure.

Select Chem Group is available only when you:

*	Select all the bonds that link your choice of contiguous atoms and bonds to the structure. (If you do not select these bonds, the entire structure is selected.)

*	Select any atom within the group of contiguous atoms and bonds.


Set Sprout Atom (Edit menu)

Specifies the single atom that will be used as the attachment point. Use Set Sprout Atom when you draw a sketch that contains a single-structure that you plan to use as a template tool or as a customized abbreviated structure.

For more information, see:

To create a template tool and add it to the tool bar

To create customized abbreviated structures


Options Menu

Zoom

Show/Snap Grid

Show Ruler

Snap To Ruler

Snap To Object

Show Atom-Maps

Show Inv/Ret Marks

Reacting Centers

Settings...

Read Journal or Custom Settings...

Apply Settings


Zoom (Options menu)

Allows you to select the size at which to display your work.

100% Size

Displays the contents of the active window at its original size.

25%, 5O%, 75%, 133%, 200%

Displays the contents of the active window at one quarter, one half, three-quarter, original plus 33%, or double size.

View Page

Displays the contents of the active window in an area that represents the default page size (as specified in the Page Setup dialog box).

Note: (1) Unless you use a scaleable font, text viewed at 25% or 50% size might not display as expected. (2) If you import sketches from a PC to view on a Macintosh, use Zoom > 133% for a direct pixel-to-pixel match. If you import sketches from a Macintosh to view on a PC, use Zoom > 75% for a direct pixel-to-pixel match.


Show/Snap Grid (Options menu)

When checked, displays the grid. In addition, any object that you draw later attempt to snap to the grid.

For more information, see:

To set up the grid


Show Ruler (Options menu)

When checked, displays the ruler at the top and left side of the drawing area. Markers show the current cursor position.

For more information, see:

To use the ruler to draw objects of a specific size


Snap To Ruler (Options menu)

When checked, any non-chemical object that you later draw is sized using the increments marked on the ruler. For example, if you specified Centimeters and 5, an object such as a box can only be drawn in 0.2 centimeter (2 millimeter) increments.

Note: Snap To Ruler does not affect the way you draw molecules.

For more information, see:

To use the ruler to draw objects of a specific size


Snap To Object (Options menu)

When checked, shows a highlight dot when you draw lines, boxes, and polygons. This shows the point where the objects can snap together so that they are accurately joined and not just close to each other.


Show Atom-Maps (Options menu)

When checked, displays the atom-to-atom map on the atoms of the reactants and products in a transformation.

Show Atom-Maps is available only when you:

*	Specify an atom-atom map on a reaction.

*	Select the atoms in the reaction whose atom-atom maps you want to display. (This setting does not apply if you use the Map or Delete Map tools.)

For more information, see:

Specifying Atom-Atom Maps on a Reaction

Searches that Require Atom-Atom Maps: RSS/Rxn or SBF


Show Inv/Ret Marks (Options menu)

When checked, displays the inversion and retention marks on the atoms of the reactants and/or products in a transformation.

Show Inv/Ret Marks is available only when you:

*	Specify inversion and/or retention marks on a reaction.

For more information, see:

To specify stereo bond query features


Reacting Centers (Options menu)

Allows you to display the reacting centers on the bonds of reactants and products in a transformation. The reacting center bonds can be displayed in a different color or with added thickness or with a set of hash marks that specify how the bonds change (or do not change) in the transformation.

Reacting Centers is available only when you:

*	Specify reacting center marks on a reaction.

For more information, see:

To specify reacting center query features


Settings... (Options menu)

Displays the Settings dialog box, allowing you to set all of ISIS/Draw's default settings.

For more information, see:

Settings


Read Journal or Custom Settings... (Options menu)

Displays a dialog box allowing you to read an existing settings file into ISIS/Draw. The settings file that you read in becomes the currently-active settings file.

For more information, see:

To read a settings file into ISIS/Draw

Drawing for Journal Publication


Apply Settings (Options menu)

Applies the current settings to an existing sketch.

For more information, see:

To apply settings to an existing sketch


Chemistry Menu

Reaction...

Create Chiral Flag

Create No-Structure...

Residue

Sequence

3D

Calculate Mol Values

R-Query

Link Node

Renumber Atoms

Disable Rgroup Chem Inspector

Run Chem Inspector


Create No-Structure... (Chemistry menu)

Displays a dialog box allowing you to create a no-structure to register into a local or remote database.

For more information, see:

The ISIS/Base Database Maintenance 2.0 manual


Run Chem Inspector (Chemistry menu)

Displays the Chem Inspector dialog, where you can find out if there are any problems that might keep you from:

*	Registering a structure, reaction, or sketch in ISIS/Base

*	Using a structure, reaction, or sketch to search a database using ISIS/Base.

For more information, see:

Verifying the Chemistry of Sketches


Disable Rgroup Chem Inspector (Chemistry menu)

Note: This menu item appears only if you have ISIS/Base and SAR Table installed.

If you create a query in ISIS/Draw that contains display Rgroups, then click [image] to return to ISIS/Base, Chem Inspector will incorrectly flag the query as invalid. You will not be able to transfer the query back to ISIS/Base.

To ensure that Chem Inspector does not incorrectly flag display Rgroup queries, make sure that Chemistry > Disable Rgroup Chem Inspector is checked.

Note: You can also copy the query and paste it into ISIS/Base to avoid the Chem Inspector check.


Reaction... (Chemistry menu)

Briefly shows you how to draw a reaction and how to verify the chemical interpretation of your reaction. You verify the chemical interpretation before you register a reaction or before you use it as a query to search a database in ISIS/Base.

For more information, see:

Drawing Reactions in the ISIS/Draw "Quick Start"

Verifying the Chemistry of Sketches


Residue (Chemistry menu)

For abbreviated structures only: Allows you to create an abbreviated structure (such as the abbreviated structure Ph for Benzene), rename an abbreviated structure, contract a structure to its abbreviated form, expand an abbreviated structure to view its underlying chemical structure, or open the underlying chemical structure so that you can then edit it.

Note: Residues, the building blocks of biopolymers, are examples of abbreviated structures.

Residue is available only when you:

*	Select a structure or an abbreviated structure.

For more information, see:

To type predefined abbreviated structures

Working With Biopolymers


Sequence (Chemistry menu)

For biopolymers only: Allows you to display or hide sequence bonds, crosslink bonds, leaving groups, residue brackets or to view and/or customize the list of residue codes that you can use to create a biopolymer.

For more information, see:

Working With Biopolymers


Create Chiral Flag (Chemistry menu)

For remote searching only: Allows you to add a chiral flag to your structure query to retrieve structures from the database that are solely absolute (not relative) stereoconfigurations. You can specify a chiral flag on either a molecule with at least one asymmetric center or on a molecule that is asymmetric.

Note: For local searching, the chiral flag is ignored.

Create Chiral Flag is available only when you:

*	Select a structure. (If you select a structure that does not contain at least one asymmetric center or is not asymmetric, the chiral flag that you add is ignored during the search.)

For more information, see:

Specifying Chiral Flags on Molecules or on Reaction Components


R-Query (Chemistry menu)

For remote searching only: Allows you to create an RGROUP query.

R-Query > Rgroup is available only when you:

*	Select the Rgroup substituents that you want to be the members of a specific Rgroup. For example, you can specify that the Rgroup substituents phenyl and carboxyl are the members of the Rgroup R1. You can specify a maximum of 32 different Rgroups (R1 through R32).

R-Query > R-Logic is available only when you:

*	Want to apply restrictions to Rgroups (called Rgroup conditions). You can specify Rgroup conditions for a maximum of 5 Rgroups (such as R1 though R5).

R-Query > Attachment is available only when you:

*	Select the atom on the Rgroup substituent that you want to be attached to the root structure. (If an Rgroup label is attached to two bonds on the root structure, such as an Rgroup label in a ring, you must designate two attachment points on the Rgroup substituent.)

R-Query > Rgroup Atom is available only when you:

*	Select the atom in the root structure that you want to be attached to an Rgroup substituent.

For more information, see:

Searching Instructions for Molecules or Reaction Components

Searching Concepts/Examples for Molecules or Reaction Components


RGROUP Query

An Rgroup (RGROUP) search finds molecule records that contain your query as a root structure with defined Rgroup substituents attached to it at any position. For example, you can define Rgroup site R1 on a root structure to be a carboxyl group and Rgroup site R2 to be either a chloride atom or a sulfur group or a nitro group.

Rgroup Conditions: You can also specify 1) the number of Rgroup sites that must be filled for a molecule to be retrieved, 2) whether or not substituents other than your defined Rgroup substituents may also attach to an Rgroup site, and 3) whether or not the presence of one Rgroup is dependent on the presence of another Rgroup.


Link Node (Chemistry menu)

For remote searching only: Allows you to specify the addition of variable numbers of repeating units to a ring or a chain to retrieve molecules with rings or chains of varying length. A repeating unit is any arrangement of atoms or bonds within a set of brackets called a link node.

Examples: Rings or Chains

Link Node is available only when you:

*	Select an atom and its two adjacent ring or chain bonds. (The atom that you select can be attached to a substituent.)

For more information, see:

To allow additional atoms and/or bonds in a chain or a ring


Renumber Atoms (Chemistry menu)

Allows you to renumber existing atom numbers on selected atoms. The selected atoms are renumbered in the order they were drawn, beginning with the numerical value that you specify (such as a numerical value of 1).

Renumber Atoms is available only when you:

*	Select all the atoms that you want to renumber.


Calculate Mol Value (Chemistry menu)

Calculates the molecular weight, exact mass, formula, and composition of selected chemical objects. You can then paste the information into the sketch.

Note: All calculations are based on atomic weights, and include implicit hydrogens used to fill open valences on atoms within the molecules.

Calculate

Based on the default set in the Molecular Calculation Settings dialog, choosing Chemistry > Calculate Mol Value > Calculate does one of the following:

*	Pastes calculated fields into the sketch

*	Displays a dialog that lists the calculated values for the selected objects. Check the fields that you want to paste into the sketch, then click Paste.

Settings...

Displays the Molecular Calculation Settings dialog where you specify defaults for the Chemistry > Calculate Mol Value command.

For more information, see the dialog-box help:

Molecular Calculations Settings


3D (Chemistry menu)

Allows you to create three dimensional (3D) queries used primarily to search 3D databases.

Create...

Fix Position

Edit Basis/Set Basis

Select Basis

Measure

Clear 3D

Restore Coordinates

For more information, see:

Creating 3D Queries


Create...

Creates a 3D object or 3D constraint from the selected reference positions (atoms, points or centroids) or other 3D objects. Displays the Create 3D Object dialog, where you specify the type of 3D object or constraint and enter values, such as range and radius, that are relevant to the object.

This command is available solely when you select a set of reference positions or 3D objects that can be used to define a 3D object or constraint.

For more information, see the dialog-box help:

Create 3D Object


Fix Position

Fixes the position of the selected atoms in the query and appends the [F] mark to them. Use this command to specify the fixed atoms in a submodel. To remove the [F] marks, choose this command again.

This command is available when you select one or more atoms.

For more information, see:

To create submodel components


Edit Basis/Set Basis

Allows you to change the reference positions (atoms, points, or centroids) or other 3D objects on which a 3D object or 3D geometric constraint is based, called the basis of the 3D object or constraint.

This command is available when a 3D object or geometric constraint is selected.

For more information, see:

To edit the basis of a 3D object


Select Basis

Highlights the reference positions (atoms, points, or centroids) or other 3D objects on which a 3D object or 3D geometric constraint is based.

This command is available when a 3D object or geometric constraint is selected.

For more information, see:

To view the basis of a 3D object or constraint


Measure

When checked, displays the measured value of 3D constraints, best-fit lines, and best-fit planes. When unchecked, displays the constraint value. Constraint values and measured values are defined as follows:

Use this command to:

*	View the measured values of 3D objects and constraints that you create in ISIS/Draw

*	View measured values on retrieved 3D structures that you transfer from ISIS/Base


Clear 3D

Clears all selected 3D query features from the structure.

This command is available when one or more 3D query features are selected.

For more information, see:

To remove 3D query features


Restore Coordinates

Allows a 3D structure that you rotated within ISIS/Draw to be restored to its original orientation.

This command is available when one or more 3D structures that have been rotated are selected.

For more information, see:

To restore the original orientation of a 3D structure or query


Object Menu

Edit <Object type>...

Bring To Front

Send To Back

Align...

Clean Molecule

Clean Brackets

Flip

Rotate

Scale

Attach Data to Objects...

Group

Ungroup

Crop

Smooth

Unsmooth

Snap To Grid


Edit <Object type>... (Object menu)

Displays a dialog box allowing you to edit properties of selected objects. The text of this command varies based on the objects that you select.

For more information, see:

5.7 Editing atoms, bonds, and structures in the ISIS/Draw "Quick Start"


Bring To Front (Object menu)

When objects overlap, brings a selected object (or group) from behind and places it on top of the other objects. You need to select only the object that you want to place on top, not the other objects.

Note: You cannot bring an object to the front when the object is completely covered and its handles are not visible; instead you must send the covering object to the back with Object > Send to Back.


Send To Back (Object menu)

When objects overlap, sends the topmost selected object (or group) to the back. You need to select only the object that you want to send to the back, not the other objects.

Object > Send to Back also uncovers objects and groups previously hidden by other objects or groups.


Align... (Object menu)

Displays the Align dialog box allowing you to align multiple objects horizontally or vertically.

For more information, see:

Aligning Objects


Clean Molecule (Object menu)

Improves the appearance of one or more selected structures by giving them uniform bond lengths and angles. When you choose Object > Clean Molecule, ISIS/Draw uses the standard bond length specified in the Settings -- Chemical Drawing tab.

Clean Molecule is available only when you select one or more structures.

For more information, see:

To modify ISIS/Draw settings


Clean Brackets (Object menu)

Improves the appearance of one or more selected set of polymer or mixture brackets and the structures contained within.

Object > Clean Brackets can affect the bracket height, position, and orientation; the position of the molecules within the brackets, and the length of crossing bonds.

Clean Brackets is available only when you select one or more sets of brackets.


Flip (Object menu)

Flips a selected object, group of objects, or group of structures (known as a Chem group) -but not text- around an axis.

Horizontal

Flips a selected object or group of objects in the horizontal plane about a vertical (top to bottom) axis midway through the objects.

Vertical

Flips a selected object or group of objects in the vertical plane about a horizontal (left to right) axis midway through the objects.

Chem Group

Flips any selected structure connected by an acyclic bond around the axis of the acyclic bond. Aromatic bonds can reposition themselves to remain chemically valid.

For more information, see:

To flip objects


Rotate (Object menu)

Rotates a structure containing a selected bond so that the bond is horizontal or vertical. All bonds connected to the rotated bond keep their relative positions.

Bond to Horizontal

Rotates the structure so that the selected bond is in a horizontal position.

Bond to Vertical

Rotates the structure so that the selected bond is in a vertical position.

For more information, see:

To rotate a structure so that a specific bond is horizontal or vertical


Scale (Object menu)

Scales objects to a specified size, or expands them to fill the current drawing area.

Standard Bond Length

Resizes selected structures to the standard bond length, as defined in the Settings -- Chemical Drawing tab. If the structure has varied bond lengths, Standard Bond Length scales them so that the average bond length equals the standard bond length set in Settings.

Fit Screen

Resizes all objects in the drawing area to fit the current size of the drawing area.

Percent

Scales all selected objects to the specified size. For example, 50% halves the current size and 200% doubles it.

Note: These commands scale only the X- and Y-coordinates of 3-D structures. To scale all three coordinates equally, choose Options > Zoom.

For more information, see:

To resize to the standard bond length


Attach Data To Objects... (Object menu)

Displays a dialog box allowing you to attach data to selected atoms, bonds, groups of atoms and bonds, or pairs of brackets.

Note: You can also use the [image] tool to attach data to objects.

For more information, see:

Creating and Editing Attached Data


Group (Object menu)

Combines selected objects into a single unit so that a command applied to the group affects the whole group.

For more information, see:

To group objects


Ungroup (Object menu)

Reverses the Group command. Ungroup dissolves a group of objects and gives each object its own individual selection handles.

For more information, see:

To ungroup objects


Crop (Object menu)

Hides parts of an object outside the rectangular area you specify.

For more information, see:

To crop objects

To uncrop objects


Smooth (Object menu)

Reshapes a selected polygon or continuous line by smoothing straight lines and vertices into rounded contours.

Object > Smooth is available solely for polygons and objects drawn with the multiline tool.

Note: Fill Color and Fill Pattern do not apply to smoothed objects.


Unsmooth (Object menu)

Reverses the Smooth command. Unsmooth returns a smoothed polygon or continuous line to its original (unsmoothed) condition.

Object > Unsmooth is available only when you select polygons or objects drawn with the multiline tool that you smoothed.

Note: Fill Color and Fill Pattern are restored if they were present before smoothing.


Snap to Grid (Object menu)

Moves part or all of a selected object to the nearest grid point (when the grid is displayed). The object snaps to the grid when it is within an area approximately one character wide surrounding each grid point.

For more information, see:

To set up the grid


Text Menu

Font...

Regular

Bold

Italic

Underline

Superscript

Subscript

Formula


Font... (Text menu)

Displays the Font Manager dialog box allowing you to set all text-related options for selected text.

Text > Font is available only when you:

*	Select one or more objects that contain text

*	Use the [image] or [image] tools.


Regular (Text menu)

When checked, removes bold, italic, underline, formula, superscript, and subscript styles from text.

Text > Regular is available only when you:

*	Select one or more objects that contain text

*	Use the [image] or [image] tools.


Bold/Italic/Underline (Text menu)

When checked, allows you to type text in the current font and font size in boldface, italic, or underline (in any combination). Uncheck the command to type without boldface, italic, or underlines.

Text > Bold, Text > Italic, and Text > Underline are available only when you:

*	Select one or more objects that contain text

*	Use the [image] or [image] tools.


Superscript (Text menu)

When checked, allows you to type superscripts in the current font and font size. Uncheck the command to type normal text. Superscript uses default values defined in the Settings -- Font dialog box.

Text > Superscript is available only when you:

*	Select one or more objects that contain text

*	Use the [image] or [image] tools.

For more information, see:

To modify ISIS/Draw settings


Subscript (Text menu)

When checked, allows you to type subscripts in the current font and font size. Uncheck the command to type normal text. Subscript uses default values defined in the Settings -- Font dialog box.

Text > Subscript is available only when you:

*	Select one or more objects that contain text

*	Use the [image] or [image] tools.

For more information, see:

To modify ISIS/Draw settings


Formula (Text menu)

When checked, automatically subscripts all numbers that you type in a line of text, in the current font and font size. Uncheck the command to type normal text. Formula uses default values defined in the Settings -- Font dialog box.

Text > Formula is available only when you:

*	Select one or more objects that contain text

*	Use the [image] or [image] tools.

For more information, see:

To modify ISIS/Draw settings


Templates Menu

The Templates menu includes the names of the template files that you have installed.

Customize Menu and Tools

Set Template Directory... (Mac)

Set Primary Template Folder... (PC)

Set Secondary Template Folder... (PC)

Open...


Open... (Templates menu)

Displays a dialog box allowing you to open an existing template page and display the contents in a separate window.

For more information, see:

Using Template Tools and Pages


Customize Menu and Tools... (Templates menu)

Displays the Customize Template Menu/Tools dialog box, allowing you to specify:

*	Which template pages appear in the Templates menu

*	Which template tools appear on the horizontal tool bar

For more information, see:

Using Template Tools and Pages


Set Template Directory... (Mac Only, Templates menu)

Displays a dialog box allowing you to specify the directory or folder where ISIS/Draw looks for template pages and template tool files.

For more information, see:

To specify the template folders


Set Secondary Template Folder... (PC Only, Templates menu)

Displays a dialog box allowing you to specify the secondary folder where ISIS/Draw looks for template pages and template tool files.

For more information, see:

To specify the template folders


Set Primary Template Folder... (PC Only, Templates menu)

Displays a dialog box allowing you to specify the primary folder where ISIS/Draw looks for template pages and template tool files.

For more information, see:

To specify the template folders


Drawing for Journal Publication

ISIS/Draw includes journal settings for the following publications:

*	Journal of American Chemical Society

*	Journal of Chemical Information & Computer Sciences

*	Journal of Medicinal Chemistry

*	Journal of Organic Chemistry

*	Perkin I/Perkin II

*	Synthesis/Synthesis Letters

*	Tetrahedron/Tetrahedron Letters

To apply journal settings to a new sketch

To apply journal settings to an existing sketch

To modify journal settings

To create journal settings


Drawing for Journal Publication

ISIS/Draw includes journal settings for the following publications:

*	Journal of American Chemical Society

*	Journal of Chemical Information & Computer Sciences

*	Journal of Medicinal Chemistry

*	Journal of Organic Chemistry

*	Perkin I/Perkin II

*	Synthesis/Synthesis Letters

*	Tetrahedron/Tetrahedron Letters

To apply journal settings to a new sketch

To apply journal settings to an existing sketch

To modify journal settings

To create journal settings


Journal Settings

Use Journal settings to make your sketches fit the publication requirements of specific journals. Journal settings include such things as standard bond length, bond line width, margin width, and so on.


To apply journal settings to a new sketch

Use this procedure to apply journal settings to a new sketch.

1.	Choose File > New.

2.	Choose Options > Read Journal or Custom Settings.

3.	Select the journal settings file whose settings you want to apply to the sketch. To see the names of the journal settings files included with ISIS/Draw 2.1, click here.

4.	Click OK.

5.	Choose Options > Apply Settings. The journal settings are applied to any new objects that you draw.


To apply journal settings to an existing sketch

Use this procedure to apply journal settings to an existing sketch.

1.	Choose File > Open.

2.	Select the sketch file to open.

3.	Click OK.

4.	Choose Options > Read Journal or Custom Settings.

5.	Select the journal settings file whose settings you want to apply to the sketch. To see the names of the journal settings files included with ISIS/Draw 2.1, click here.

6.	Click OK.

7.	Choose Options > Apply Settings. The journal settings are applied to the sketch.


To modify journal settings

Use this procedure to modify a journal setting file. You might do this if publication style requirements change. Journal settings files are read-only, so save your modified settings under another name.

1.	Choose Options > Settings.

2.	Click Read.

3.	Select the journal settings file whose settings you want to modify.

4.	Click OK.

5.	Click a tab and modify one or more settings.

6.	Click Save As.

7.	Enter a name for the new settings file.

8.	Click OK.


To create journal settings

Use this procedure to create a new journal settings file.

1.	Choose Options > Settings.

2.	Click a tab to see settings that affect a specific area of ISIS/Draw.

3.	Modify one or more settings.

4.	(Optional) Click another tab and modify more settings.

5.	Click Save As.

6.	Enter a name for the new journal settings file.

7.	Click OK.

8.	Click OK.


Journal Setting File Names

	PC	Macintosh
Journal of American Chemical Society	JACS.CFG	JACS Settings
Journal of Chemical Information & Computer Sciences	JCICS.CFG	JCICS Settings
Journal of Medicinal Chemistry	JMC.CFG	JMC Settings
Journal of Organic Chemistry	JOC.CFG	JOC Settings
Perkin I/Perkin II	PERKIN.CFG	Perkin Settings
Synthesis/Synthesis Letters	SYNTH.CFG	Synth Settings
Tetrahedron/Tetrahedron Letters	TETRA.CFG	Tetra Settings


Aids for Precision Drawing

To use the ruler to draw objects of a specific size

To set up the grid

To create crosshairs

To draw bonds aligned to the grid

To draw rings aligned to the grid

To view a sketch at different magnifications

To view the page as it will look when printed


To use the ruler to draw objects of a specific size

1.	Choose Options > Settings, and then click the Ruler/Grid tab.

2.	To display the ruler, you require this setting: Show ruler.

3.	To specify that any object that you draw is sized using the increments marked on the current ruler, you require this setting: Snap to ruler.

4.	(Optional) To change the ruler divisions, click the Divisions box and enter or choose a value. You might not see all divisions at less than 200% scale.

5.	Do one of the following:

*	To display the ruler in inches, click [image] Inches.

*	To display the ruler in centimeters, click [image] Centimeters.

6.	Click OK.

7.	Click the drawing tool that you want to use.

8.	Move the cursor to the drawing area. Examine the moving marks on both rulers to position the cursor where you want the object to begin.

9.	Drag the mouse. The object is drawn and the moving ruler markers show the current pointer position.

10.	Release the mouse where you want the object to end.


To set up the grid

Use this procedure to set up the grid.

1.	Choose Options > Settings, and then click the Ruler/Grid tab.

2.	To display the grid and to have objects that you draw snap to the grid, you require this setting: Show/snap grid.

3.	Do one of the following:

*	To use a hexagonal grid pattern, click [image] Hexagonal.

*	To use a square grid pattern, click [image] Square.

4.	To enter a default length for the grid, click the Standard bond/grid length box and enter or choose a value. Then, choose the unit of measure.

5.	Do one of the following:

*	To use a horizontal grid, click [image] Horizontal.

*	To use a vertical grid, click [image] Vertical.

*	To define your own grid, click [image] Others.... You see a dialog where you can enter X and Y values for the line origin and vector values.

 	Note: When you enter coordinates to define a grid, the standard bond length is modified.

6.	Click OK.


Grid

The grid is a set of points arranged in a hexagonal or square pattern. The points are spaced an equal distance apart, and that distance represents the standard bond length. You draw bonds from grid point to grid point to draw structures with standard bond lengths and angles.


To create crosshairs

Use this procedure to create crosshairs. You can then use the crosshairs for more precise placement of objects.

1.	Click

2.	Press the Shift key as you draw a horizontal line.

3.	Press the Shift key as you draw a vertical line.

4.	Drag the vertical line over the horizontal line so that they intersect.

5.	Choose Edit > Select All.

6.	Choose Object > Group. The two lines are now grouped as one object that you can move around.


To draw bonds aligned to the grid

Use this procedure to draw bonds that are aligned to the grid. This procedure assumes that the grid is active.

1.	Click [image], [image], or

2.	Point to the grid point where you want the bond to begin.

3.	Drag the mouse to another grid point. The bond snaps to the grid point.

4.	Release the mouse button.


To draw rings aligned to the grid

Use this procedure to draw rings that are aligned to the grid. This procedure assumes that the grid is active.

1.	Click a template tool, or choose a ring from a template page.

Note: Use only the Benzene ring or 6-ring tool with the hexagonal grid. Other types of rings will distort when they snap to the grid.

2.	Do one of the following:

*	To align a ring to the vertical hexagonal grid: Click a grid point.

*	To align a ring to the horizontal hexagonal grid: Point to a grid point, and then drag the mouse horizontally to the next grid point.

*	To fuse a ring to an existing bond: Click the bond.

*	To attach a ring to an existing atom by a single bond: Click the atom. The ring is attached to the atom by an acyclic bond.


To view a sketch at different magnifications

1.	Choose Options > Zoom.

2.	Do one of the following:

*	To view the active window at one quarter, one half, or three quarters size: Choose 25%, 50%, or 75%.

*	To view the active window in its original size: Choose 100%

*	To view the active window in its original size plus 33%: Choose 133%. Use this setting if you import sketches from a PC to view on a Macintosh and want to see a direct pixel-to-pixel match.

*	To view the active window in an area that represents the default page size (as specified in the Page Setup dialog box): Choose View Page.

*	To view the active window at double size: Choose 200%.

View Page

Displays the contents of the active window

Note: Unless you use a scaleable font, text viewed at 25% or 50% size might not display as expected.


To view the page as it will look when printed

When Print Preview is active, you can see how your sketch will print out, and you can edit, delete, create, or move objects.

1.	To enter Print Preview, choose File > Print Preview.

2.	(Optional) Edit, delete, create, or move objects as necessary.

3.	To exit Print Preview, choose File > [image] Print Preview.

Note: Print Preview displays the default page size, which is specified in the Print or Page Setup dialog box.


Creating Molecule Queries

A molecule query is a structure or group of structures that you use to search a database. To draw a molecule query, you first draw the structure that you want to find, then add the stereochemistry restrictions of your choice, and finally add additional restrictions on atoms and/or bonds (called query features).

Note: You create a molecule query in ISIS/Draw, enter it into the form in ISIS/Base, and then conduct the search.

Click one of the following:

*	Drawing a molecule with ISIS/Draw "Quick Start"

*	Specifying stereochemistry

*	Specifying query features

*	Specifying multiple structures in a single query

*	Specifying polymer queries

*	Specifying mixture queries

*	Specifying attached data


To specify multiple fragments in a single query

A molecule contains multiple fragments if its structure cannot be drawn in one connected set of bonds. If you create a query that contains more than one fragment (functional group), each of your retrieved molecules must contain all the fragments embedded wholly within it (and not solely one or some of the fragments). None of these fragments overlap each other. Examples

Note: If one of the fragments retrieves no molecules, then none of the fragments together retrieve any molecules. If there are molecules in the database that contain overlapping fragments, then you do not retrieve these molecules.

1.	Transfer to ISIS/Draw.

2.	Draw all the structures. If you need help, click either

Drawing a 2D Substructure or

Specifying ISIS Query Features or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Examples


Specifying Query Features on a Molecule

A query feature on a molecule is a restriction on an atom and/or a bond that specifies the retrieval of certain types of molecule records from a database using ISIS/Base.

Click one of the following:

*	Specifying atom query features

*	Specifying bond query features

*	Specifying Rgroup query features

*	Specifying attached data


Specifying Query Features

A query feature on a molecule is a restriction on an atom and/or a bond that specifies the retrieval of certain types of molecule records from an ISIS/Base database.

Click one of the following:

*	Specifying atom query features

*	Specifying bond query features


Specifying Query Features on a Reaction Component

A query feature on a reaction component is a restriction on an atom and/or a bond that specifies the retrieval of certain types of reaction records from the database.

Click one of the following:

*	Specifying atom query features

*	Specifying bond query features


Specifying Query Features on a Reaction Component

A query feature on a reaction component is a restriction on an atom and/or a bond that specifies the retrieval of certain types of reaction records from the database.

Caution: You can only specify Rgroups on reaction components that do not also contain a reaction arrow.

Click one of the following:

*	Specifying atom query features

*	Specifying bond query features

*	Specifying Rgroup query features


Specifying Atom Query Features

Click one of the following:

*	To allow or exclude specific atoms

*	To allow explicit hydrogen atoms

*	To prohibit hydrogens on an atom

For remote searching only:

*	To allow an unsaturated atom

*	To allow a specific number of attachments (substituents)

*	To allow a specific number of ring bond attachments

*	To allow additional atoms and/or bonds in a chain or a ring

See also:

To remove query features from atoms

To transfer the query back to ISIS/Base


Specifying Bond Query Features

Click one of the following:

*	To allow a specific bond type

*	To allow solely chain bonds

*	To allow solely ring bonds

For remote searching only:

*	To allow additional atoms and/or bonds in a chain or a ring

See also:

To remove query features from bonds

To transfer the query back to ISIS/Base


To remove query features from bonds

1.	Select the bonds(s) whose query features you want to remove.

2.	Double-click the selected bond(s).

3.	(Optional) To remove Any, Aromatic, S/D, S/A, or D/A: Click the Bond tab, and then click the Bond type box and choose any other bond type.

4.	(Optional) To remove a stereo box: Click the Bond tab, and then set Stereo search to

5.	(Optional) To remove either chain or ring query features and restore the bonds to their previous bond types: Click the Bond tab, and then click the Topology box and choose None.

6.	Click OK.

See also:

To transfer the query back to ISIS/Base


To prohibit implicit hydrogens on an atom
To prohibit hydrogens on an atom

Use this procedure to mark atoms with HO to prohibit any hydrogen attachments to the atom. Examples

1.	Select the atom(s) on which to prohibit hydrogens.

2.	Double-click the selected atom(s).

3.	Click the Query Atom tab.

4.	To prohibit hydrogens, you require this setting: No implicit hydrogens.

5.	Click OK.

See also:

To transfer the query back to ISIS/Base


Examples


To allow a specific number of ring bond attachments

This procedure is for these remote searches only. Use this procedure to specify the number of allowed ring bonds on an atom.

Click to see examples:	r0	r2	r3	r4	r*
1.	Select the atoms that you want to specify as having ring bond attachments.

2.	Double-click the selected atoms.

3.	Click the Query Atom tab.

4.	Click the Ring bond count box.

5.	Do one of the following:

*	To specify no ring bond attachments, choose 0.

*	To specify exactly 2 or 3 ring bond attachments, choose 2 or 3.

*	To specify at least 4 ring bond attachments, choose 4.

*	To specify solely those existing ring bond attachments that you see, choose * (asterisk).

*	To remove the existing ring bond notation, choose Off.

6.	Click OK.

See also:

To transfer the query back to ISIS/Base


Ring Bond

A ring bond is a bond that is part of a ring structure.


r0

The query atom feature r0 allows you to specify that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:


r2

The query atom feature r2 allows you to specify that the records retrieved have solely two ring bond attachments at the specified position. For example:


r3

The query atom feature r3 allows you to specify that the records retrieved have solely three ring bond attachments at the specified position. For example:


r4

The query atom feature r4 allows you to specify that the records retrieved have at least four ring bond attachments at the specified position. For example:


r4
r*

The query atom feature r* allows you to specify that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:


To allow a specific number of attachments

This procedure is for these remote searches only. Use this procedure to specify the number of allowed non-hydrogen attachments (substituents) on an atom.

Click to see examples:

s0	s1	s2	s3	s4	s5	s6	s*
1.	Select the atoms that you want to specify as having non-hydrogen attachments.

2.	Double-click the selected atoms.

3.	Click the Query Atom tab.

4.	Click the Substitution count box.

5.	Do one of the following:

*	To specify no non-hydrogen attachments, choose 0.

*	To specify exactly 1, 2, 3, 4, or 5 non-hydrogen attachments, choose 1, 2, 3, 4, or 5.

*	To specify at least 6 non-hydrogen attachments, choose 6.

*	To specify solely those existing non-hydrogen attachments that you see, choose * (asterisk).

*	To remove the existing attachment notation, choose Off.

Note: Count double or triple bonds as one attachment.

6.	Click OK.

See also:

To transfer the query back to ISIS/Base


s0

The query atom feature s0 allows you to specify that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of a single atom with attached hydrogens (if any).


s1

The query atom feature s1 allows you to specify that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:


s2

The query atom feature s2 allows you to specify that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:


s3

The query atom feature s3 allows you to specify that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:


s4

The query atom feature s4 allows you to specify that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:


s5

The query atom feature s5 allows you to specify that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:


s6

The query atom feature s6 allows you to specify that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:


s*

The query atom feature s* allows you to specify that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:


To allow an unsaturated atom

This procedure is for these remote searches only. Use this procedure to mark an atom unsaturated (U) to specify that the atom must be attached to at least one multiple bond: double, triple, or aromatic. Examples

1.	Select the atom(s) that you want to specify as unsaturated.

2.	Double-click the selected atom(s).

3.	Click the Query Atom tab.

4.	To mark atom(s) as unsaturated, you require this setting: Unsaturated atoms.

5.	Click OK. The selected atom(s) are marked with (U).

See also:

To transfer the query back to ISIS/Base


Examples


To allow additional atoms and/or bonds in a chain or a ring

This procedure is for these remote searches only. Use a link node to specify the addition of variable numbers of identical repeating units to a ring or chain.

1.	To select a repeating unit, select an atom and its two adjacent ring or chain bonds. (The atom that you select can be attached to a substituent.)

2.	Choose Chemistry > Link Node.

3.	Enter the maximum number of repeating units allowed in your ring or chain. Your number must be a value between 2 and 32,000.

4.	Click OK. You see the link node on your ring or chain, such as [L1-3], which specifies a maximum of three repeating units.

5.	(Optional) To remove the link node, delete either bracket.

See also:

To transfer the query back to ISIS/Base


Examples

Click one of the following:

Rings

Chains


Repeating Units in Link Node Brackets

A repeating unit is any arrangement of atoms or bonds within a set of brackets called link nodes, for which you specify a range of multiples of the repeating unit. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the label [L1-3]:

Note: To represent a fixed number of identical repeating units, use a multiple group. To represent an unspecified number of identical repeating units within a polymer, use SRU brackets (n).


Repeating Units in Link Node Brackets

A repeating unit is any arrangement of atoms or bonds within a set of brackets called link nodes, for which you specify a variable number of multiples of the repeating unit. For example, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the label [L1-3]:


Repeating Units in Link Node Brackets

A repeating unit is any arrangement of atoms or bonds within a set of brackets called link nodes, for which you specify a variable number of multiples of the repeating unit. A link node permits the retrieval of rings or chains of varying length.

Examples: Rings or Chains


Rings

For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the label [L1-3]:


Chains

For example, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the label [L1-3]:


To remove query features from atoms

1.	Select the atom(s) whose query features you want to remove.

2.	Double-click the selected atom(s).

3.	Do one of the following:

*	To remove A, Q, List, or Not List: Click the Atom tab, and then click the Symbol box and enter or choose a different atom symbol.

*	To remove atom values: Click the Atom tab, and then click the Value box and delete all the numbers.

*	To remove HO: Click the Query Atom tab, and then set No implicit hydrogens to

*	To remove a stereo box: Click the Query Atom tab, and then click the Reaction stereo box and choose Off.

*	To remove the ring bond count: Click the Query Atom tab, and then click the Ring bond count box and choose Off.

*	To remove the unsaturated atom label: Click the Query Atom tab, and then set Unsaturated atoms to

*	To remove the substitution count: Click the Query Atom tab, and then click the Substitution count box and choose Off.

4.	Click OK.

See also:

To transfer the query back to ISIS/Base


To allow a specific bond type

This procedure is for a limited number of local or remote searches. You can retrieve molecules that allow variations in bond type at specified positions. Click to see examples.

1.	Select a bond or a group of bonds.

2.	Double-click the selected bonds.

3.	Click the Bond tab.

4.	Click the Bond Type box.

5.	Do one of the following:

*	To allow any bond type at these positions, choose Any.

*	To allow solely aromatic bonds at these positions, choose Aromatic.

*	To allow either single or double bonds at these positions, choose Single/Double.

*	To allow either single or aromatic bonds at these positions, choose Single/Aromatic. (For these remote searches only)

*	To allow either double or aromatic bonds at these positions, choose Double/Aromatic. (For these remote searches only)

6.	Click OK.

See also:

To transfer the query back to ISIS/Base


Examples


To allow or exclude specific atoms

You can retrieve molecules that allow or exclude atoms at specified positions. Click to see examples.

1.	Select an atom.

2.	Double-click the selected atom.

3.	Click the Query Atom tab.

4.	Click the Symbol box.

5.	Do one of the following:

*	To allow any atom except hydrogen at that position, choose A.

*	To allow any atom except hydrogen or carbon at that position, choose Q.

*	To allow one atom from a list of atoms of your choice at that position, choose List. Click an atom symbol to add it to your list of allowed atoms. (Click an atom symbol a second time to deselect it.) Click OK. Examples

Note: To specify more than one list of atoms, you need to specify Rgroup query features.

*	To exclude both hydrogens and any atom on your list at that position, choose Not List. You see the Periodic Table. Click an atom symbol to add it to the list of excluded atoms. (Click an atom symbol a second time to deselect it.) Click OK. (This query feature also specifies no hydrogen atoms.)

6.	Click OK.

See also:

To transfer the query back to ISIS/Base


Examples


Examples

To specify the retrieval of a salt that contains a halogen at a specified position, click Br, Cl, I, and F. For example:

Note: The hydrogens that you see are explicitly drawn to block the retrieval of salts with non-hydrogen substituents at the specified positions.


To allow solely ring bonds

This procedure is for these remote searches only. Use this procedure to mark a bond Rn to specify that the bond must be part of a ring. The ring can be of any size:

1.	Select the bond(s) that you want to mark.

2.	Double-click the selected bond(s).

3.	Click the Bond tab.

4.	Click the Topology box and choose Ring.

5.	Click OK. The selected bonds(s) are marked with Rn.

See also:

To transfer the query back to ISIS/Base


To allow solely chain bonds

This procedure is for these remote searches only. Use this procedure to mark a bond Ch to specify that the bond must be part of a chain. The chain can be of any size:

1.	Select the bond(s) that you want to mark.

2.	Double-click the selected bond(s).

3.	Click the Bond tab.

4.	Click the Topology box and choose Chain.

5.	Click OK. The selected bonds(s) are marked with Ch.

See also:

To transfer the query back to ISIS/Base


Specifying Rgroup Query Features

Rgroup query features allow you to:

*	Specify the structural fragments (such as functional groups or atoms) of your choice at specific sites within a molecule.

*	Exclude structural fragments of your choice at specific sites within a molecule.

*	Specify that the presence of one structural fragment requires the presence of another (Rgroup conditions).

Example

Note: You can only create an Rgroup query with a molecule (or a reaction component without a reaction arrow).

Do the following steps in order:

1.	Draw the root structure.

2.	Draw Rgroup substituents.

3.	Specify attachment points for Rgroup substituents.

4.	Specify the members of each Rgroup.

5.	Specify Rgroup conditions.

See also:

To move Rgroup query components

To transfer the query back to ISIS/Base


Drawing the Root Structure

Click here for step-by-step instructions

A root structure contains that portion of a molecule that does not vary among the molecules retrieved. In the following example, the phenyl ring is the invariant portion of the structure:

Each Rgroup label represents a list of Rgroup substituents that you allow to be attached to the root structure. You draw the root structure by drawing the invariant portion of the structure, drawing bonds for Rgroup labels, then specifying Rgroup labels:


To draw the root structure

You draw the root structure of an Rgroup by drawing the invariant portion of the structure, adding bonds to the atoms that you want to be Rgroup labels, then specifying Rgroup labels. For example:

1.	Draw the invariant portion of the root structure.

2.	Draw bonds for Rgroup labels.

3.	Specify Rgroup labels on the root structure.


Drawing the Invariant Portion of the Root Structure

A root structure contains that portion of a molecule that does not vary among the molecules retrieved. In the following example, the phenyl ring is the invariant portion of the structure:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Drawing Mixtures: MDL Requirements for Database Searching and Registration

*	Verifying the Chemistry of Sketches


Drawing Bonds For Rgroup Labels

You draw the root structure of an Rgroup by drawing the invariant portion of the structure, drawing bonds to the atoms that you want to be Rgroup labels, then specifying Rgroup labels. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


Specifying Multiple Rgroups at a Single Position

Click here for step-by-step instructions

You can specify multiple Rgroups at a single site on the root structure. For example:


Specifying the Members of an Rgroup

Click here for step-by-step instructions

The members of an Rgroup are the Rgroup substituents that are associated with a single Rgroup (such as R1 or R2). In the following example query, R1 contains one member and R2 contains two members:


Specifying the Members of an Rgroup

The members of an Rgroup are the Rgroup substituents that are associated with a single Rgroup (such as R1 or R2). In the following example query, R1 contains one member and R2 contains two members:


Specifying Rgroup Conditions

Click here for step-by-step instructions

Default Rgroup Conditions

Rgroup conditions are the set of restrictions that you can apply to each Rgroup in your query. With the Rgroup condition:

*	Occurrence, you can specify the number of Rgroup sites that must be occupied in the records retrieved. For example, the occurrence designation R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved.

*	RestH, you can specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site.

*	If/then, you can specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.


Default Rgroup Conditions

If you do not apply Rgroup conditions, ISIS assigns the following default conditions:

*	Occurrence > 0

*	RestH off (for each Rgroup)


Drawing the Root Structure

Click here for step-by-step instructions

A root structure contains that portion of a molecule that does not vary among the molecules retrieved. In the following example, the phenyl ring is the invariant portion of the structure:

Each Rgroup label represents a list of Rgroup substituents that you allow to be attached to the root structure. You draw the root structure by drawing the invariant portion of the structure, drawing bonds for Rgroup labels, then specifying Rgroup labels:


To draw the root structure

You draw the root structure of an Rgroup by drawing the invariant portion of the structure, adding bonds to the atoms that you want to be Rgroup labels, then specifying Rgroup labels. For example:

1.	Draw the invariant portion of the root structure.

2.	Draw bonds for Rgroup labels.

3.	Specify Rgroup labels on the root structure.

See also:

To remove an Rgroup label

To transfer the query back to ISIS/Base


Drawing an Rgroup Substituent

Rgroup substituents are functional groups or atoms that you allow to be attached to the root structure at a particular position in the records retrieved. For example, you can specify that the Rgroup label R1 on the root structure allows a carboxyl group at its position and that R2 allows a chlorine atom, a sulfonic acid group, or a carboxyl group at its position:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	To specify attachment points on an Rgroup Substituent

*	Specifying a Nested Rgroup Substituent Within Another Rgroup Substituent

*	Specifying Atom Query Features

*	Specifying Bond Query Features

*	Specifying Stereochemistry

*	Verifying the Chemistry of Sketches


Specifying a Nested Rgroup Substituent Within Another Rgroup Substituent

Click here for step-by-step instructions

A nested Rgroup is an Rgroup that is a place holder within another Rgroup rather than within the root structure. (You cannot nest an Rgroup any lower than this level.) In the following example, Rgroup R2 is nested within the Rgroup R1:

Nested Rgroups are equivalent to the following structures:

Note


Note

You cannot specify more than one nested occurrence of a single Rgroup substituent (such as R2) within another (unnested) Rgroup substituent (such as R1). For example, you cannot specify that the nested Rgroup R2 be retrieved at both positions 1 and 2 within the R1 Rgroup substituent benzene. Instead, create a query in which a set of nested Rgroups (such as R2 and R3) contains identical substituents. Then specify the occurrence of each nested Rgroup only one time. For example, specify that the nested Rgroup R2 be retrieved at position 1 and that the nested Rgroup R3 be retrieved at position 2 within the R1 Rgroup substituent benzene.


To specify a nested Rgroup substituent within another Rgroup substituent

1.	Select an atom on the Rgroup substituent that you want to be attached to the nested Rgroup.

2.	Choose Chemistry > R-Query > Rgroup Atom.

3.	Click an Rgroup label that is unused, such as R2.

4.	Click OK. You see the nested Rgroup label on the Rgroup substituent.

See also:

Drawing the Rgroup Substituents for the Nested Rgroup Label

Specifying the Members of an Rgroup

Specifying Rgroup Conditions

Transfer the query back to ISIS/Base


Drawing an Rgroup Substituent for a Nested Rgroup Label

Click one of the following:

*	ISIS/Draw “Quick Start”

*	To specify an attachment point on an Rgroup Substituent

*	Specifying Atom Query Features

*	Specifying Bond Query Features

*	Specifying Stereochemistry

*	Verifying the Chemistry of Sketches


To specify the members of an Rgroup

This procedure assumes that you have drawn all the members of an Rgroup, and that you want to assign the list of members (the Rgroup substituents) to an Rgroup, such as R1 or R2.

1.	Select all the Rgroup members (and their attachment points).

2.	Choose Chemistry > R-Query > Rgroup.

3.	Click the name of the Rgroup to create, such as R1 or R2.

4.	Click OK. You see the Rgroup designation, such as R1= or R2=, next to the Rgroup members.

See also:

To add an additional member to an existing Rgroup

To edit an Rgroup member

To delete an Rgroup member

To delete all Rgroup members

To dissolve an Rgroup into its substituents

To transfer the query back to ISIS/Base


To specify Rgroup conditions

Use this procedure to specify Rgroup conditions on the Rgroup substituents in the query. This procedure assumes that you have defined a root structure and the list of Rgroup substituents.

1.	Choose Chemistry > R-Query > R-logic.

2.	To specify the Rgroup that the conditions apply to, enter the Rgroup number.

3.	(Optional) To specify the Rgroup condition Occurrence for an Rgroup site, click the Occurrence text box, and then enter the number of Rgroup sites that must be occupied.

4.	(Optional) To specify the RestH condition for an Rgroup site, do one of the following:

*	To allow non-hydrogen substituents in addition to your defined Rgroup substituents to be attached to the Rgroup site, you require this setting:  in the RestH text check box.

*	To allow solely your Rgroup substituents to be attached to the Rgroup site, you require this setting:  in the RestH text check box.

5.	(Optional) To specify the If R (I) Then condition for a set of Rgroups, click in the If/Then text box, and then enter the number of the dependent Rgroup.

6.	Click OK.

See also:

Default Rgroup Conditions

To edit Rgroup conditions

To transfer the query back to ISIS/Base


Occurrence

Use the Rgroup condition Occurrence to specify the number of Rgroup sites that must be occupied in the records retrieved. For example, the occurrence designation R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved.


RestH

Use the Rgroup condition RestH to specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site.


If/Then
If R(i) Then

Use the Rgroup condition If R (I) Then to specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.


To specify Rgroup labels on the root structure

This procedure assumes that you have drawn the portion of the Rgroup query that does not vary among the molecules retrieved, have drawn bonds for the atoms that you want to represent Rgroups, and are now ready to specify Rgroup labels. Example

1.	Select the atom that you want to label as an Rgroup site.

2.	Choose Chemistry > R-Query > Rgroup Atom.

3.	Do one of the following:

*	To add a single Rgroup label: Click an Rgroup label, such as R1 or R2.

*	To add multiple Rgroup labels: Click all the Rgroup labels of your choice, such as R1R2 or R1R2R3.

Note: To deselect a label, click it a second time.

4.	Click OK. You see each Rgroup label on the root structure.

5.	(Optional) To label additional positions on the root structure, repeat Steps 1 through 4.

See also:

Specifying Multiple Rgroups at a Single Position

Specifying a Nested Rgroup Substituent Within Another Rgroup Substituent


To specify multiple Rgroups at a single position

1.	Select the atom that you want to label as an Rgroup site.

2.	Choose Chemistry > R-Query > Rgroup Atom.

3.	Click all the Rgroup labels of your choice, such as R1R2 or R1R2R3.

Note: To deselect a label, click it a second time.

4.	Click OK. You see each Rgroup label on the root structure.


To remove an Rgroup label

Use this procedure to remove an Rgroup label from the root structure.

1.	Select the atom(s) that are marked with the Rgroup label.

2.	Choose Object > Edit Atom.

3.	Click the Symbol box and enter or choose an atom symbol.

4.	Click OK. The selected atom(s) display the atom symbol you specified.


To specify attachment points on an Rgroup substituent

Use this procedure to specify the atoms on the Rgroup substituent that you want to attach to the root structure at the positions specified with Rgroup labels, such as R1. (If an Rgroup is attached to two bonds on the root structure, you must designate two attachment points.)

1.	Select one atom on the Rgroup substituent that you want to be attached to the root structure.

Note: If you want to designate two attachment points, your selected atom must be the one that will attach to the lower atom number on the root structure. To view the atom numbers on the root structure, click here.

2.	Choose Chemistry > R-Query > Attachment.

3.	Enter 1.

4.	(Optional) To specify a second attachment point, select the second atom on the Rgroup substituent, choose Chemistry > R-Query > Attachment, and then enter 2. Your selected atom must be the one that will attach to the higher atom number on the root structure.

5.	Click OK. You see an arrow that points to an asterisk (*). If you designated two attachment points, you also see a single quote for the first attachment point and a double quote for the second attachment point.

6.	If you came in from the procedure "Specifying Rgroup Query Features", click Back (at the top of the help screen) to return to the previous screen and continue with Step 4.

See also:

To specify attachment points on an Rgroup substituent using the keyboard

To delete an attachment point on an Rgroup substituent


To specify attachment points on an Rgroup substituent using the keyboard

Use this procedure to specify the atoms on the Rgroup substituent that you want to attach to the root structure at the positions specified with Rgroup labels, such as R1. (If an Rgroup is attached to two bonds on the root structure, you must designate two attachment points.)

1.	Select one atom on the Rgroup substituent that you want to be attached to the root structure.

Note: If you want to designate two attachment points, your selected atom must be the one that will attach to the lower atom number on the root structure. To view the atom numbers on the root structure, click here.

2.	Type *1 and press Return. You see an arrow that points to an asterisk (*).

3.	(Optional) To specify a second attachment point, select the second atom on the Rgroup substituent, type *2, and the press Return. Your selected atom must be the one that will attach to the higher atom number on the root structure. If you designated two attachment points, you see a single quote for the first attachment point and a double quote for the second attachment point.

4.	If you came in from the procedure "Specifying Rgroup Query Features", click Back (at the top of the help screen) twice to return to that screen and continue with Step 4.


To delete an attachment point on an Rgroup substituent

1.	Select the atom on the Rgroup substituent whose attachment point you want to delete.

2.	Choose Chemistry > R-Query > Attachment.

3.	Enter 0.

4.	Click OK. You see the Rgroup substituent without an attachment point. (You can now change the attachment point or delete the Rgroup substituent.)

Alternatively, you can select the atom whose attachment point you want to delete, type *0, and then press Return.


To display and position atom numbers

Use this procedure to display atom numbers and specify where the atom numbers appear.

1.	In ISIS/Draw, select the structure.

2.	Choose Options > Edit Molecules (or Edit Objects).

3.	Click the Atom tab.

4.	Click the Number position box and choose the position of your choice.


To edit Rgroup conditions

Use this procedure to edit the occurrence, RestH condition, or If R (I) Then logic for an Rgroup query.

1.	Choose Chemistry > R-Query > R-logic.

2.	(Optional) To edit the Rgroup condition Occurrence for an Rgroup site, click the Occurrence text box, and then enter the number of Rgroup sites that must be occupied.

3.	(Optional) To edit the RestH condition for an Rgroup site, do one of the following:

*	To allow non-hydrogen substituents in addition to your defined Rgroup substituents to be attached to the Rgroup site, you require this setting:  in the RestH text check box.

*	To allow solely your non-hydrogen Rgroup substituents to be attached to the Rgroup site, you require this setting:  in the RestH text check box.

4.	(Optional) To edit the If R (I) Then condition for a set of Rgroups, click in the If/Then text box, and then enter the number of the dependent Rgroup.

5.	Click OK.


To delete an Rgroup

1.	Select all the members of the Rgroup.

2.	Choose Edit > Cut.


To dissolve an Rgroup

Use this procedure to dissolve an Rgroup into individual Rgroup substituents.

1.	Select the Rgroup designation of the Rgroup to dissolve, such as R1=.

2.	Choose Edit > Cut.


To edit an Rgroup member

Use this procedure to edit the molecule structure or attachment point on an existing Rgroup member. If you do not delete a member, the Rgroup stays assembled.

1.	Select the Rgroup member.

2.	Edit the Rgroup member as you would any ISIS/Draw object.


To delete an Rgroup member

If you delete an Rgroup member, the Rgroup automatically dissolves. Use this procedure to delete an Rgroup member and then reassemble the Rgroup.

1.	Select the Rgroup member(s) to delete.

2.	Choose Edit > Cut.

3.	Select the remaining Rgroup members.

4.	Choose Chemistry > R-Query > Rgroup.

5.	Click the name of the Rgroup to create, such as R1.

6.	Click OK. You see the Rgroup designation, such as R1=, next to the Rgroup members.


To add an additional member to an existing Rgroup

To add a member to an existing Rgroup, you must first dissolve the Rgroup, then reassemble it with the new member.

1.	Select the Rgroup designation of the Rgroup to dissolve, such as R1=.

2.	Choose Edit > Cut. The original Rgroup is dissolved.

3.	Select the Rgroup members, including the new member.

4.	Choose Chemistry > R-Query > Rgroup.

5.	Click the name of the Rgroup to create, such as R1.

6.	Click OK. You see the Rgroup designation, such as R1=, next to the Rgroup members.


To move Rgroup query components

Use this procedure to move Rgroup members, designations, conditions, or the root structure. When you move the components, the chemical significance of the Rgroup query is not affected.

1.	Select the object that you want to move.

2.	Drag the object to its new position.


To specify chirality

In a remote database, you can create a query with a chiral flag on a molecule with at least one asymmetric center or on a molecule that is asymmetric to retrieve solely the absolute stereoconfiguration but not relative stereoconfigurations. (In a local database, the chiral flag is ignored.) Example

1.	Select the structure that you want to label as chiral.

2.	Choose Chemistry > Create Chiral Flag. You see the word "Chiral" at the right of the structure.

See also:

To delete a chiral flag

To transfer the query back to ISIS/Base


Example

In a remote database:

For information on using queries with geometric and tetrahedral stereochemistry, click here.


To delete a chiral flag

When you create a query without a chiral flag on a molecule that contains at least one asymmetric center or on a molecule that is asymmetric, you retrieve all the relative stereoconfigurations.

1.	Select the chiral flag.

2.	Choose Edit > Cut.

See also:

To transfer the query back to ISIS/Base


Settings

Set all of the ISIS/Draw default settings with the Settings dialog box. You save settings in a settings file. This settings file is updated whenever you modify settings and then save the modifications.

To modify ISIS/Draw settings

To apply settings to an existing sketch

To apply settings to a new sketch

To create your own settings file

To read a settings file into ISIS/Draw


To modify ISIS/Draw settings

1.	Choose Options > Settings.

2.	Click a tab to see settings that affect a specific area of ISIS/Draw.

3.	Modify one or more settings.

4.	(Optional) To save your modifications to the currently-open settings file, click Save. If you don't do this, the modifications to settings will not be saved the next time you run ISIS/Draw.

5.	Click OK. If this is a new sketch, the new settings are applied to any new objects that you draw.

If this a sketch with objects that already exist, a dialog asks if you want to apply the new settings to the objects. Do one of the following:

*	To apply new settings to the existing objects, click Yes.

*	To apply new settings only to new objects you create, click No.

*	To cancel the operation and return to the Settings dialog, click Cancel.

Note (1): If you chose not to apply settings to an existing sketch, you can still do so later.

Note (2): You can also modify settings when you resize all molecules in a sketch. You see a dialog box where you can specify that you want your settings to reflect the resizing.


To apply settings to a new sketch

ISIS/Draw automatically applies the currently-active settings to any new sketch that you draw.


To create your own settings file

Use this procedure to save the current settings to a new settings file.

1.	Choose Options > Settings.

2.	Click a tab to see settings that affect a specific area of ISIS/Draw.

3.	Modify one or more settings.

4.	(Optional) Click another tab and modify more settings.

5.	Click Save As.

6.	Navigate to the Settings directory or folder.

7.	Enter a name for the settings file.

PC users: The file name must end with the .CFG extension.

8.	Click OK.

9.	Click OK.


ISIS/Draw Settings File

A settings file contains program settings (defaults) that have been saved. The default ISIS/Draw settings file (ISISDRAW.CFG) is created the first time that you run ISIS/Draw. You can save different sets of settings to multiple settings files.


To apply settings to an existing sketch

Use this procedure to apply the current settings to a sketch that already exists. You might want to do this if you modified your current settings in one sketch, and want to apply these same modified settings to other existing sketches.

1.	Choose File > Open.

2.	Select the sketch file to open.

3.	Click OK.

4.	Choose Options > Apply Settings. The current settings are applied to the open sketch.


To read a settings file into ISIS/Draw

1.	Choose Options > Read Journal or Custom Settings.

2.	Select a settings file.

3.	Click OK.

4.	If this is an existing sketch, do one of the following:

*	To apply the new settings to the existing sketch, click OK.

*	If you do not want the new settings applied to the existing sketch, click Cancel.

The settings file you selected becomes the currently-active settings file.

5.	If this is a new sketch, you see the message Settings from <settings file> are now active, where <settings file> is the name of the settings file you selected.


Grayed Button


No-Structure

In a molecule or 3D database, a no-structure entry is a molecule record that does not contain a structure. The record contains solely data.

In a reaction database, a no-structure entry is a reaction record that does not contain one or more of the components of the reaction.

For information on how to register and retrieve no-structures, see the ISIS/Base Database Maintenance 2.0 manual.


Using Template Tools and Pages

You can save time when drawing structures by using template tools and template pages.

To use a template tool

To add a template tool

To remove a template tool

To create a template tool and add it to the horizontal tool bar

To use a template page

To add a template page to the Templates menu

To remove a template page from the Templates menu

To rename a template page on the Templates menu

To create a template page and add it to the Templates menu

To specify the template folders


To use a template tool

1.	Click one of the template tools on the horizontal tool bar.

2.	Do one of the following:

*	To draw the template with standard length bonds: Click in the drawing area.

*	To draw a template of any size: Press the Shift key, then drag the mouse to create a template of the size and orientation that you want.

*	To fuse to a bond: Click an existing bond.

*	To attach the template to an atom with a single bond: Click a non-terminal atom. (This works only with atoms that have more than one bond attached to them.)


To add a template tool

Use this procedure to add a template tool to the horizontal tool bar. ISIS/Draw can display up to 10 template tools on the horizontal tool bar.

1.	Choose Templates > Customize Menu and Tools.

2.	Click the Template Tools tab.

3.	In the Templates area, click the icon that represents the template tool that you want to add to the horizontal tool bar. The Templates area displays icons for all of the available template tools.

Note: The icons on the bottom row labeled 1 through 10 represent the 10 custom template tools. Icon 1 is linked to the file TPL41.SKC, icon 2 is linked to TPL42.SKC, and so on. For information on how to create a template tool, click here.

4.	In the Template Tools area, near the bottom of the dialog, click the position where you want the template tool to display.

5.	Click OK.

Note: Any changes that you make to template tools are saved in the TPL.CFG file. TPL.CFG is saved when you exit ISIS/Draw.


To remove a template tool

Use this procedure to remove a template tool from the horizontal tool bar.

1.	Choose Templates > Customize Menu and Tools.

2.	Click the Template Tools tab.

3.	In the Template Tools area, near the bottom of the dialog, click the template tool that you want to remove.

4.	Click Remove.

5.	Click OK.

Note: Any changes that you make to template tools on the horizontal tool bar are saved in the TPL.CFG file.


To create a template tool and add it to the tool bar

Use this procedure to take one structure that you use often and make it available as a template tool from the horizontal tool bar.

1.	Create, import, or modify one structure that you want to access from the horizontal tool bar.

2.	Click [image] or

3.	Select the atom on the template that will attach the template to structures that you draw.

4	Choose Edit > Set Sprout Atom.

5.	Choose File > Save.

6.	Navigate to the Templates directory or folder and name the sketch TPL41.SKC (Mac: the file-name extension is optional).

Note (1): You can create 9 more of your own template tools, but you must save them as TPL42.SKC through TPL50.SKC.

Note (2): You must save the sketch files to the Primary Templates directory.

7.	(Optional) For Windows 95/NT users only: To specify a name to display when you move the mouse over the tool on the horizontal tool bar, click Save Name/Comments. Then, click the Name box, enter the name to display, and then click OK.

8.	Click OK (Mac=Save).

9.	Add the sketch file as a template tool to the horizontal tool bar.


To use a template page

1.	Choose a template page from the Templates menu.

2.	Click the attachment point of the template structure that you want to use in your sketch.

3.	With your sketch active, do one of the following:

*	To draw an unattached template: Click an empty area.

*	To attach the template to an atom with a single bond: Click a non-terminal atom. (This works only with atoms that have more than one bond attached to them.)

*	To size and rotate the template: Press the Shift key, then drag the mouse. As you drag the mouse, the template is resized. Release the mouse button to fix the size of the template.

4.	To bring up the template page again, do one of the following:

*	Click

*	Click any visible part of the template page.

5.	To recall the last template that you chose from a template page, click [image]. Then fuse or sprout the template, or click an empty area in the sketch.


To add a template page to the Templates menu

1.	Choose Templates > Customize Menu and Tools.

2.	Click the Template Menu tab.

3.	To position the template page on the Templates menu: Click the name under which you want to place the new template page on the Templates menu.

4.	Click Insert.

5.	Navigate to the disk and directory or folder that contains the sketch file to use as a template page.

Note: We recommend that you save sketch files that you want to use as template pages in the Templates directory or folder.

6.	Highlight the name of the sketch file.

7.	Click OK (Mac=Open).

8.	Enter the name for the template page that you want to see on the Templates menu.

Note: This does not change the name of the sketch file, only the name on the Templates menu.

9.	Click OK. You see the name of the new template page in the list box.

10.	Click OK.

Note: Any changes that you make to the Templates menu are saved in the TPL.CFG file. TPL.CFG is saved when you exit ISIS/Draw.


To remove a template page from the Templates menu

1.	Choose Templates > Customize Menu and Tools.

2.	Click the Template Menu tab.

3.	Select the name of the template to remove. You might have to use the scroll bar.

4.	Click Remove.

5.	Click OK.

Note: Any changes that you make to the Templates menu are saved in the TPL.CFG file.


To rename a template page on the Templates menu

1.	Choose Templates > Customize Menu and Tools.

2.	Click the Template Menu tab.

3.	Select the name of the template to rename. You might have to use the scroll bar.

4.	Click Rename.

5.	Enter the new name.

6.	Click OK.

Note: Any changes that you make to the Templates menu are saved in the TPL.CFG file.


To create a template page and add it to the Templates menu

Use this procedure to take graphics that you use often and make them available as a template page.

1.	Create, import, or modify the image(s) that you want to include in the template page.

2.	Save the image(s) as a sketch file.

3.	Add the sketch file to the Templates menu.


To specify the template folders

Use this procedure to specify the primary or secondary folder where ISIS/Draw looks for template pages and template tools.

When you click a template tool or choose a template file, ISIS/Draw looks first in the primary template folder. If it cannot find the template file, it then looks in the secondary folder.

Note (1): You can specify one folder for personal template files on your local machine, and the other folder for shared template files located on the network.

Note (2): On the Macintosh, you can only specify the primary directory.

1.	Do one of the following:

*	Choose Templates > Set Primary Template Folder. (PC Only)

*	Choose Templates > Set Secondary Template Folder. (PC Only)

*	Choose Templates > Set Templates Directory. (Mac Only - this specifies the primary directory)

2.	Navigate to the disk and folder where you want ISIS/Draw to look for template pages and template tools.

3.	Click OK (Mac=Open).


Template Tools

A template tool is an icon that you click to quickly draw a single structural fragment, such as a benzene ring. You see the template tools on the top menu bar.


Template Page

A template page is a sketch file that contains many structural fragments, such as rings or chains. You create and edit template pages as you would any sketch file. You display template pages by choosing them from the Templates menu.


Attachment Point

The attachment point is the atom or bond on the template that attaches the template to the structure that you build.


Verifying the Chemistry of Sketches

Use Chem Inspector(TM) to verify that you can:

*	Register a structure or reaction in a database using ISIS/Base

*	Use a structure or reaction to search an ISIS/Base database

We recommend that you use Chem Inspector before you:

*	Copy a reaction from ISIS/Draw and paste it into ISIS/Base for searching or registration

*	Export a sketch as a REACCS rxnfile

*	Export a sketch as a CPSS rxnfile

Chem Inspector is activated automatically when you:

*	Click [image] to transfer a sketch to ISIS/Base

*	Export a sketch as a molfile

*	Export a sketch as a rxnfile

To use Chem Inspector

To turn individual Chem Inspector warnings on or off


To use Chem Inspector

1.	Click [image] or choose Chemistry > Run Chem Inspector.

2.	Do one of the following:

*	To verify the entire sketch, click [image] Check entire sketch.

*	To verify part of the sketch, first select the objects that you want to verify, and then click [image] Check selected objects.

Note

3.	Click the Intended Use box and choose an option. For example, if you want to register a reaction into a remote database, choose Host Database > Reaction > Registration as the intended use. Chem Inspector can then look for features (such as fonts or pen size) that are not supported by remote databases. Note

4.	(Optional) If ISIS/Draw finds any problems, you see the number of errors and warnings listed below the Results box. Click the arrow next to the Results box. You see a scrolling list of results divided into three categories: Errors, Warnings, and Information.

5.	(Optional) To see more information on a specific result, scroll to that result and click it. ISIS/Draw highlight the objects referred to in the warning or error message. To see a detailed explanation of the result, click [image].

6.	Fix any errors in the drawing. (The Chem Inspector dialog box stays on top.) You must fix any errors that Chem Inspector finds to successfully:

*	Register a structure or reaction

*	Use a structure or reaction to search a database

*	Export a reaction as a rxnfile.

*	Manually atom-atom map a reaction.

7.	(Optional) To verify the sketch again, click


Note

When you click [image] to transfer a sketch from ISIS/Draw to ISIS/Base, Chem Inspector always verifies the entire sketch.

If you copy a sketch from ISIS/Draw and then paste it into ISIS/Base, ISIS/Base automatically checks the sketch. If there are errors in the sketch, you see an error message. You do not see the Chem Inspector dialog box in ISIS/Base.


Note

ISIS/Draw saves the Type of Sketch setting. However, if the active window is linked to ISIS/Base, the Type of Sketch is reset according to the ISIS/Base mode when another transfer is made.


Errors

The structure, reaction, or sketch cannot be registered or searched for.


Warnings

There might be a mismatch between ISIS/Draw's chemical interpretation of the sketch and what the scientist might mean. The structure or sketch can be registered and searched for.


Information

ISIS/Draw provides information such as molecular weight, molecular formula, and composition of the selected structure(s). ISIS/Draw displays this information even if there are no errors or warnings.


To turn individual Chem Inspector warnings on or off

Use this procedure to specify the types of issues that Chem Inspector examines when you:

*	Click [image] or choose Chemistry > Run Chem Inspector.

*	Click [image] to transfer a sketch to ISIS/Base

*	Export a sketch as a molfile or rxnfile

1.	Choose Options > Settings.

2.	Click the Chem Inspector tab.

3.	(Optional) To see information on the Chem Inspector warnings, click Help.

4.	Do one of the following:

*	To have Chem Inspector warn you of a particular issue, you require this setting:  next to the warning type.

*	To have Chem Inspector ignore a particular issue, you require this setting:  next to the warning type.

5.	(Optional) To save your modifications to the currently-open settings file, click Save.

6.	Click OK.


Using Atom Values

To add an atom value to an existing atom

To edit or delete existing atom values


To add an atom value to an existing atom

Use this procedure to attach an atom value to an existing atom.

1.	Select the atom to which you want to attach an atom value.

2.	Double-click the atom.

3.	Click the Atom tab.

4.	Click the Value box and enter an atom value. The number can be a real number, such as 7.3, or a range of real numbers separated by a dash, such as 6.71 - 8.45. Do not type the angle brackets; they are generated automatically.

5.	Click OK.


To edit or delete existing atom values

Use this procedure to edit or delete an existing atom value.

1.	Select the atom whose atom value you want to edit or delete.

2.	Double-click the atom.

3.	Click the Atom tab.

4.	Click the Value box.

5.	Do one of the following:

*	To edit the atom value: Enter a number. The number can be a real number, such as 7.3, or a range of real numbers separated by a dash, such as 6.71 - 8.45. Do not type the angle brackets; they are generated automatically.

*	To delete the atom value: Delete all the numbers in the Value box.

6.	Click OK.


Using Atom Aliases

To add an atom alias or atom symbol

To edit or delete an atom alias or atom symbol


To add an atom alias or atom symbol

Use this procedure to add an atom alias or an atom symbol to an atom.

1.	Click

2.	Click the atom to which you want to attach the atom alias or atom symbol. You see a text entry field.

3.	(Optional) Enter an atom alias into the text field. An alias can be any text or numbers. Numbers automatically display as subscripts.

*	To add numbers that are not subscripts, enter \n before and after the number.

*	To add numbers or letters that are superscripts, enter \S before and after the number or letter.

*	To add a letter as a subscript, enter \s before and after the letter.

*	To position a charge to the left of an atom, enter \S+\S or \S-\S before the letter.

*	To sprout a bond from a specific symbol within an alias, enter ^ (caret character) before the letter you want the bond to be attached to. Click elsewhere and then draw a bond under the alias. You can include only one caret for one attachment point.

4.	(Optional) Enter an atom symbol, such as N or Cu. ISIS/Draw sees it as an atom symbol, not an atom alias.

5.	Click elsewhere.

Note: If you transfer a structure to ISIS/Base that contains one or more atom aliases, you can customize Chem Inspector to warn you that atom aliases can be registered.

See also:

To transfer the query back to ISIS/Base


To edit or delete an atom alias or atom symbol

Use this procedure to edit or delete an atom alias or atom symbol attached to an atom.

1.	Click

2.	Click the atom with the atom alias or atom symbol that you want to edit or delete. You see a text entry field.

3.	Do one of the following:

*	To edit the atom alias or atom symbol: Edit the text in the text field.

*	To delete the atom alias or atom symbol: Delete the text in the text field.

4.	Click elsewhere.

See also:

To transfer the query back to ISIS/Base


Learning Essential ISIS/Draw Skills

All of the essential ISIS/Draw information that you need is in the ISIS/Draw "Quick Start."

The ISIS/Draw "Quick Start" is a 14-page document written in a new, compact style. We designed it to be printed.

Read the ISIS/Draw "Quick Start" to learn the basic information that you need to use ISIS/Draw.

To see the ISIS/Draw "Quick Start," click here.


Learning Essential ISIS/Draw Skills

All of the essential ISIS/Draw information that you need is in the ISIS/Draw "Quick Start."

The ISIS/Draw "Quick Start" is a 14-page document written in a new, compact style. We designed it to be printed.

Read the ISIS/Draw "Quick Start" to learn the basic information that you need to use ISIS/Draw.

To see the ISIS/Draw "Quick Start," click here.


Learning Essential ISIS/Draw Skills

All of the essential ISIS/Draw information that you need is in the ISIS/Draw "Quick Start."

The ISIS/Draw "Quick Start" is a 14-page document written in a new, compact style. We designed it to be printed.

Read the ISIS/Draw "Quick Start" to learn the basic information that you need to use ISIS/Draw.

To see the ISIS/Draw "Quick Start," click here.


Learning Essential ISIS/Draw Skills

All of the essential ISIS/Draw information that you need is in the ISIS/Draw "Quick Start."

The ISIS/Draw "Quick Start" is a 14-page document written in a new, compact style. We designed it to be printed.

Read the ISIS/Draw "Quick Start" to learn the basic information that you need to use ISIS/Draw.

To see the ISIS/Draw "Quick Start," click here.


Learning Essential ISIS/Draw Skills

All of the essential ISIS/Draw information that you need is in the ISIS/Draw "Quick Start."

The ISIS/Draw "Quick Start" is a 14-page document written in a new, compact style. We designed it to be printed.

Read the ISIS/Draw "Quick Start" to learn the basic information that you need to use ISIS/Draw.

To see the ISIS/Draw "Quick Start," click here.


Learning Essential ISIS/Draw Skills

All of the essential ISIS/Draw information that you need is in the ISIS/Draw "Quick Start."

The ISIS/Draw "Quick Start" is a 14-page document written in a new, compact style. We designed it to be printed.

Read the ISIS/Draw "Quick Start" to learn the basic information that you need to use ISIS/Draw.

To see the ISIS/Draw "Quick Start," click here.


Learning Essential ISIS/Draw Skills

All of the essential ISIS/Draw information that you need is in the ISIS/Draw "Quick Start."

The ISIS/Draw "Quick Start" is a 14-page document written in a new, compact style. We designed it to be printed.

Read the ISIS/Draw "Quick Start" to learn the basic information that you need to use ISIS/Draw.

To see the ISIS/Draw "Quick Start," click here.


Learning Essential ISIS/Draw Skills

All of the essential ISIS/Draw information that you need is in the ISIS/Draw "Quick Start."

The ISIS/Draw "Quick Start" is a 14-page document written in a new, compact style. We designed it to be printed.

Read the ISIS/Draw "Quick Start" to learn the basic information that you need to use ISIS/Draw.

To see the ISIS/Draw "Quick Start," click here.


Learning Essential ISIS/Draw Skills

All of the essential ISIS/Draw information that you need is in the ISIS/Draw "Quick Start."

The ISIS/Draw "Quick Start" is a 14-page document written in a new, compact style. We designed it to be printed.

Read the ISIS/Draw "Quick Start" to learn the basic information that you need to use ISIS/Draw.

To see the ISIS/Draw "Quick Start," click here.


To draw a new query

The type of search query that you need to draw depends entirely on the ISIS search that you want to do.

To obtain specific help, click The ISIS/Base Chemical Searches - and How to do Them, and click the specific search that you need. You see a help screen that contains all of the information that you need to draw a new query.

Note: There are, for example, six types of substructure searches (SSS) on the ISIS/Base Chemical Searches - and How to do Them screen. Whether you search a remote or local database for molecule, 3D structure, or reaction records is significant when you decide on a search. Thus, your choice must be accurate.


Importing Data Into ISIS/Draw

To import molfiles, rxnfiles, and TGFfiles

To import a sequence or residue

To import TIFF, HPGL, EPS, and CGM files

Note: ISIS/Draw cannot import ASCII files, MACCS-II files, ChemText files, or ChemBase .FRM files.


Exporting Data From ISIS/Draw

To export molfiles

To export TGFfiles

To export CPSS rxnfiles and REACCS rxnfiles

To export a sequence as ASCII text

To export WMF, HPGL, EPS, and CGM files

To export a sketch to another platform

To paste molfiles or rxnfiles into other applications

Note: Structures in an ISIS/Draw sketch are chemically significant. When you import or cut and paste a structure into another MDL program, it retains its chemical significance.


Sketch File

A sketch file is a binary file, containing a collection of ISIS/Draw objects, that you create when you choose File > Save As. It uses the .SKC file-name extension.

Note: For the Macintosh, a file-name extension is optional.

If you create a sketch file on one platform, you cannot open that file on another platform. To transfer a sketch from one platform to another, save it as a .TGF file.


To import molfiles, rxnfiles, and TGFfiles

Use this procedure to import molfiles, rxnfiles, and TGFfiles.

1.	Choose File > Import > Molfile (or Rxnfile or TGFfile).

Macintosh users: To import a file that was created on the PC, press and hold down the Option key before beginning this step.

2.	Navigate to the disk and directory or folder that contains the file to import.

3.	Highlight the name of the file to import.

4.	Click OK (Mac=Open).


To import TIFF, HPGL, EPS, and CGM files

ISIS/Draw cannot directly import TIFF, HPGL, EPS, or CGM files.

However, you might find a utility program that converts these types of files to the native file format for your computer. The native file formats are PICT and PICT II for the Macintosh, and Windows metafile (.WMF) for the PC.

If you can read the converted file into an application that supports the native format, you can then copy and paste the image into ISIS/Draw.


To export molfiles

Use this procedure to export molfiles.

1.	Select one structure.

2.	Choose File > Export > Molfile.

Macintosh users: To export a molfile for use on the PC, press and hold down the Option key before beginning this step. This saves the molecule as a text (ASCII format) file.

3.	Navigate to the disk and directory or folder where you want to save the exported file.

4.	Enter a name for the file. A file-name extension is optional except when you export molfiles to ChemText and ChemBase.

5.	(Optional) To save a name and comment with the file, click Save/Name Comments and then enter a name and a comment. Then, click OK.

6.	Click OK (Mac=Save).


To export CPSS rxnfiles and REACCS rxnfiles

Use this procedure to export CPSS Rxnfiles and REACCS Rxnfiles.

1.	Select one complete reaction.

2.	Do one of the following:

*	Choose File > Export > CPSS Rxnfile

*	Choose File > Export > REACCS Rxnfile

Macintosh users: To export a CPSS rxnfile or REACCS rxnfile for use on the PC, press and hold down the Option key before beginning this step. This saves the reaction as a text (ASCII format) file.

Note: You can export only one reaction (or step of a multi-step reaction) at a time.

3.	Navigate to the disk and directory or folder where you want to save the exported file.

4.	Enter a name for the file. A file-name extension is optional except when you export rxnfiles to ChemText and ChemBase.

5.	(Optional) To save a name and comment with the file, click Save/Name Comments and then enter a name and a comment. Then, click OK.

6.	Click OK (Mac=Save).


To export TGFfiles

Use this procedure to export TGFfiles.

1.	Choose File > Export > TGFfile.

Macintosh users: To export a TGFfile for use on the PC, press and hold down the Option key before beginning this step. This saves the sketch as a text (ASCII format) file.

2.	Navigate to the disk and directory or folder where you want to save the exported file.

3.	Enter a name for the file.

4.	(Optional) To save a name and comment with the file, click Save/Name Comments and then enter a name and a comment. Then, click OK.

5.	Click OK (Mac=Save).


To export a sketch to another platform

To export an ISIS/Draw sketch to another platform, export it as a TGFfile.

A sketch that is exported as a TGFfile can then be imported by ISIS/Draw on another supported computer platform.

When you export a sketch as a TGFfile, structures in the sketch retain their chemical significance.

If you export sketches from a PC to view on a Macintosh, use Zoom > 133% for a direct pixel-to-pixel match.

If you export sketches from a Macintosh to view on a PC, use Zoom > 75% for a direct pixel-to-pixel match.


To paste molfiles and rxnfiles into other applications

You can paste chemically significant structures and reactions into any application that recognizes MDL's molfile or rxnfile (Chemical Table) file format. Use this procedure to paste a molecule or reaction from ISIS/Draw to an opened application that supports the molfile or rxnfile format.

1.	Choose Options > Settings.

2.	Click the General tab.

3.	To paste chemical information to the Clipboard, you require this setting: Copy Mol/Rxnfile to the Clipboard

4.	(Optional) If you are going to be regularly pasting chemical information to the Clipboard, click Save. This saves your modifications to the currently-open settings file.

5.	Click OK.

6.	Select the structure or reaction that you want to paste into another application.

7.	Choose Edit > Copy. Some of the ISIS/Draw features are not supported when pasted to the Clipboard. If your molecule or reaction contains any of these features, you see a warning that shows the features that will be removed. Click OK.

8.	In the other application, choose Edit > Paste.


To export WMF, HPGL, EPS, and CGM files

Use this procedure to export the image in the active window as a Windows Metafile (.WMF), HPGL, CGM Metafile, or EPS, file. This procedure assumes that you have ConSystant 3.0 installed. For information on ConSystant, see the ConSystant & Chemeleon Reference Manual.

1.	Choose File > Export > Other.

2.	Select the file format for the exported file.

3.	Click OK.

4.	Navigate to the disk and directory or folder where you want to save the exported file.

5.	Enter a name for the file.

6.	Click OK (Mac=Save).


ConSystant & Chemeleon Reference Manual

This manual is included in the individual, boxed copies of ISIS/Draw 2.1. At companies with site licenses, a certain number of these manuals have been provided free of charge. Additional copies can also be purchased. See your ISIS Administrator for details.


TGFfile

A Transportable Graphics File (.TGF) is an ASCII file that contains an exact copy of an ISIS/Draw sketch (including molecules and reactions, if present). When you export a sketch as a TGFfile, ISIS/Draw saves all chemical structures, geometric objects, and text in the current window. Structures in the sketch retain their chemical significance. ISIS/Draw also saves properties, such as pen width, pen color, and font style.

Use TGF files to transfer sketches between versions of ISIS/Draw on supported platforms. For example, you can create a sketch on a PC, export it as a TGFfile, and transfer it to a colleague to import into ISIS/Draw on a Macintosh.

Macintosh Users: (1) A file-name extension is optional. (2) If you are transferring TGFfiles between the Macintosh and other platforms, press and hold down the Option key when importing or exporting TGFfiles. This saves the sketch as a text (ASCII format) file.


Molfile

A molfile contains information about one structure in an ISIS/Draw sketch. It uses the .MOL file-name extension.

Note: For the Macintosh, a file-name extension is optional.


Rxnfile

A rxnfile contains information about one reaction in an ISIS/Draw sketch. It uses the .RXN file-name extension. ISIS/Draw automatically recognizes and reads REACCS-type and CPSS-type rxnfiles.

Note: For the Macintosh, a file-name extension is optional.


REACCS Rxnfile

Contains information about one REACCS-type reaction. Uses the .RXN file-name extension.

Note: For the Macintosh, a file-name extension is optional.


CPSS Rxnfile

Contains information about one CPSS-type reaction. Uses the .RXN file-name extension.


ISIS/Draw Tools

To view information about a tool, click the tool.


ISIS/Base Transfer Icon

Available when you have transferred structures from ISIS/Base to ISIS/Draw for editing in an ISIS/Draw Transfer window. When you press the ISIS/Base Transfer icon, the material in the ISIS/Draw Transfer window is transferred back to ISIS/Base.


Chem Inspector

Click to have ISIS/Draw check to see if there are any problems that might keep you from:

*	Registering a structure or reaction in ISIS/Base

*	Using a structure or reaction to search a database using ISIS/Base

For information on using Chem Inspector, see Verifying the Chemistry of Sketches.


Sequence Tool

Press and hold down the mouse to view a palette where you can choose the Sequence or Sequence Shape tools. For information on creating and shaping sequences, see Working with Biopolymers.


Page Tool

Available after you have opened a template page. Click the highlighted tool to see the last page of templates that you chose. You can then select a fragment.


Previous Template Tool

Available after you have clicked and used a fragment from a template page. Click the highlighted tool to reuse that fragment.


Template Tools

Click one of the template tools to draw a template. For information on using template tools, see Using Template Tools and Pages.


Select Tool

Press and hold down the mouse to view a palette where you can choose the Lasso, Select, or Molecule Select tools.

For information on selecting and deselecting objects, see Section 5.5 of the ISIS/Draw "Quick Start". The ISIS/Draw "Quick Start" is a 14-page document, written in a quick-reference style, that explains most of the basic functionality of ISIS/Draw. We strongly recommend that you print and read this document.


Rotate Tool

Press and hold down the mouse to view a palette where you can choose the 2D or 3D Rotate tools. Use the 2D Rotate tool to rotate objects in the horizontal plane. Use the 3D Rotate tool to rotate structures in the third dimension. For more information, see To rotate an object or To rotate a 3D structure or query


Eraser Tool

Use this tool to delete selected bonds or objects. (If you select an atom, the Eraser tool deletes the selected atom and any bonds adjacent to the atom.)


Atom Tool

Use this tool to add, edit, or delete atom aliases and atom symbols. For information on drawing atoms, see Section 5.4 of the ISIS/Draw "Quick Start". The ISIS/Draw "Quick Start" is a 14-page document, written in a quick-reference style, that explains most of the basic functionality of ISIS/Draw. We strongly recommend that you print and read this document.


Bond Tool

Press and hold down the mouse to view a palette where you can choose the Single, Double, or Triple bond tools.

For information on drawing bonds, see Section 5.3 of the ISIS/Draw "Quick Start". The ISIS/Draw "Quick Start" is a 14-page document, written in a quick-reference style, that explains most of the basic functionality of ISIS/Draw. We strongly recommend that you print and read this document.


Stereo Bond Tool

Press and hold down the mouse to view a palette where you can choose from 6 different types of stereo bonds.

For information on drawing bonds, see Section 5.3 of the ISIS/Draw "Quick Start". The ISIS/Draw "Quick Start" is a 14-page document, written in a quick-reference style, that explains most of the basic functionality of ISIS/Draw. We strongly recommend that you print and read this document.


Chain Tool

Press and hold down the mouse to view a palette where you can choose the Chain or Multi-Bond tool.

For information on drawing chains, see Section 5.3 of the ISIS/Draw "Quick Start". The ISIS/Draw "Quick Start" is a 14-page document, written in a quick-reference style, that explains most of the basic functionality of ISIS/Draw. We strongly recommend that you print and read this document.


Plus Tool

Press to draw a + when you create reactions.

For information on drawing reactions, see Section 5.14 of the ISIS/Draw "Quick Start". The ISIS/Draw "Quick Start" is a 14-page document, written in a quick-reference style, that explains most of the basic functionality of ISIS/Draw. We strongly recommend that you print and read this document.


Arrow Tool

Press and hold down the mouse to view a palette where you can choose from 30 different arrows that you can use when drawing reactions or other sketches.

For information on using tools to draw objects, see Section 5.3 of the ISIS/Draw "Quick Start". The ISIS/Draw "Quick Start" is a 14-page document, written in a quick-reference style, that explains most of the basic functionality of ISIS/Draw. We strongly recommend that you print and read this document.


Map Tool

Press and hold down the mouse to view a palette where you can choose the Atom-Atom Map or Delete Atom-Atom Map tools.

For information on adding and removing atom-atom maps, see Specifying atom-atom maps on a reaction.


Text Tool

Use this tool to enter text, or to attach data to atoms, bonds, or brackets.

For information on working with text, see Section 5.16 of the ISIS/Draw "Quick Start". The ISIS/Draw "Quick Start" is a 14-page document, written in a quick-reference style, that explains most of the basic functionality of ISIS/Draw. We strongly recommend that you print and read this document.

For information on attaching data to objects, see Creating and Editing Attached Data.


Line Tool

Press and hold down the mouse to view a palette where you can choose the Straight Line, Continuous Line, Circular Arc, or Elliptical Arc tools.

For information on using tools to draw objects, see Section 5.3 of the ISIS/Draw "Quick Start". The ISIS/Draw "Quick Start" is a 14-page document, written in a quick-reference style, that explains most of the basic functionality of ISIS/Draw. We strongly recommend that you print and read this document.


Rectangle Tool

Press to view a palette where you can choose the Box, Rounded Box, Ellipse, or Polygon tools.

For information on using tools to draw objects, see Section 5.3 of the ISIS/Draw "Quick Start". The ISIS/Draw "Quick Start" is a 14-page document, written in a quick-reference style, that explains most of the basic functionality of ISIS/Draw. We strongly recommend that you print and read this document.


Bracket Tool

Use this tool to draw brackets when creating polymers and mixtures.

For more information, see Working with Polymers or Working with Mixtures.


To create braces

Use this procedure to create braces for use in presentations.

1.	Click

2.	Draw the following line. To do so, click the mouse at points 1, 2, and 3; then double-click at point 4.

3.	Choose Edit > Duplicate.

4.	Choose Object > Flip Vertical.

5.	Manually align the copy beneath the original:

6.	Select the two portions, then choose Object > Group.

7.	To create the complimentary brace, select the sketch and choose Edit > Duplicate.

8.	Choose Object > Flip Vertical.

9.	To resize the braces, select both, and then drag a corner handle until the braces are the desired size.


To specify an Up or a Down or an Either bond

1.	Do one of the following:

*	To sprout an Up bond from an atom, click

*	To sprout a Down bond from an atom, click

 	*	To sprout either an Up or a Down bond from an atom, click [image]. This is an ISIS bond-query feature that you can use solely with searches that allow query features. For more information on the searches that allow query features, see the ISIS/Base SearchSelector or the ISIS/Base Search Types.

2.	Click the atom of your choice.

See also:

To change an unspecified bond to an Up or a Down bond

To change an Up or a Down bond to an unspecified bond

To change an Up or a Down bond to a single, a double, or a triple bond

To change the direction of an Up or a Down bond

To transfer the query back to ISIS/Base


To specify an Up or a Down bond

1.	Do one of the following:

*	To sprout an Up bond from an atom, click

*	To sprout a Down bond from an atom, click

2.	Click the atom of your choice.

See also:

To change an unspecified bond to an Up or a Down bond

To change an Up or a Down bond to an unspecified bond

To change an Up or a Down bond to a single, a double, or a triple bond

To change the direction of an Up or a Down bond

To transfer the query back to ISIS/Base


To change an unspecified bond to an Up or a Down bond

1.	Do one of the following:

*	To change an unspecified bond or an EITHER bond to an Up bond, click

*	To change an unspecified bond or an EITHER bond to a Down bond, click

2.	Click the bond of your choice.


Either Bond

An EITHER bond allows you to specify that you want an undefined stereo bond at a specific position rather than an Up bond or a Down bond at that position. For example:


To change an Up or a Down bond to an Either bond

Use this procedure to change an Up or a Down bond to an Either bond. An Either bond retrieves molecules with either an Up or a Down bond in the specified position. You can use Either bonds solely with searches that allow ISIS bond-query features. For more information on the searches that allow query features, see the ISIS/Base SearchSelector or the ISIS/Base Search Types.

1.	Click

2.	Click the existing Up or the Down bond of your choice.


To change an Up or a Down bond to a single, a double, or a triple bond

1.	Click [image], [image], or

2.	Click the existing Up or the Down bond of your choice.


To change the direction of an Up or a Down bond

1.	Do one of the following:

*	To change the direction of an Up bond, click

*	To change the direction of a Down bond, click

2.	Click the existing Up bond or Down bond of your choice.


To specify stereo boxes on cis or trans configurations

To retrieve either cis or the trans stereoconfigurations (but not both) from a substructure search, use the following procedure. To retrieve either cis or the trans stereoconfigurations for all other searches, you must draw the exact cis or trans stereoconfiguration. Example

1.	Select the asymmetric double bond of your choice. The bond must be attached to one of the following atoms: C, N, O, P, S, or Si.

2.	Double-click the selected bond.

3.	Click the Bond tab.

4.	To specify stereo boxes, you require this setting:  Stereo Search.

5.	Click OK.

See also:

To delete stereo boxes


Example

The cis configuration is not retrieved:


To delete stereo boxes

To retrieve both cis and trans stereoconfigurations with a substructure query, use the following procedure. This procedure assumes that you have a structure in ISIS/Draw that contains a stereo box.

Note: To retrieve cis and trans stereoconfigurations with a structure query, draw either the cis or the trans stereoconfiguration and conduct a FLEX search.

1.	Select the double bond that contains the stereo box.

2.	Double-click the selected bond.

3.	Click the Bond tab.

4.	To delete stereo boxes, you require this setting:  Stereo Search.

5.	Click OK.


To specify an Either bond

1.	Click

2.	Click the atom of your choice.

See also:

To change an Either bond to an Up or a Down bond

To change an Either bond to a single, a double, or a triple bond


To specify an Either bond

1.	Click

2.	Click the atom of your choice.

See also:

To change an Either bond to an Up or a Down bond

To change an Either bond to a single, a double, or a triple bond


To specify an Either bond

1.	Click

2.	Click the atom of your choice.

See also:

To change an Either bond to an Up or a Down bond

To change an Either bond to a single, a double, or a triple bond


To change an Either bond to an Up or a Down bond

1.	Do one of the following:

*	To change an EITHER bond to an Up bond: Click

*	To change an EITHER bond to a Down bond: Click

2.	Click the bond of your choice.


To change an Either bond to a single, a double, or a triple bond

1.	Click [image], [image], or

2.	Click the bond of your choice.


Sketch Tables

Click here for step-by-step instructions

A sketch table is made up of text or graphical objects arranged in rows and columns. You create sketch tables in ISIS/Draw; and these can include any text or graphical object.

Sketch tables are not the same as tables that you see in database forms in ISIS/Base. You create tables in ISIS/Base forms within the database.


Drawing Sketch Tables

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Aligning columns vertically	6.1

*	Aligning numbers on a decimal point	6.2

*	Equalizing the white space between rows	6.3

*	Aligning a row of data or column titles horizontally 	6.4

*	Aligning multi-line column titles or row titles vertically	6.5

*	Moving rows or columns	6.6

*	Adding horizontal lines	6.7

*	Making a sketch table into an overhead transparency	6.8

We recommend that you print this 6-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

Sketch tables are made up of text or graphical objects, aligned in rows and columns, and saved as a sketch file (not as a "table"). This document emphasizes the ways you might use the Align command to make your data look neater. Here is a typical example of text and structures that you might want to convert into a sketch table:

The next illustration shows a sketch table with rows and columns aligned, and horizontal lines added. The procedures that follow use this table as an example.

To draw a sketch table, you typically perform the following operations in the order shown:

*	Align columns vertically

*	Align numbers on a decimal point

*	Equalize the white space between rows

*	Align a row of data or column titles horizontally

*	Align multi-line column or row titles vertically

*	Move rows or columns

*	Adding horizontal lines

6.1 To align columns vertically

Use this procedure to vertically align a column of text or structures:

1.	(Optional) If you cannot view all of your columns at the same time, choose Options > Zoom > 75%.

2.	Select the text or structures in the column. Include the column title if you want to align it with the data.

3.	Choose Object > Align.

4.	Click Left Sides, Left/Right Centers, or Right Sides in the Vertical box.

5.	Click None in the Horizontal box.

6.	Click OK.

6.2 To align numbers on a decimal point

Use this procedure to vertically align numbers on a decimal point:

1.	(Optional) If you cannot view all of your columns at the same time, choose Options > Zoom > 75%.

2.	Click

3.	Press the Shift key as you draw a vertical line over the numbers that you want to align.

4.	Click

5.	Select one of the numbers to align.

6.	Press the left or right arrow key to move the number left or right.

7.	Repeat Steps 5 and 6 until all the numbers are correctly aligned.

8.	Select the vertical line, and then choose Edit > Clear.

6.3 To equalize the white space between rows

Use this procedure to equalize the space that is between each horizontal row. Before you begin this procedure, determine which column includes the largest sketch object.

Note: Do not use this procedure for text in column headings.

1.	(Optional) If you cannot view all of your columns at the same time, choose Options > Zoom > 75%.

2.	Select all of the objects in the column that includes the largest object.

3.	Choose Object > Align.

4.	Click Left Sides, Left/Right Centers, or Right Sides in the Vertical box.

5.	Click None in the Horizontal box.

6.	You require the following setting: Space Evenly.

7.	Click OK.

6.4 To align a row of data or column titles horizontally

Use this procedure to align data in a horizontal row. You can also align column titles, including multi-line titles, horizontally across the width of the page:

1.	(Optional) If you cannot view all of your columns at the same time, choose Options > Zoom > 75%.

2.	Select the data or titles in the row that you want to align horizontally.

3.	Choose Object > Align.

4.	Click None in the Vertical box.

5.	Click Tops, Top/Bottom Centers or Bottoms in the Horizontal box.

6.	Click OK.

6.5 To align multi-line column titles or row titles vertically

Use this procedure to align a multi-line column or row title vertically so that the left or right edges of the text line up, or the text is centered:

1.	(Optional) If you cannot view all of your columns at the same time, choose Options > Zoom > 75%.

2.	Select the multi-line row or column title that you want to align.

3.	Choose Text > Font.

4.	Click Left, Center, or Right in the left section of the Text Alignment box.

5.	Click Top, Center, or Bottom in the right section of the Text Alignment box.

6.	Click OK.

6.6 To move rows or columns

Use this procedure to rearrange your sketch table by moving a row or column to another position:

1.	(Optional) If you cannot view all of your columns at the same time, choose Options > Zoom > 75%.

2.	Select all of the objects in the row or column (including title) that you want to move.

3.	Choose Object > Group.

4.	Press the left, right, up, or down arrow key to move the row or column in one pixel increments.

5.	Choose Object > Ungroup.

6.7 To add horizontal lines

1.	(Optional) If you cannot view all of your columns at the same time, choose Options > Zoom > 75%.

2.	Click

3.	Press the Shift key and draw a horizontal line where you need it.

4.	Choose Edit > Duplicate and make as many copies of the horizontal line as necessary.

5.	Click

6.	Select and move each horizontal line to the desired location.

7.	Select all of the horizontal lines and choose Object > Align.

8.	Click Left Sides or Right Sides in the Vertical box.

9.	Click None in the Horizontal box.

10.	Click OK.

6.8 To make a sketch table into an overhead transparency

Print the sketch table. Put a sheet of special transparent film into the paper tray of the photocopier, then photocopy the sketch table onto the plastic film.

To create effective overhead transparencies:

*	Limit the amount of text on a transparency. Be concise. Your overheads should show only the main ideas, and your talk should provide details. When you show the audience only the key points, you help them to focus on the central ideas.

*	Include 3 to 5 ideas on an overhead. Your overhead transparencies will be hard to read if you include too many ideas. Do not reduce the font size to add extra text.

*	Increase the font size to make the transparencies more readable. For a presentation to a small group that is close to the screen, use 18-point type for the body of the text and 24-point type for titles. For a larger audience, use 24-point type for the body of the text with 48-point type for titles.

*	Use two kinds of overhead transparencies: all-graphics and all-text. If you mix graphics and text, the text will be hard for those in a large audience to read.

*	Use graphs instead of a sketch table. Graphs that contain different pen and line styles give the same information to your audience as a sketch table and are much easier to understand.

*	Give each transparency a title that indicates its contents. The audience can see immediately the topic that you are discussing.


Predefined Abbreviated Structures Available Via the Keyboard

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Alpha-D-Sugars	7.1

*	Amino Acids	7.2

*	Aromatics	7.3

*	Beta-D-Sugars	7.4

*	Carbonyls	7.5

*	D-Sugars	7.6

*	L-Amino Acids	7.7

*	Down L-Amino Acids	7.8

*	Up L-Amino Acids	7.9

*	Nitrogen	7.10

*	Phosphorus	7.11

*	More Rings	7.12

We recommend that you print this 5-page Request-A-Document and then browse through it. To print this document, click the Printer icon at the top of the screen.

This document lists the predefined abbreviated structures that are included with ISIS/Draw 2.1. An abbreviated structure is all or part of a structure that has been abbreviated to a text label. Structures that you abbreviate keep their chemical significance, but their underlying structure is hidden.

In this example, the phenyl rings in the 2,5-diphenylfuran are abbreviated to the text string Ph:

Abbreviated structures are saved as ISIS/Draw sketch files. You can add them to your sketch with the keyboard.

Note: Sketches that you want to use as abbreviated structures must be located in the same directory or folder as your template files.

Before you can use the keyboard abbreviated structures included with ISIS/Draw, choose Options > Settings and click the General tab. You require the following setting: Abbreviate typed-in templates.

7.1 Alpha-D-Sugars

ADALLOS	ADLYXOP

ADALTRO	ADMANNO

ADARABIF	ADPSICO

ADARABIP	ADRIBOF

ADERYTH	ADRIBOP

ADGALAC	ADSORBO

ADGULAO	ADTAGAT

ADGLUCO	ADTALOS

ADIDOSE	ADTHREO

ADLYXOF	ADXYLOF

ADXYLOP

7.2 Amino Acids

ALA	LEU

ARG	LYS

ASN	MET

ASP	PHE

CYS	PRO

GLN	SER

GLU	THR

GLY	TRP

HIS	TYR

IIE	VAL

Caution: These abbreviated structures use the same three-letter abbreviations as some entries in the extended Periodic Table. How you enter the three-letter abbreviation determines what ISIS/Draw adds to your sketch.

*	To add the complete structure of the amino acid, enter the name in uppercase letters, such as CYS.

*	To represent the amino acid as a pseudoatom in the extended Periodic Table, enter the name in lowercase or mixed case letters, such as cys or Cys.

Note: The same issue exists when you enter NO. In addition, custom template files created by users might conflict with entries in the standard and extended Periodic Tables.

7.3 Aromatics

PH

NAPH

CPH3

BZ

OBN

OBZ

PY

PYRIM

7.4 Beta-D-Sugars

BDALLOS	BDLYXOP

BDALTRO	BDMANNO

BDARABIF	BDPSICO

BDARABIP	BDRIBOF

BDERYTH	BDRIBOP

BDFRUCT	BDSORBO

BDGALAC	BDTAGAT

BDGLUCO	BDTALOS

BDGULOS	BDTHREO

BDIDOSE	BDXYLOF

BDLYXOF	BDXYLOP

7.5 Carbonyls

CHO	COOET

COOH	CONET

CONH2	CONET2

COSH	COBR

COF	COTBU

COME	COOTBU

COOME	COPH

CONME	COCO

CONME2	COCF3

COCL	COONA

COET	COOPH

7.6 D-Sugars

DALLOS	DMANNO

DALTRO	DPSICO

DARABI	DRIBOS

DERYTH	DRIBUL

DERYTHU	DSORBO

DFRUCT	DTAGAT

DGALAC	DTALOS

DGLUCO	DTHREO

DGLUCOS	DXYLOS

DIDOSE	DXYLUL

DLYXOS

7.7 L-Amino Acids

These use the following convention to represent stereochemistry:

LALA	LLEU

LARG	LLYS

LASN	LMET

LASP	LPHE

LCYS	LPRO

LGLN	LSER

LGLU	LTHR

GLY	LTRP

LHIS	LTYR

LILE	LVAL

7.8 Down L-Amino Acids

These have the same abbreviations as L-Amino Acids, but use the following convention to represent stereochemistry:

LALA	LLEU

LARG	LLYS

LASN	LMET

LASP	LPHE

LCYS	LPRO

LGLN	LSER

LGLU	LTHR

GLY	LTRP

LHIS	LTYR

LILE	LVAL

7.9 Up L-Amino Acids

These have the same abbreviations as L-Amino Acids and Down L-Amino Acids, but use the following convention to represent stereochemistry:

LALA	LLEU

LARG	LLYS

LASN	LMET

LASP	LPHE

LCYS	LPRO

LGLN	LSER

LGLU	LTHR

GLY	LTRP

LHIS	LTYR

LILE	LVAL

7.10 Nitrogen

CN	NO

N2	NO2

N3	NO3

NC	NOH

NCO	NBS

NCS	NET3

NME2	NET4

NME3	NBU4

7.11 Phosphorus

PO3	POOET2

PO4	PPH2

POET2	PPH3

POET3	PF6

7.12 More Rings

RING3	RING12

RING4	RING13

RING5	RING14

RING6	RING15

RING7	RING16

RING8	RING18

RING9	RING20

RING10	RING21

RING11


ISIS/Base Remote Chemical Searches (Subset)

New users: If you do not know exactly which remote search you need, see How To Choose the Best Type of Search -- and How to Do It.

Molecule Record (Remote Searches):

QB    RGROUP    SBF    SSS    SSS/Biopoly

Reaction Records (Remote Searches):

QB   RGROUP    RSS/Comp    RSS/Rxn    SBF    SSS

3D Structure Records (Remote Searches):

CFS   CFS/Biopoly    QB    SBF    SSS3D     SSS3D/Biopoly


ISIS/Base Local Chemical Searches (Subset)

New users: If you do not know exactly which search you need, see How To Choose the Best Type of Search -- and How to Do It.

Molecule Record (Local Searches):

QB    SBF    SSS    SSS/Biopoly

Reaction Records (Local Searches):

QB    RSS/Comp    RSS/Rxn    SBF    SSS

3D Structure Records (Local Searches):

QB    SBF


ISIS/Base Remote Chemical Searches

New users: If you do not know exactly which search you need, see How To Choose the Best Type of Search -- and How to Do It.

Reaction Records (Remote Searches):

QB   RSS/Comp    RSS/Rxn


Specifying Stereochemistry

Click one of the following items:

*	For an exact match search in a remote database (such as MEXACT or REXACT/Rxn).

*	For an exact match search in a local database (such as MEXACT or REXACT/Rxn).

*	For a molecule or reaction substructure search in a remote database (such as SSS or RSS).

*	For a molecule or reaction substructure search in a local database (such as SSS or RSS).

*	For a search in the Query Builder in a remote database.

*	For a search in the Query Builder in a local database.


Specifying Stereochemistry

There are 3 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Stereo Boxes on Cis or Trans Configurations

*	Chiral Flags on Molecules


Specifying Stereochemistry

There are 3 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Cis or Trans Configurations

*	Chiral Flags on Molecules


Specifying Stereochemistry

There are 2 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Stereo Boxes on Cis or Trans Configurations


Specifying Stereochemistry

There are 2 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Cis or Trans Configurations


Specifying Stereochemistry

There are 3 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Cis or Trans Configurations

*	Chiral Flags on Molecules


Specifying Stereochemistry

There are 2 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Cis or Trans Configurations


Specifying Stereochemistry

There are 3 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Cis or Trans Configurations

*	Chiral Flags on Molecules


Specifying Stereochemistry

There are 3 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Cis or Trans Configurations

*	Chiral Flags on Molecules


Specifying Stereochemistry

There are 3 ways to specify stereochemistry in biopolymers.

Click one of the following:

*	Up and Down Bonds

*	Stereo Boxes on Cis or Trans Configurations

*	Chiral Flags on Biopolymers


Specifying Stereochemistry

There are 2 ways to specify stereochemistry in biopolymers.

Click one of the following:

*	Up and Down Bonds

*	Stereo Boxes on Cis or Trans Configurations


Atom-Atom Mapping Guidelines

Use the following guidelines to help you to atom-atom map your query correctly:

Always atom-atom map a query that contains an entire reaction (at least a reactant and a product). Do not attempt to atom-atom map a query that contains solely a reaction component and a reaction arrow.

Note: We strongly recommend that you draw solely the reacting fragments (and use query features where relevant) rather than draw each reactant and product in detail.

Only map those specific atoms that you see in both the reactants and the products. For example, do not map the oxygen atom that you see only in the product:

To simplify the atom-atom mapping process, map your query automatically with the automap feature. However, there are specific times when you need to map a portion of your query manually, and then apply the automap feature to finish the task. For example, map a portion of your query manually if it is unbalanced or if it is mapped incorrectly with the automap feature.

An unbalanced reaction query is a reaction query that contains multiple mappings of a single atom. You need to manually map enough of the atoms to allow the automap feature to map your query correctly. (This typically requires two to three mapped atoms that surround the reacting center bond.) Then select the entire query and automap it. For example:

*	Select a reactant atom and a product atom that you want to specify as Atom 1 and map them manually.

*	Select the same atom in the reactant and another atom in the product that you want to specify as Atom 1 (a multiple mapping of Atom 1) and map them manually. For example, you see the following:

*	Select the entire query and automap it.

Inspect the atom-atom maps on a reaction query before you use the query to conduct a search. If you notice that a map is incorrect, delete it entirely. You need to manually map enough of the atoms to allow the automap feature to map your query correctly. Then select the entire query and re-automap it.

Always atom-atom map a reaction query last, after you add all other structures, stereochemistry, and/or query features to your query.


Up And Down Bonds

Click here for step-by-step instructions

You can create a query with an Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si:


Up And Down Bonds

Click here for step-by-step instructions

You can create a query with an Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si:


Stereo Boxes on Cis or Trans Configurations

Click here for step-by-step instructions

To retrieve molecules that match the cis or trans configuration (but not both) in your query, draw the configuration, and then place a stereo box on the asymmetric double bond that is attached to atoms C, N, O, P, S, or Si. (Without the stereo box, you retrieve both the cis and the trans configuration.) For example:

The cis configuration is not retrieved:


Cis or Trans Configurations

To retrieve molecules that match the cis or trans configuration (but not both) in your query, draw the configuration that you want to find. For example:

The cis configuration is not retrieved:


Cis or Trans Configurations

To retrieve molecules that match the cis or trans configuration (but not both) in your query, draw the configuration that you want to find. For example:


Cis or Trans Configurations

To retrieve molecules that match the cis or trans configuration (but not both) in your query, draw the configuration that you want to find. For example:


Cis and Trans Configurations

In a QB search, the way that you specify cis and trans configurations in a graphical query depends on the type of search operator that you use.

Click one of the following items:

*	The Search Operator is SSS.

*	The Search Operator is not SSS, such as = (equal sign), FLEXMATCH, ISOMER, MSIMILAR, PARENT, and TAUTOMER.


Cis and Trans Configurations

In a QB search, the way that you specify cis and trans configurations in a graphical query depends on the type of search operator that you use.

Click one of the following items:

*	The Search Operator is SSS.

*	The Search Operator is = (equal sign).


Chiral Flags on Molecules

Click here for step-by-step instructions

In a remote database, you can create a query with a chiral flag on a molecule with at least one asymmetric center or on a molecule that is asymmetric to retrieve solely the absolute stereoconfiguration but not relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

For information on using queries with geometric and tetrahedral stereochemistry, click here.


Using Queries with Geometric and Tetrahedral Stereochemistry

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.


Either Bonds

Click here for step-by-step instructions

You can create a query with an EITHER bond to retrieve molecules with an undefined single stereo bond at a specified position rather than an Up bond or a Down bond at that position. For example:


Specifying Stereochemistry

There are 3 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Stereo Boxes on Cis or Trans Configurations

*	Chiral Flags on Reaction Components


Specifying Stereochemistry

There are 3 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Cis or Trans Configurations

*	Chiral Flags on Reaction Components


Specifying Stereochemistry

There are 3 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Cis or Trans Configurations

*	Chiral Flags on Reaction Components


Specifying Stereochemistry

There are 3 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Cis or Trans Configurations

*	Chiral Flags on Molecules


Specifying Stereochemistry on a Reaction Component

There are 3 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Stereo Boxes on Cis or Trans Configurations

*	Chiral Flags on Reaction Components


Cis and Trans Configurations

In a QB search, the way that you specify cis and trans configurations in a graphical query depends on the type of search operator that you use.

Click one of the following items:

*	The Search Operator is SSS or RSS.

*	The Search Operator is not SSS or RSS, such as = (equal sign), FLEXMATCH, ISOMER, MSIMILAR, PARENT, RSIMILAR, SUBSET, and TAUTOMER.


Cis and Trans Configurations

In a QB search, the way that you specify cis and trans configurations in a graphical query depends on the type of search operator that you use.

Click one of the following items:

*	The Search Operator is SSS or RSS.

*	The Search Operator is not SSS or RSS, such as = (equal sign), FLEXMATCH, ISOMER, MSIMILAR, PARENT, RSIMILAR, SUBSET, and TAUTOMER.


Cis and Trans Configurations

In a QB search, the way that you specify cis and trans configurations in a graphical query depends on the type of search operator that you use.

Click one of the following items:

*	The Search Operator is SSS or RSS.

*	The Search Operator is = (equal sign).


Cis and Trans Configurations

In a QB search, the way that you specify cis and trans configurations in a graphical query depends on the type of search operator that you use.

Click one of the following items:

*	The Search Operator is SSS or RSS.

*	The Search Operator is = (equal sign).


Specifying Stereochemistry

There are 2 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Stereo Boxes on Cis or Trans Configurations


Specifying Stereochemistry

There are 2 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Cis or Trans Configurations


Specifying Stereochemistry

There are 3 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Cis or Trans Configurations

*	Chiral Flags on Reaction Components


Specifying Stereochemistry

There are 2 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Cis or Trans Configurations


Specifying Stereochemistry

There are 2 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Cis or Trans Configurations


Specifying Stereochemistry

There are 2 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Cis or Trans Configurations


Specifying Stereochemistry

There are 3 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Cis or Trans Configurations

*	Chiral Flags on Reaction Components


Specifying Stereochemistry

There are 2 ways to specify stereochemistry.

Click one of the following:

*	Up and Down Bonds

*	Cis or Trans Configurations


Up or Down Bonds

Click here for step-by-step instructions

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve reactions with matching stereochemistry on the reaction components. For example:


Up or Down Bonds

Click here for step-by-step instructions

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve reactions with matching stereochemistry on the reaction components. For example:


Stereo Boxes on Cis or Trans Configurations

Click here for step-by-step instructions

To retrieve reaction records with reaction components that match the cis or trans configuration (but not both) in your query, draw the configuration, and then place a stereo box on the asymmetric double bond that is attached to atoms C, N, O, P, S, or Si. (Without the stereo box, you retrieve both the cis and the trans configuration.) For example:

The cis configuration is not retrieved:


Stereo Boxes on Cis or Trans Configurations

Click here for step-by-step instructions

To retrieve molecule records or reaction records with reaction components that match the cis or trans configuration (but not both) in your query, draw the configuration, and then place a stereo box on the asymmetric double bond that is attached to atoms C, N, O, P, S, or Si. (Without the stereo box, you retrieve both the cis and the trans configuration.) For example:

The cis configuration is not retrieved:


Cis or Trans Configurations

To retrieve reactions with reaction components that match the cis or trans configuration (but not both) in your query, draw the configuration that you want to find. For example:

The cis configuration is not retrieved:


Cis or Trans Configurations

To retrieve reactions that match the cis or trans configuration (but not both) in your query, draw the configuration that you want to find. For example:

The cis configuration is not retrieved:


Cis or Trans Configurations

To retrieve reactions that match the cis or trans configuration (but not both) in your query, draw the configuration that you want to find. For example:

The cis configuration is not retrieved:


Chiral Flags on Reaction Components

Click here for step-by-step instructions

In a remote database, a chiral flag on a reaction component with at least one asymmetric center or on a reaction component that is asymmetric allows you to retrieve solely the absolute stereoconfiguration but not relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

For information on using queries with geometric and tetrahedral stereochemistry, click here.


To display an implicit hydrogen

Use this procedure to display an implicit hydrogen on an atom.

Note: ISIS does not recognize implicit hydrogens in a search query, even if you display them. If you want to create a search query that allows solely hydrogen atoms at specified positions in the structures retrieved, you must draw explicit hydrogens. To create an explicit hydrogen, click here.

Examples of Implicit and Explicit Hydrogens

1.	Select the atom from which you want to sprout the explicit hydrogen.

2.	Choose Object > Edit Atom.

3.	Click the Symbol box and choose H.

4.	(Optional) To specify the position of the implicit hydrogen, click the Hydrogens box and choose an option.

5.	Click OK.


Examples


Radicals

To specify a radical in ISIS/Draw, enter one of the following characters after the atom symbol:

:	(singlet diradical)

.	(doublet monoradical)

^^	(triplet diradical)


Explicit Hydrogen

An explicit hydrogen is a hydrogen that is attached to an atom by a visible bond. For example:

Note: You can add explicit hydrogens to a search query at specific positions to block substitutions.


Implicit Hydrogen

An implicit hydrogen is a hydrogen that is either assumed to be present (invisible) or attached to an atom by an invisible bond. For example:

Note: ISIS does not recognize implicit hydrogens in a search query, even if you show them.


To allow explicit hydrogen atoms

To allow solely hydrogen atoms at specified positions in the structures retrieved, you must draw explicit hydrogens in your search query. You can also draw explicit hydrogens to block substitutions at specific positions in the structures retrieved. Use the following procedure to draw an explicit hydrogen on an existing atom.

Note: ISIS does not recognize implicit hydrogens in a search query, even if you show them. For information on how to create implicit hydrogens, click here.

1.	Click

2.	Click an existing atom (non-hydrogen) and sprout a single bond.

3.	Click

4.	Click the terminal atom where you only want hydrogens in the structures that you retrieve.

5.	Choose H.

6.	Click elsewhere.


Working with Abbreviated Structures

An abbreviated structure is all or part of a structure (molecule or reaction component) that has been abbreviated to a text label. Structures that you abbreviate keep their chemical significance, but their underlying structure is hidden. Examples

You can use queries (including reaction queries) that contain abbreviated structures to search a database using ISIS/Base. ISIS/Base uses the underlying chemistry and ignores the name.

Note: In earlier versions of ISIS/Draw, abbreviated structures were called superatoms.

Click one of the following:

To create an abbreviated structure

To expand an abbreviated structure

To contract an abbreviated structure

To edit an abbreviated structure

To rename an abbreviated structure

To type predefined abbreviated structures using the keyboard

To create a predefined abbreviated structure

Note: If your structure contains a specific number of identical repeating units, you can use a multiple group to draw the structure in condensed form.


To create an abbreviated structure

Use this procedure to create an abbreviated structure.

1.	Select the portion of the structure whose underlying chemistry you want to hide. You must select the one (and only) bond that connects the part of the structure that you want to abbreviate to the rest of the structure.

2.	Choose Chemistry > Residue > Create.

3.	Enter a name of your choice for the abbreviated structure. The name can be anything that you choose.

If you use a query that contains an abbreviated structure to search a database using ISIS/Base, ISIS/Base ignores the name and uses the underlying chemistry for the search.

4.	Click OK.


To expand an abbreviated structure

Use this procedure to display the underlying chemistry of an abbreviated structure.

1.	Select the name of the abbreviated structure.

2.	Choose Chemistry > Residue > Expand.

3.	(Optional) To hide the underlying chemistry, choose Chemistry > Residue > Contract.

Note: If you use a query that contains an abbreviated structure to search a database using ISIS/Base, ISIS/Base ignores the name and uses the underlying chemistry for the search. It doesn't matter if the underlying chemistry is visible or hidden.


To edit an abbreviated structure

Use this procedure to first display the underlying chemistry of an abbreviated structure, and then edit it.

1.	Select the name of the abbreviated structure.

2.	Choose Chemistry > Residue > Expand.

3.	Edit the structure.

4.	(Optional) To hide the underlying chemistry, select the portion of the structure whose underlying chemistry you want to hide. You must select the one (and only) bond that connects the part of the structure that you want to abbreviate to the rest of the structure. Then, choose Chemistry > Residue > Contract.


To rename an abbreviated structure

Use this procedure to rename an abbreviated structure.

1.	Select the name of the abbreviated structure.

2.	Choose Chemistry > Residue > Rename.

3.	Enter a new name for the abbreviated structure. The name can be anything that you choose.

If you use a query that contains an abbreviated structure to search a database using ISIS/Base, ISIS/Base ignores the name and uses the underlying chemistry for the search.

4.	Click OK.


Example
Examples

In the following examples, the phenyl rings in the structures are abbreviated to the text string Ph:


To contract an abbreviated structure

Use this procedure to hide the underlying chemistry of an abbreviated structure that already exists. To create a new abbreviated structure, see To create an abbreviated structure.

1.	Select the portion of the structure whose underlying chemistry you want to hide. You must select the one (and only) bond that connects the part of the structure that you want to abbreviate to the rest of the structure.

2.	Choose Chemistry > Residue > Contract.


Working with Biopolymers

The following help screen assumes that you know how to draw molecules in ISIS/Draw. To learn the essential ISIS/Draw skills, read the ISIS/Draw Quick Start.

Click any of the following:

*	What is a Biopolymer?

*	The Steps for Drawing Biopolymers

*	Customizing a List of Residue Codes

*	Customizing the Sequence Menu

*	Importing Biopolymers

*	Pasting Biopolymers into ISIS/Draw

*	Exporting Biopolymers

*	Searching for Biopolymers


      What is a Biopolymer?

A biopolymer sequence is a linear chain of connected repeating structures that are called residues. In the following example, you see the residue codes for one of the protein Bovine Insulin, which contains 21 amino acid residues:

H2N-G I V E Q C C A S V C S L Y Q L E N Y C N-COOH

In ISIS, the list of residue codes that you can use are defined in a Residue Map file that uses the structures from a Residue Template file. In this example, the Residue Map file contains the list of 1-letter residue codes for the amino acid residues. MDL provides you with Residue Map files for 1- and 3-letter residue codes for amino acids and for the nucleic acids DNA and RNA. The sequence bond between each residue is formed by the connection of atoms that are specified within the Residue Template file.

If the list of residue codes or their underlying structures are not sufficient for your specific needs, you can edit an existing Residue Map file or Residue Template file or create your own.

To improve the readability of a sequence, you can group residues into suitably sized blocks, limit the number of residues per line, or change the spacing between blocks or residues:


The Steps for Drawing a Biopolymer

Do these steps in the order shown:

1.	(Optional) Customize the display settings.

2.	Specify the list of residue codes to use.

3.	Enter all the residue codes (build the sequence).

4.	(Optional) Edit any portion of the sequence.

5.	(Optional) Expand a residue and edit its underlying chemical structure.

6.	(Optional) Shape a line of residue codes.

7.	(Optional) Check the chemistry of the sequence or residue.


The Steps for Drawing Biopolymer Fragments

Do these steps in the order shown:

1.	(Optional) Customize the display settings.

2.	Specify the list of residue codes to use.

3.	Enter all the residue codes (build the sequence).

4.	(Optional) Edit any portion of the sequence.

5.	(Optional) Expand a residue and edit its underlying chemical structure.

6.	(Optional) Shape a line of residue codes.

7.	(Optional) Check the chemistry of the sequence or residue.


Customizing the Display Settings

You can customize the settings for the ways that you want biopolymer sequences to be displayed as you create them. For example, the default setting displays all residues of a biopolymer sequence on the same line that might extend beyond the width of the drawing window. You can customize the number of residues per line so that additional residues wrap to the next line.

You can also group the residues within each line into blocks of any length, hide or display sequence bonds, crosslink bonds, leaving groups, and residue brackets; or change the delimiters.

Note: You can change your customized settings at any time.

Click here for step-by-step instructions


To customize the display settings

You can change the following default settings for drawing sequences:

*	Spacing Between Residues

*	Spacing Between Blocks

*	Spacing Between Lines

*	Number of Blocks in a Line

*	Number of Residues in a Block

*	Show/Hide Sequence Bonds

*	Show/Hide Crosslink Bonds

*	Show/Hide Residue Brackets

*	Show/Hide Leaving Groups

*	Define the Delimiter

To change these defaults, choose Options > Settings and click the Sequence Tab. Change the defaults of your choice, and then click OK. For more information, click Help in the dialog box, or click here.


Specifying the List of Residue Codes to Use

In ISIS, a list of residue codes is the set of residue codes that you use to create the sequence. For example, you might want to specify that your list of residue codes is the set of amino acid residue codes or the set of DNA residue codes.

Also, you might want to specify that your list of residue codes is 1-letter instead of 3-letter. Thus, to create a sequence with the amino acid residue Arginine, you can enter the 1-letter code R instead of the 3-letter code Arg.

Click here for step-by-step instructions


To specify the list of residue codes

Use the following procedure to specify the list of residue codes that you want to use to build a biopolymer sequence. Every list of residue codes that are available for use must be listed on the Sequence menu.

1.	Choose Chemistry > Sequence, and then choose the list of residue codes that you want. MDL provides you with the following lists of residue codes on the Sequence menu: Amino Acids - 1 letter (for 1-letter amino acid structures); Amino Acids- 3 letter (for 3-letter amino acid structures); DNA - 1 letter (for deoxyribonucleic acid structures); or RNA - 1 letter (for ribonucleic acid structures).

Note: To use a list of residue codes that is not on the Sequence menu or to customize a list, click Customizing a List of Residue Codes.

2.	To view the current list of residue codes that you chose in Step 1, choose Chemistry > Sequence. You require [image] Show Residue List.

If you do not see the current list, click [image].


Entering All the Residue Codes

You can either type in your residue codes from the keyboard or click the residue codes from a list. Either method displays residues that are in a contracted form.

Click one of the following:

To type in residue codes from the keyboard

To click residue codes from a list


To type a sequence from the keyboard

You can type a sequence of residues directly from the keyboard:

1.	Click [image].

2.	(Optional) To see the list of residues, choose Chemistry > Sequence. You require [image] Show Residue List.

3.	Type in the residue codes of your choice. You see the contracted residues and terminal leaving groups.

4.	(Optional) To enter a residue code that you do not see on the list, click Customizing a Residue.

5.	(Optional) To specify the end of a block of residues as you enter residues into the ISIS/Draw window, press the Space key.

6.	(Optional) Customize the settings for the way that you want biopolymer sequences to be displayed.

Caution: If you do not specify the number of residues per line, all the residue codes that you type will remain on a single line that might extend past the drawing window. However, you can insert a line break anywhere if you press the Return key.

See also:

Using Editing Keys


Example

For example, if you enter the amino acid residue codes F (for phenylalanyl), R (for arginyl), C (for cysteinyl), A (for alanyl), and T (for threonyl), you see:


Delimiter

A delimiter is the character that you type to specify at the end of a delimited residue code. (To use residue codes that are of different lengths, click Delimited in the Code Length list box.) A delimited residue code is a residue code of variable length.

A delimiter can be one of the following: A hyphen (-), a colon (:), a semicolon (;), a period (.), a space, the TAB key, the Return key, or any other character of your choice.


To click residue codes from a list

You can create a sequence by selecting residue codes from a list of residue codes:

1.	Click [image].

2.	To see the list of residues, choose Chemistry > Sequence. You require [image] Show Residue List.

3.	Click in the drawing area where you want to begin the sequence.

4.	Double-click the residue codes of your choice from the list of residue codes. You see the contracted residues and terminal leaving groups.

5.	(Optional) To enter a residue code that you do not see on the list, click Customizing a Residue.

6.	(Optional) Customize the settings for the way that you want biopolymer sequences to be displayed.

Caution: If you do not specify the number of residues per line, all the residue codes that you type will remain on a single line that might extend past the drawing window. However, you can insert a line break anywhere if you press the Return key.

See also:

Using Editing Keys


Customizing a Residue

If you want to enter a residue that you do not see on the list of residue codes available for your use, you can either customize a residue and then use it one time only or customize the list of residue codes so that you can use a customized residue more than one time only.

Click one of the following:

To customize a residue for one-time usage

To customize a list of residue codes


To customize a residue for one-time usage

Use this procedure to customize a residue for one-time usage.

1.	Click [image].

2.	Click the area in ISIS/Draw where you want to enter the customized residue.

3.	Type in a residue code from the keyboard or double click a residue code from the list of residue codes. (Use the simplest code, such as glycine, or the code that most closely resembles the residue that you want.)

4.	Click [image].

5.	Double-click the residue code in the ISIS/Draw window. You see the chemical structure of the generic residue in the Edit window.

6.	To edit the underlying chemical structure, do any of the following:

*	To learn how to add, delete, or replace atoms and/or bonds, click the ISIS/Draw "Quick Start".

*	To add, delete, or replace stereochemistry, click here.

Hint

*	To specify query features on atoms and/or bonds, click here.

7.	Click Close. You see the ISIS/Draw dialog box where you are prompted to change the name of the edited residue.

8.	To rename the edited residue, enter a new name in the ISIS/Draw text box, and then click Yes. You see the residue code in the ISIS/Draw window.

9.	(Optional) To customize another residue, repeat Steps 2 through 8 as needed.

Note: You do not see customized residues on the list of residue codes. To see customized residues on the list, click Customizing a List of Residue Codes.


Editing Any Portion of the Sequence

You can edit any portion of a sequence to:

*	Delete or insert or rename or replace any incorrectly entered residue codes.

*	Improve the readability of a sequence by its division into blocks or lines of residue codes.

*	Cleave the sequence into smaller sequences or join the sequence to another sequence.

*	Delete or display/hide the sequence bonds.

*	Add or delete or display/hide the crosslink bonds.

*	Delete or display/hide the leaving groups.


To cleave a sequence into smaller sequences

Use this procedure to cleave a sequence that is in the ISIS/Draw window into smaller sequences.

1.	Click [image].

2.	Click the sequence bond where you want to cleave the sequence. You see the leaving groups on the cleaved residues.


To join the sequence to another sequence

Use this procedure to join together two sequences that are in the ISIS/Draw window.

1.	Click [image].

2.	Press and hold the mouse button on a terminal leaving group of one of the sequences.

3.	Drag the mouse to a terminal leaving group on the other sequence, and then release it. The sequences join together.

4.	(Optional) To undo Steps 2 and 3, choose Edit > Undo. The sequences move back to their original location.

5.	(Optional) Move connected residues from different lines to the same line.


To move connected residues

Use this procedure to move connected residues into positions that suit you. You can move any number of residues to any location.

1.	Select the residues that you want to move.

2.	Press and hold the mouse button on the selected residues.

3.	Drag the mouse to the location of your choice, and then release the mouse. You see the selected residues in the new location.


Using Editing Keys

You can use editing keys to help you to build or edit sequences that contain lines or blocks of contracted residues. However, before you use an editing key, you must first click a residue code. (You see a box around the residue code that disappears if you move the mouse. You see the cursor at the left of the residue code.)

Editing Function	IBM Keys	Macintosh Keys

Begin new line	Return	Return

Begin new block	Space	Space

Create selected block	Shift Left/Right Arrow	Drag mouse

Delete selected block	Delete	Delete

Delete left residue	Back Space	Delete/Back Space

Delete right residue	Delete

Move left/right	Left/Right Arrow	Left/Right Arrow

Move up one line	Up Arrow	Up Arrow

Move down one line	Down Arrow	Down Arrow

Move to start of line	Home

Move to end of line	End

Move to start of sequence	Ctrl-Home

Move to end of sequence	Ctrl-End


Expanding a Residue and Editing its Underlying Chemical Structure

To edit the underlying chemical structure of a residue, you must first expand the residue in either the Edit window or the ISIS/Draw window.

Caution: Although you can expand more than one residue at a time in the ISIS/Draw window, you might see overlapping structures or structures that are difficult to edit. Thus, we strongly recommend that you edit a residue in the Edit window.

You can edit an expanded residue as follows: Add, delete, or replace atoms, bonds, or stereochemistry. In addition, you can add query features to atoms and/or bonds to specify the retrieval of certain types of biopolymers from your database.

Click one of the following:

To expand/edit a residue in the Edit window

To expand/edit one or more residues in the ISIS/Draw window


To expand a residue and edit it in the Edit window

This procedure assumes that you want to expand a single, contracted residue and edit its underlying chemical structure in the Edit window.

Caution: Do not use this procedure to edit the letter codes of a residue, such as P, R, or C, which represent the amino acid residues Proline, Arginine, or Cysteine. To edit a residue code, click here.

1.	Click [image].

2.	Double click the contracted residue that you want to edit. You see the chemical structure in the Edit window.

3.	To edit the underlying chemical structure, do any of the following:

*	To learn how to add, delete, or replace atoms and/or bonds, click the ISIS/Draw "Quick Start".

*	To add, delete, or replace stereochemistry, click here.

Hint

*	To specify query features on atoms and/or bonds, click here.

4.	Click Close. You see the ISIS/Draw dialog box where you are prompted to change the name of the edited residue.

5.	To rename the edited residue, do one of the following:

*	Use the name that is provided (the residue code with an asterisk). Click Yes.

*	Enter a name that is not provided in the ISIS/Draw text box, and then click Yes.

You see the edited residue in contracted form in ISIS/Draw.

6.	(Optional) Repeat Steps 2 through 5 for each residue that you want to edit.

Note: You do not see customized residues on the list of residue codes. To see customized residues on the list, click Customizing a List of Residue Codes.


Hint

MDL provides you with a list of residue codes with stereochemistry on the amino acid residues. The list AAS_BOTH contains L-amino acid residues with both Up bonds (residues are in capital letters) and Down bonds (residues are in small letters).

To add the list AAS_BOTH to the Sequence menu and then make this list the current list, you must first add this list of residue codes to the Sequence menu, and then change the current list to AAS_BOTH.


To expand one or more residues in the ISIS/Draw window

Use this procedure to expand any number of contracted residues. Example

Caution: This procedure might produce overlapping structures or structures that are difficult to edit. Thus, we recommend that you expand a single residue code in the Edit window. To do so, click here.

1.	Click [image].

2.	Select the set of residues that you want to expand.

3.	Choose Chemistry > Residue > Expand. You see the chemical structures.

4.	(Optional) You can edit the underlying chemical structures.

5.	(Optional) To change the display of the residues, click any of the following:

Residue Brackets:  Display/Hide

Leaving Groups:  Delete,  Display/Hide,

Sequence Bonds:  Display/Hide

Crosslink Bonds:  Add,  Delete,  Display/Hide

6.	(Optional) To change the orientation of any of the residues, click here.

7.	(Optional) To contract a set of expanded structures in the ISIS/Draw window, select them, and then choose Chemistry > Residue > Contract.


Example

When you expand the contracted amino acid residues R R E K H, you see the underlying chemical structures of the residues, as follows:


Shaping a Line of Residue Codes

You can create a biopolymer sequence with a spatial arrangement that is significant to you. Example.

You enter the sequence, and then either shape it into any position or snap it to either a line or a circle.

Click one of the following:

To shape a sequence to any position

To snap a sequence to a pre-existing object


Example

For example, you can build the protein Bovine Insulin:

This protein consists of two sequences (chains) of amino acid residues. In this example, you see internal crosslink bonds that connect the sulfur groups of Cysteine (C) residues together to form disulfide bridges between the two sequences.


To shape a sequence to any position

This procedure assumes that you have a sequence in ISIS/Draw that you want to shape.

1.	Click [image].

2.	Press and hold the mouse button on a residue. This residue is now the anchor.

3.	Drag the mouse to the shape of your choice, and then release it. The residues that succeed the anchor move to the new shape.


To snap a sequence to a pre-existing object

Use this procedure to snap a sequence to a pre-existing object (shape template). This procedure assumes that you have a pre-existing shape template in ISIS/Draw. A shape template can be any circle or line object that is created in ISIS/Draw with the Sketch tools.

Note: MDL does not provide pre-existing shape templates.

1.	Choose Options > Snap To Object.

2.	Click

3.	Do one of the following:

*	If you have a sequence in the ISIS/Draw window, press and hold the mouse button on a residue. This residue is now the anchor. Drag the mouse to the shape of the object, and then release it. The residues that succeed the anchor move to the new shape.

*	If you do not have a sequence in the ISIS/Draw window, position the cursor on the shape template where you want to see the first residue. Type the letter codes for the residues of your choice. Each residue snaps to the object along the sequence path that the object creates via its shape.

See also:

Creating a shape template


Creating a Shape Template

All of the essential information that you need to create any shape in ISIS/Draw is in the ISIS/Draw "Quick Start."

The ISIS/Draw "Quick Start" is an 11-page document written in a new, compact style. We designed it to be printed.

Read the ISIS/Draw "Quick Start" to learn nearly everything you need to use ISIS/Draw.

To see the ISIS/Draw "Quick Start," click here.


Checking the Chemistry of a Sequence or Residue

Before you can use a biopolymer (or a portion of it) to search an ISIS/Base database, you must check its chemistry: You must check a residue to ensure that the underlying structure is chemically correct. You must check a sequence (or a fragment of a sequence) to ensure that the underlying structure of each residue is chemically correct and that each residue is connected to the sequence.

Click here for step-by-step instructions


To check the chemistry of a sequence or residue

1.	Click [image] or choose Chemistry > Run Chem Inspector.

2.	Do one of the following:

*	To verify the entire sketch, click [image] Check entire sketch.

*	To verify part of the sketch, first select the objects that you want to verify, and then click [image] Check selected objects.

Note

3.	Click the Intended Use box and choose an option. For example, if you want to register a reaction into a remote database, choose Host Database > Reaction > Registration as the intended use. Chem Inspector can then look for features (such as fonts or pen size) that are not supported by remote databases. Note

4.	(Optional) If ISIS/Draw finds any problems, you see the number of errors and warnings listed below the Results box. Click the arrow next to the Results box. You see a scrolling list of results divided into three categories: Errors, Warnings, and Information.

5.	(Optional) To see more information on a specific result, scroll to that result and click it. ISIS/Draw highlight the objects referred to in the warning or error message. To see a detailed explanation of the result, click [image].

6.	Fix any errors in the drawing. (The Chem Inspector dialog box stays on top.) You must fix any errors that Chem Inspector finds to successfully:

*	Register a structure or reaction

*	Use a structure or reaction to search a database

*	Export a reaction as a rxnfile.

*	Manually atom-atom map a reaction.

7.	(Optional) To verify the sketch again, click

See also:

To turn individual Chem Inspector warnings on or off


Customizing a List of Residue Codes

You use a list of residue codes to create a biopolymer sequence. You can either specify different letter codes for an existing list of residue codes or create your own list of residue codes.

Click one of the following:

To specify different letter codes for an existing list of residue codes

To create your own list of residue codes


Customizing the Sequence Menu

All the lists of residue codes that you intend to use must be on the Sequence menu. You can add a list of residue codes to the Sequence menu, remove a list, or rename it.

Click one of the following:

To add a list of residue codes to the Sequence menu

To remove a list of residue codes from the Sequence menu

To rename a list of residue codes on the Sequence menu

To change to a different list of residue codes


To add a list of residue codes to the Sequence menu

Use this procedure to add an existing list of residue codes to the Sequence menu that contains all the available lists of residue codes that you can use.

1.	Choose Chemistry > Sequence > Customize Menu.

2.	Click Insert.

3.	Click the name of an existing Residue Map file in the File Name list box (change your directory or folder if necessary). You see the name of the file in the File Name text box. (On the PC, the file names contain the *.MAP extension.)

4.	(Optional) If you want to rename the list of residue codes, enter a new name.

5.	Click OK (Mac=Open).


To change to a different list of residue codes

Use this procedure to change to a different list of residue codes than your current list of residue codes.

1.	Choose Chemistry > Sequence, and then choose the list of residue codes that you want. MDL provides you with the following lists of residue codes on the Sequence menu: Amino Acids - 1 letter (for 1-letter amino acid structures); Amino Acids- 3 letter (for 3-letter amino acid structures); DNA - 1 letter (for deoxyribonucleic acid structures); or RNA - 1 letter (for ribonucleic acid structures).

Note: To use a list of residue codes that is not on the Sequence menu or to customize a list, click Customizing a List of Residues

2.	To view the current list of residue codes that you chose in Step 1, choose Chemistry > Sequence. You require [image] Show Residue List.

If you do not see the current list, click [image].


To specify different letter codes for an existing list of residue codes

When you create a biopolymer sequence, you can enter the letter codes (also called residue codes) of your choice. For example, you can enter 1-letter codes (such as P for the amino acid residue Proline) instead of 3-letter codes (such as Pro for Proline).

Use this procedure to specify a different set of letter codes (such as 1-letter instead of 3-letter) for the list of residue codes on the Residue List.

Note: To customize specific residues, click Customizing a Residue.

1.	Choose Chemistry > Sequence > Customize Menu. You see the Sequence menu that shows your current list of residue codes.

2.	Click a different code length in the Code Length list box. For example, to change from 1-letter to 3-letter residue codes, click 3-letter. (To use residue codes that are of different lengths, click Delimited in the Code Length list box.)

Note: If you do not see the code length that you want, you need to enter a Residue Map file that contains the code length of your choice onto the Sequence menu. For more information, click Customizing a List of Residue Codes or Customizing the Sequence Menu.

3.	Click OK.


To create your own list of residue codes

Use this procedure to create your own list of residue codes, to add your list to the Sequence menu that contains all the available lists of residue codes that you can use, and then to make your list the current list.

1.	You must have a Residue Template file that contains all the chemical structures (templates) for each of the residues and leaving groups that you want to use. Do one of the following:

*	Edit an existing Residue Template file.

*	Create a new Residue Template file.

2.	You must have a Residue Map file that maps all the templates to the code names for each of the residues and leaving groups that you want to use. Do one of the following:

*	Edit an existing Residue Map file.

*	Create a new Residue Map file.

3.	All of the available lists of residue codes that you can use must be on the Sequence menu. Click To add a list of residue codes to the Sequence menu.

4.	You must make your list of residue codes the current list. Click To make your list of residue codes the current list.


To make your list of residue codes the current list

Use this procedure to make your list current so that you can use your list.

1.	Choose Chemistry > Sequence, and then choose your own list of residue codes.

2.	Click [image] (if not highlighted).

Note: To see your list of residue codes, choose Chemistry > Sequence. You require [image] Show Residue List.


To edit an existing Residue Template file

Use this procedure to edit an existing Residue Template file that you can use when you create your own list of residue codes. A Residue Template file contains all the residue and leaving group templates that you need to create a biopolymer sequence in ISIS/Draw. A template is a structure that can be used as many times as you want.

1.	In the ISIS/Draw window, open an existing Residue Template file that contains the types of residues that you want to use. For example, open the amino acid structures Residue Template file AAS.SKC.

2.	Click [image]. You see each template for the residues and leaving groups. For example, you see the residue template:

A(l)--Ala--B(r)

Where Ala represents the amino acid residue Alanine; the first letter of the leaving-group designator (A or B) refers to the leaving group ID in the Residue Map file; and the letter in parentheses indicates a left (l), right (r), or a crosslink (x) attachment of the leaving group within the sequence.

3.	To create duplicate residue template (such as Ala), select an existing residue template, choose Edit > Copy, click an empty area in the ISIS/Draw window, choose Edit > Paste, and then double-click on the residue template. You see the underlying chemical structure of the residue template in the Edit window.

4.	Double click the duplicate residue template, and then edit it. If you need help, click any of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Specifying Stereochemistry.

5.	Click Close. You see the ISIS/Draw dialog box where you are prompted to change the name of the edited residue.

6.	Do one of the following:

*	Use the name that is provided (the residue code with an asterisk). Click Yes.

*	Enter your own name in the ISIS/Draw text box, and then click Yes.

You see the edited residue in contracted form in the ISIS/Draw window.

7.	Repeat Steps 3 through 7 as needed.

8.	To save the Residue Template file, choose File > Save As. Navigate to the disk and directory or folder that contains the original Residue Template file. Enter a name for the file. PC Only: The file name must end with the *.SKC extension. Click OK (Mac=Save).


To create a new Residue Template file

Use this procedure to create a new Residue Template file that you can use when you create your own list of residue codes. A Residue Template file contains all the residue and leaving group templates that you need to create a biopolymer sequence in ISIS/Draw. A template is a structure that can be used as many times as you want.

1.	In the ISIS/Draw window, click [image].

2.	Create the underlying chemical structure of a residue. If you need help, click any of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Specifying Stereochemistry.

3.	To the residue in Step 2, add the following two attachment bonds (with their atom aliases) to represent the leaving groups that you will draw:

A(l)--Your Chemical Structure--B(r)

Where the first letter of the leaving-group designator (A or B) refers to the leaving group ID in the Residue Map file; and the letter in parentheses indicates a left (l), right (r), or a crosslink (x) attachment of the leaving group within the sequence.

4.	To create the residue template, select the residue and the two attachment bonds [but do not select the atom alias A(l) or B(r)], and then choose Chemistry > Residue > Create. Enter a name for the residue. This name is not necessarily the name that you will type when you enter a residue to create a sequence. (The residue code that you will type is specified in the Residue Map file.)

5.	Create all additional residue templates as follows: Select an existing residue template, choose Edit > Copy, click an empty area in the ISIS/Draw window, choose Edit > Paste, and then double-click on the residue template. You see the underlying chemical structure of the residue template in the Edit window. Edit the residue template. Click Close. You see the ISIS/Draw dialog box where you are prompted to change the name of the edited residue. Enter your own name in the ISIS/Draw text box, and then click Yes.

6.	Create the underlying chemical structures of each leaving group. For example, draw the leaving groups --H (a bond to an explicit hydrogen) and --OH (a bond to an oxygen that also shows the hydrogen atom).

7.	To create each leaving group template, select the specific leaving group, and then choose Chemistry > Residue > Create. Enter a name for the leaving group. This name is not necessarily the name that you will see on the leaving group when you enter a residue to create a sequence. (The leaving group name that you will see is specified in the Residue Map file.)

8.	To save the Residue Template file, choose File > Save As. Navigate to the disk and directory or folder that contains the original Residue Template file. Enter a name for the file. PC Only: The file name must end with the *.SKC extension. Click OK (Mac=Save).


To edit an existing Residue Map file

Use this procedure to edit an existing Residue Map file that you can use when you create your own list of residue codes. A Residue Map file contains all the residue and leaving group code names and Residue Template file names that you need to create a biopolymer sequence in ISIS/Draw.

1.	In any ASCII text editor, open the Residue Map file that you want to edit.

2.	(Optional) On line one of the file, to change the type of residues (also called Residue Class ID), delete the current name and enter your own name. For example, enter:

ResidueClassID: AAS

Note: You need to minimize the number of characters for in the ResidueClassID (such as AAS instead of Amino Acid Structures) to minimize the space that this line displaces in molfiles and databases.

3.	(Optional) On line two of the file, to change the type of delimiter, delete the current delimiter and enter your own delimiter. For example, enter (a semicolon as the delimiter):

Delimiter: ;

4.	(Optional) On line three of the file, to configure the chemical groups on all residues automatically so that you see their expanded structures in the alternating up-and-down orientation, add the following:

FlipAlternateResidues:

5.	Beneath the heading Leaving Groups, edit the leaving groups of your choice. Each leaving group that you can use must be in this file and contain the following information: An ID (such as A), the label (such as NH2), and a template name [such as AAS.SKC (H), where AAS.SKC is the Residue Template file name and (H) is the abbreviation of a leaving group in the Residue Template file]. For example, enter:

LeavingGroups:

A	NH2	AAS.SKC (H)

B	COOH	AAS.SKC (OH)

C	SH	AAS.SKC (H)

(Enter all the leaving groups, and do not allow any blank lines.)

6.	Beneath the heading Residue Codes, edit the residue codes of your choice. Each residue code that you can use must be in this file and contain the following information: The label that you type when you enter a residue to draw a sequence (such as A for the amino acid Alanine), the label or detailed text that you see in the Residue list box [such as A (Ala)], and a template name [such as AAS.SKC (L-Ala)]. For example, enter:

Residues:

A	A (Ala)	AAS.SKC (L-Ala)

R	R (Arg)	AAS.SKC (L-Arg)

N	N (Asn)	AAS.SKC (L-Asn)

(Enter all the residues, and do not allow any blank lines.)

7.	To save the Residue Map file, choose File > Save As. Navigate to the disk and directory or folder that contains the original Residue Map. Enter a name for the file. PC Only: The file name must end with the *.MAP extension. Click OK (Mac=Save).


The Contents of Residue Map Files

Each Residue Map file contains:

*	The type of residues (also called Residue Class ID), such as amino acid structures or DNA.

*	The type of delimiter. (For customized residue code lengths that are variable in length, to specify where one residue code ends and where another begins, enter delimited rather than any of the existing delimiters.)

*	(Optional) A statement that changes the orientation of the residues. For more information, click here.

*	The set of leaving groups that are available for use. Each leaving group that you can use must be in this file and contain the following information: An ID (such as A or B), the label (such as NH2 or COOH), and a template name [such as AAS.SKC (H) or AAS.SKC (OH), where AAS.SKC is the Residue Template file name and (H) and (OH) are the abbreviations of the leaving groups in the Residue Template file].

*	The set of residue codes that are available for use. Each residue code that you can use must be in this file and contain the following information: The label that you type when you enter a residue to draw a sequence (such as R for the amino acid Arginine), the label or detailed text that you see in the Residue list box [such as R (Arg)], and a template name [such as AAS.SKC (L-Arg)].


To create a new Residue Map file

Use this procedure to create a new Residue Map file that you can use when you create your own list of residue codes. A Residue Map file contains all the residue and leaving group code names and Residue Template file names that you need to create a biopolymer sequence in ISIS/Draw.

1.	Open any ASCII text editor.

2.	On line one of the file, enter the type of residues (also called Residue Class ID). For example, enter:

ResidueClassID: Amino Acid Structures

3.	On line two of the file, enter the type of delimiter. For example, enter (a semicolon as the delimiter):

Delimiter: ;

4.	(Optional) On line three of the file, to configure the chemical groups on all residues automatically so that you see their expanded structures in the alternating up-and-down orientation, add the following:

FlipAlternateResidues:

5.	Beginning on the next available line of the file, enter the heading Leaving Groups:, followed by the set of leaving groups that are available for use. Each leaving group that you can use must be in this file and contain the following information: An ID (such as A), the label (such as NH2), and a template name [such as AAS.SKC (H), where AAS.SKC is the Residue Template file name and (H) is the abbreviation of a leaving group in the Residue Template file]. For example, enter:

LeavingGroups:

A	NH2	AAS.SKC (H)

B	COOH	AAS.SKC (OH)

C	SH	AAS.SKC (H)

(Enter all the leaving groups, and do not allow any blank lines.)

6.	On the line of the file immediately following the last leaving group, enter the heading Residues:, followed by the set of residue codes that are available for use. Each residue code that you can use must be in this file and contain the following information: The label that you type when you enter a residue to draw a sequence (such as A for the amino acid Alanine), the label or detailed text that you see in the Residue list box [such as A (Ala)], and a template name [such as AAS.SKC (L-Ala)]. For example, enter:

Residues:

A	A (Ala)	AAS.SKC (L-Ala)

R	R (Arg)	AAS.SKC (L-Arg)

N	N (Asn)	AAS.SKC (L-Asn)

(Enter all the residues, and do not allow any blank lines.)

7.	To save the Residue Map file, choose File > Save As. Navigate to the disk and directory or folder that contains the original Residue Map. Enter a name for the file. PC Only: The file name must end with the *.MAP extension. Click OK (Mac=Save).


To remove a list of residue codes from the Sequence menu

Use this procedure to remove a list of residue codes from the Sequence menu that allows you to choose your own list to use.

1.	Choose Chemistry > Sequence > Customize Menu.

2.	Select the file name of a list of residues that you want to remove.

3.	Click Remove.

4.	Click OK (Mac=Open).


To rename existing lists of residue codes

Use this procedure to rename a list of residue codes on the Sequence menu that allows you to choose your own list to use.

1.	Choose Chemistry > Sequence > Customize Menu.

2.	Select the file name of a list of residues that you want to rename.

3.	Click Rename.

4.	Enter a different name for the file. (On the PC, the file names contain the *.MAP extension.)

5.	Click OK (Mac=Open).


To import a sequence or residue

Use this procedure to import an existing sequence or a residue (also called a sequence file) into ISIS/Draw.

Note

1.	(Optional) To import a sequence into the ISIS/Draw window in the format of the stored file, choose Options > Settings, and then click the Sequence Tab. Enter the numerical value of 0 (zero) in both the Wrap after and Blocksize list boxes. (Any blank line in the imported sequence translates into the start of a new sequence.)

2.	Choose File > Import > Sequence. (To retrieve a PC-sequence file on the Macintosh, press and hold the Option key while you complete this step.)

3.	Navigate to the disk and directory or folder that contains the file to import.

4.	Highlight the name of the file to import .On the PC, the file names contain the .SEQ extension.

5.	Click OK (Mac=Open). You see the Choose Sequence Type dialog box.

6.	Click the type of sequence that the file contains, such as DNA - 1 letter. The selected sequence or residue is imported into your form.

7.	(Optional) To show the leaving groups, you require [image] Show Leaving Groups on the Chemistry > Sequence menu.

8.	(Optional) To show the sequence bonds, you require [image] Show Sequence Bonds on the Chemistry > Sequence menu.

9.	(Optional) To show the crosslink bonds, you require [image] Show Crosslink Bonds on the Chemistry > Sequence menu.

See also:

To abandon the importing process


To abandon the importing process

1.	To abandon the importing process:

*	On the PC, press and hold the Esc key.

*	On the Macintosh, press and hold the Command key and the period key.


Note

For each residue code that was not on your current list of residue codes prior to importing the sequence, you see a question mark on the list of residue codes.


To paste a sequence into ISIS/Draw from the Clipboard

This procedure assumes that you have a sequence from any ASCII text editor on the Clipboard in ISIS/Draw.

1.	Choose Chemistry > Sequence, and then choose the list of residue codes that you want. MDL provides you with the following lists of residue codes on the Sequence menu: Amino Acids - 1 letter (for 1-letter amino acid structures); Amino Acids- 3 letter (for 3-letter amino acid structures); DNA - 1 letter (for deoxyribonucleic acid structures); or RNA - 1 letter (for ribonucleic acid structures).

2.	Click [image].

3.	Click the area in the ISIS/Draw window where you want to see the start of the sequence.

4.	Choose Edit > Paste.


To specify blocks of residues in a sequence

Use this procedure to specify blocks of residues in a sequence to improve the readability of contracted residues.

1.	Do one of the following:

*	To specify the end of a block of residues as you type in residues via the keyboard into the ISIS/Draw window, press the Space key. (You cannot use the Space key if you click residues from a list of residue codes.)

*	To specify the default number of residues per block, choose Options > Settings. You see the Settings dialog box. Click the Sequence Tab, and then click the number of residues that you want per block in the Blocksize list box. You can enter a value between 0 and 999. [A default setting of 0 (zero) specifies that there are no blocks of residues (zero residues per block.)]

To save the specifications that you entered and to apply them to your current work, click Save, click OK, and then click Yes. (Or, click No to apply these settings solely to future work.)

Note: To change the block size for a sequence that you already entered, select the sequence, choose Edit > Objects, and then click the Sequence Tab. Click the number of residues that you want per block in the Blocksize list box.


To specify lines of residues in a sequence

You must specify a new line for the residues in a sequence that would otherwise extend past the drawing window. Use this procedure to specify lines of contracted residues in a sequence.

1.	Do one of the following:

*	To specify the end of a line of residues as you enter residues into the ISIS/Draw window, press the Return key.

*	To specify the default number of residues per line, choose Options > Settings. You see the Settings dialog box. Click the Sequence Tab, and then click the number of residues that you want per line in the Wrap after list box. You can enter a value between 0 and 999. [A default setting of 0 (zero) specifies that there is solely a single line of residues.]

To save the specifications that you entered and to apply them to your current work, click Save, click OK, and then click Yes. (Or, click No to apply these settings solely to future work.)

Note: To change the number of residues per line for a sequence that you already entered, select the sequence, choose Edit > Objects, and then click the Sequence Tab. Click the number of residues that you want per line in the Wrap after list box.


Configuring residues in a sequence

When you view a set of expanded residues in a sequence, you see each residue in the opposite orientation from the previous residue. For example:

If you do not see this (or you want all residues to be configured in the same orientation), you can change the configuration of the residues.

Click one of the following:

To configure specific residues in a sequence

To configure all residues in a sequence


To configure specific residues in a sequence

Use this procedure to configure the chemical groups on specific residues in the up- or down-configuration. This procedure assumes that you have a set of expanded residues in the ISIS/Draw window.

Note: To configure all residues automatically, click here.

1. 	Select the a residue whose chemical group you want to configure in the opposite orientation. (You can select more than one residue if the residues are in succession.)

2.	Choose Options > Flip > Chem Group.

3.	Repeat Steps 1 and 2 as needed.


To configure all residues in a sequence

Use this procedure to configure the chemical groups on all residues automatically so that you see their expanded structures in the alternating up-and-down orientation.

1.	In any ASCII text editor, open the Residue Map file that you want to use.

2.	Beneath the line of text that begins with the word Delimiter, enter the following line of text:

FlipAlternateResidues

3.	To save the Residue Map file, choose File > Save As. Navigate to the disk and directory or folder that contains the original Residue Map. Enter a name for the file. PC Only: The file name must end with the *.MAP extension. Click OK (Mac=Save).

4.	Choose Chemistry > Sequence > Customize Menu.

5.	Click the name of the Residue Map file that you saved in Step 3. This file is now your current list of residue codes that you can use to enter a sequence.


To delete a residue in a sequence

Use this procedure to delete contracted residues in the ISIS/Draw window.

1.	Click [image].

2. 	Click the residue that you want to delete. You see the cursor at the left of the residue code.

3.	Do one of the following:

*	To delete the residue at the left of the cursor, press the Back Space key. (Macintosh=Back Space or Delete key)

*	For the PC only: To delete the residue at the right of the cursor, press the Delete key.

4.	(Optional) To delete a set of residues in succession, repeat Step 3 as needed.

See also:

Using Editing Keys


To insert a residue in a sequence

Use this procedure to insert a contracted residue into a sequence at any location.

1.	Click [image] (if it is not highlighted).

2.	(Optional) To view the list of residues that you can use, click here.

3.	Click the exact middle of the residue that is at the right of your insertion point. You see a box around the residue.

4.	Type in the residue codes of your choice. (Alternatively, double-click the residue from the list of residues.) The insertion of a new residue moves the succeeding residues one position to the right.

Caution: If you previously specified a default setting for the number of residues per line and the insertion of your residue exceeds that default setting, a new line is not created.

5.	(Optional) Insertions can create gaps (additional spacing) between succeeding residues. To eliminate a gap, click [image]. Choose Edit > Objects, and then click the Sequence Tab. Edit the sequence.

See also:

Using Editing Keys


To rename a residue in a sequence

Use this procedure to rename the residue code of a contracted residue.

1.	Click [image].

2.	Select the residue code that you want to rename.

3.	Choose Chemistry > Residue > Rename.

4.	Enter a unique name for the residue code.

5.	Click OK.


To replace a residue in a sequence

Use this procedure to replace the residue code of a contracted residue with a different residue code. The procedure inserts a new residue, and then deletes the residue that you want to be replaced.

1.	Click [image] (if it is not highlighted).

2.	(Optional) To see the list of residue codes that you can insert, choose Chemistry > Sequence. You require [image] Show Residue List.

3.	Click the exact middle of the residue that is at the right of the residue that you want to replace. You see a box around the residue.

4.	Press the Back Space key.

5.	Type in the residue code of your choice. Alternatively, double-click the residue from the list of residues.

See also:

Using Editing Keys


Contracting Residues

You can either contract a single, expanded residue in the Edit window or you can contract one or more expanded residues in the ISIS/Draw window.

Click one of the following:

To contract a single residue in the Edit window

To contract residues in the ISIS/Draw window


To contract residues in the ISIS/Draw window

Use this procedure to contract a set of expanded residues in the ISIS/Draw window. This procedure assumes that you have a set of expanded residues in the ISIS/Draw window.

Note: If you have a single, edited residue in the Edit window, do not use this procedure. Instead, click here.

1.	Click [image].

2.	Select the set of residues that you want to contract.

3.	Choose Chemistry > Residue > Contract. You see the residue codes.

Note: 3D residues that are contracted might produce misaligned 3D sequences.


To contract a single residue in the Edit window

This procedure assumes that you have a single, expanded residue in the Edit window that you want to contract.

1.	Click Close. You see the ISIS/Draw dialog box where you are prompted to change the name of the edited residue.

2.	To rename the residue code, do one of the following:

*	Use the name that is provided (the residue code with an asterisk). Click Yes.

*	Enter your own name in the ISIS/Draw text box, and then click Yes.

You see the edited residue in contracted form in ISIS/Draw.

Note: 3D residues that are contracted might produce misaligned 3D sequences.


To display or hide residue brackets

You can either display or hide residue brackets on expanded residues in the ISIS/Draw window. (You do not see brackets on a contracted residue.)

1.	Choose Chemistry > Sequence.

2.	Do one of the following:

*	To display the residue brackets, you require [image] Show Residue Brackets.

*	To hide the residue brackets, you require Show Residue Brackets.


To delete leaving groups from a residue

Use this procedure to delete a leaving group on a contracted residue.

1.	Click [image].

2.	Click the leaving group that you want to delete.

Note: After you delete a leaving group, you cannot add it back to the residue. Instead, you must replace the residue with a residue whose leaving group you did not delete. To replace a residue, click here.


To display or hide leaving groups

You can either display or hide leaving groups on contracted residues in the ISIS/Draw window.

1.	Choose Chemistry > Sequence.

2.	Do one of the following:

*	To display the leaving groups, you require [image] Show Leaving Groups.

*	To hide the leaving groups, you require Show Leaving Groups.


To display or hide sequence bonds

You can either display or hide sequence bonds on contracted residues in the ISIS/Draw window.

1.	Choose Chemistry > Sequence.

2.	Do one of the following:

*	To display the sequence bonds, you require [image] Show Sequence Bonds.

*	To hide the sequence bonds, you require Show Sequence Bonds.


To delete sequence bonds

Use this procedure to delete sequence bonds (that are displayed or hidden) between two residues.

1.	Click [image].

2.	Click the sequence bonds of your choice. Leaving groups sprout on those residues without a sequence bond.


To display or hide crosslink bonds

You can either display or hide crosslink bonds on contracted or residues in the ISIS/Draw window.

Note: If you hide the crosslink bonds, you see markers, such as x1 or x2, that designate those pairs of residues that are crosslinked. Example

1.	Choose Chemistry > Sequence.

2.	Do one of the following:

*	To display the crosslink bonds, you require [image] Show Crosslink Bonds.

*	To hide the crosslink bonds, you require Show Crosslink Bonds.


Example


Adding Crosslink Bonds to Sequences

You can crosslink the bonds between any residues. However, if you crosslink the bonds between residues that contain leaving groups, it is the leaving groups that form the crosslink bonds.

Click one of the following:

To add crosslink bonds to contracted residues

To add crosslink bonds to expanded residues in the ISIS/Draw window


To add crosslink bonds to contracted residues

Use this procedure to add crosslink bonds between two residues that have crosslinking groups (such as two Cysteines in a sequence of amino acids).

This procedure assumes that the contracted residues that you want to crosslink contain leaving groups.

Note: If you want to add crosslink bonds between two residues that do not have crosslinking groups, draw a bond between the contracted residues.

1.	Click [image].

2.	Press and hold the mouse on one of the leaving groups that you want to crosslink.

3.	Drag the mouse to the other leaving group that you want to crosslink, and then release the mouse.

4.	Choose Chemistry > Sequence.

5.	Do one of the following:

*	To display the crosslink bonds, you require [image] Show Crosslink Bonds.

*	To hide the crosslink bonds, you require Show Crosslink Bonds.

Note: If you hide the crosslink bonds, you see markers, such as x1 or x2, that designate those pairs of residues that are crosslinked. Example


To add crosslink bonds to expanded residues in the ISIS/Draw window

Use this procedure to add crosslink bonds to a sequence that contains expanded residues in the ISIS/Draw window.

Caution: After you add crosslink bonds on expanded residues in the ISIS/Draw window, you cannot contract the residues. Thus, we recommend that you add crosslink bonds solely to contracted residues. You can then expand, view and/or edit, and contract the residues.

1.	Click [image].

2.	Select the residues that you want to expand. (To select two non-adjacent residues, hold down the Shift key.)

3.	Choose Chemistry > Residue > Expand. You see the chemical structures.

4.	Draw a crosslink bond between the atoms of the expanded residues that you want to crosslink. To learn how to add, delete, or replace atoms and/or bonds, click the ISIS/Draw "Quick Start".


To delete crosslink bonds

Use this procedure to delete a crosslink bond between two leaving groups on different residue codes.

1.	Select the bond that you want to delete.

2.	Press the Delete key.


To display or hide the list of residue codes

To create a sequence, you can either type in residue codes from the keyboard or you can choose the codes from a list. Use this procedure to display or hide the list of residue codes.

1.	Choose Chemistry > Sequence.

2.	Do one of the following:

*	To display the list of residue codes, you require [image] Show Residue List.

*	To hide the list of residue codes, you require Show Residue List.


To export a sequence as ASCII text

Use this procedure to export a sequence or residue as ASCII text. You can then use this information with third-party applications.

Note

1.	Select the sequence or residue that you want to export.

2.	(Optional) If the residue codes that you are exporting contain more than one letter, such as Arg for the amino acid Arginine, a delimiter character is written between each residue code. To specify a delimiter character, choose Options > Settings and click the Sequence Tab. Specify one of the following: A hyphen (-), a colon (:), a semicolon (;), a period (.), a space, the TAB key, or the Return key. Click OK. (If you do not specify a delimiter character, a hyphen will be written.)

3.	Choose File > Export > Sequence.

Macintosh users: To save a sequence file for use on the PC, press and hold the Option key while you complete this step.

4.	Navigate to the disk and directory or folder where you want to save the exported file.

5.	Enter a name for the file. PC Users: Use the .SEQ extension in the file name.

6.	Click OK (Mac=Open). Your sequence is exported as ASCII text in the format that you created it.


Notes

Note: A blank line in the sequence file that you export translates into the start of a new sequence.


Searching for Biopolymers

You can store biopolymers in your ISIS database, search for them, and manipulate your list of search results to obtain a set that suits your specific needs. To search for stored biopolymers, you can conduct any of the following searches:

For remote database only: 3DEXACT or ALL or CFS/Biopoly or ID or MSim or QB or SBF or SSS/Biopoly or SSS3D/Biopoly

For local database only: SSS/Biopoly or 3DEXACT or ID or QB or ALL or SBF

Note: You cannot conduct a sequence search to compare sequence homologies in this version of ISIS.


To create a structure for a new residue code

This procedure assumes that you have the ISIS/Draw window open and that you want to create a structure for use as a residue.

1.	Click [image].

2.	(Optional) To modify an existing structure, do one of the following:

*	To open a structure file that was saved on your disk, choose File > Open. Navigate to the disk and directory or folder that contains the file that you want to open. Highlight the name of the ISIS/Draw file. Click OK (Mac=Open).

*	To import a structure file (a MOLfile), choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.) Navigate to the disk and directory or folder that contains the file that you want to import. Highlight the name of the file. Click OK. (Mac=Open).

3. 	(Optional) To create your own structure, draw it. If you need help, click any of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches

4.	(Optional) To specify stereochemistry, click here.

6.	(Optional) To create a residue code from this structure, click here.


To create a residue code from an existing structure

Use this procedure to create a residue code from a structure in the ISIS/Draw window.

1.	Click [image] (if it is not highlighted).

2.	Select the structure in the ISIS/Draw window.

3.	Choose Chemistry > Residue> Create.

4.	Enter the residue name.

5.	Click OK. You see the residue code in the ISIS/Draw window instead of the structure.


Working With Polymers

Drawing Polymers: MDL Requirements for Database Searching and Registration

Click any of the following:

*	Creating a Polymer

*	Editing Polymers

*	Creating and Editing Attached Data


Creating Polymers

Drawing Polymers: MDL Requirements for Database Searching and Registration

Click any of the following:

*	To draw a structure-based representation of a polymer or copolymer

*	To draw a source-based representation of a polymer or copolymer

*	To draw a modified polymer or copolymer

*	To draw a graft polymer or copolymer

*	To draw a cross-linked polymer


Editing Polymers

Drawing Polymers: MDL Requirements for Database Searching and Registration

Click any of the following:

*	Change the definition of a polymer (the definition is the set of atoms, bonds, and brackets that comprise the polymer)

*	Change the bracket display of a polymer

*	Create or edit attached data to annotate a polymer


Changing the Definition of a Polymer

Drawing Polymers: MDL Requirements for Database Searching and Registration

Click any of the following:

*	To add a bracket to a set of brackets

*	To delete a bracket from a set of brackets

*	To move a bracket to a different bond

*	To edit the structure within a polymer

*	To delete fragments from a polymer

*	To change the polymer type

*	To change the polymer repeat pattern

*	To include or exclude additional fragments

*	To edit default end groups in a polymer


To add a bracket to a set of brackets

Use this procedure to add an additional bracket to an existing set of polymer brackets.

1.	Click

2.	Click the set of polymer brackets to which you want to add the bracket.

3.	Click the crossing bond to which you want to associate the new bracket.

4.	Click Apply.

5.	(Optional) To verify the chemical validity of the polymer, click


To delete a bracket from a set of brackets

Use this procedure to delete a bracket from an existing set of polymer brackets.

1.	Click

2.	Click the set of polymer brackets from which you want to delete a bracket.

3.	Click the crossing bond associated with the bracket that you want to delete.

4.	Click Apply.

5.	(Optional) To verify the chemical validity of the polymer, click


To move a bracket to a different bond

Use this procedure to move a bracket associated with a specific crossing bond to a different crossing bond.

1.	Click

2.	Move the cursor over the bracket that you want to move, then click the mouse.

Note: Make sure that the cursor appears as a hand, not as an arrow.

3.	Drag the bracket over to the desired bond.

4.	(Optional) To verify the chemical validity of the polymer, click


To delete fragments from a polymer

1.	Click

2.	Select the fragments that you want to delete from the polymer.

3.	Choose Edit > Cut.

4.	(Optional) To verify the chemical validity of the polymer, click


Editing End Groups
Editing Default End Groups

Click here for step-by-step instructions

The end groups of polymers are often unknown. Therefore, when you draw the brackets of a polymer structure, ISIS automatically changes terminal carbon atoms to a special type of atom called a *atom (star atom). These are the default end groups. You can edit the *atoms to draw the end groups explicitly. For example:


To edit end groups on a polymer
To edit default end groups on a polymer

This procedure assumes that you have drawn the polymer or copolymer and that you want to change the default end groups (*atoms) to a specific end group.

For more information on drawing polymers, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

1.	Click

2.	Click the *atom outside the end group. This sprouts a bond from the *atom and changes it to a carbon.

3.	Draw the structures that you want at the end group.


To change polymer type

Use this procedure to change an existing polymer from one type to another.

1.	Click

2.	Click the polymer brackets whose type you want to change.

3.	Click the Bracket type box and choose a polymer type. For information about the different polymer types available, click here.

4.	Click Apply.


To change the polymer repeat pattern

Use this procedure to change polymer repeat pattern.

1.	Click

2.	Click the brackets that define the polymer whose repeat pattern you want to change.

3.	Click the Polymer repeat pattern box and choose a repeat pattern.

4.	Click Apply.


To include or exclude additional fragments

Use this procedure to include an additional fragment, or to exclude an existing fragment from a polymer definition.

1.	Click

2.	Click the brackets that define the polymer from which you want to exclude or include additional fragments. The brackets and structures that are part of the definition shimmer.

3.	Do one of the following:

*	To include an additional fragment as part of the polymer definition, press Shift and click the fragment. You see the fragment shimmer.

*	To exclude a fragment that is part of the polymer definition, press Shift and click the fragment.

4.	Click Apply.


Including/Excluding Polymer Fragments

Click here for step-by-step instructions

You include additional fragments in polymers when you want to ensure that the structural repeating unit (SRU) includes additional fragments (such as salt counterions) that are part of the SRU but are not connected to the other bonds. For example:

You might also need to exclude fragments that are not part of the SRU.

 Caution: When you register a polymer that contains SRU brackets, you must verify that the SRU(s) in the polymer contain the desired fragments. If you do not, other users might not be able to retrieve your structures.


Working With Mixtures

Polymer Mixtures: See Drawing Polymers: MDL Requirements for Database Searching and Registration

Non-Polymer Mixtures: See Drawing Mixtures: MDL Requirements for Database Searching and Registration

Click any of the following:

*	Drawing an Unordered Mixture

*	Drawing an Ordered Mixture

*	Editing Mixtures

*	Creating and Editing Attached Data


Editing Mixtures

Polymer Mixtures: See Drawing Polymers: MDL Requirements for Database Searching and Registration

Non-Polymer Mixtures: See Drawing Mixtures: MDL Requirements for Database Searching and Registration

Click any of the following:

*	To change an unordered mixture to an ordered mixture

*	To add a new component to an unordered mixture

*	To delete a component from an unordered mixture

*	To change an ordered mixture to an unordered mixture

*	To add a new component to an ordered mixture

*	To delete a component from an ordered mixture

*	To create or edit attached data to annotate a mixture


To change an unordered mixture to an ordered mixture

Use this procedure to change an unordered mixture into an ordered mixture.

1.	Click

2.	Click the brackets that define the first component of the unordered mixture.

3.	Click the Order box and enter 1.

4.	Click Apply.

5.	Click the brackets for the next component of the unordered mixture.

6.	Click the Order box, then enter the number of the component.

7.	Click Apply.

8.	Repeat steps 5 through 7 for each component of the unordered mixture.

9.	Click the outer brackets.

10.	Click the Bracket type box and choose mixture, ordered (f).

11.	Click Apply.

12.	To close the Create Brackets dialog, click another tool.


To change an ordered mixture to an unordered mixture

Use this procedure to change an ordered mixture into an unordered mixture.

1.	Click

2.	Click the brackets that define the first component of the ordered mixture.

3.	Click the Order box and delete the number within.

4.	Click Apply.

5.	Repeat steps 2 through 4 for each component of the ordered mixture.

6.	Click the outer brackets (labeled f).

7.	Click the Bracket type box and choose mixture, unordered (mix).

8.	Click Apply.

9.	To close the Create Brackets dialog, click another tool.


To add a new component to an ordered mixture

Use this procedure to add a new component to an ordered mixture.

1.	Draw the structure(s) that you want to include in the new component.

2.	Click

3.	Draw a set of brackets around the new component.

4.	Click the Bracket type box and choose component (c).

5.	Click the Order box and enter the number for the new component.

6.	Click Apply.

7.	Click

8.	Click the outer bracket (labeled f) and move the cursor until it changes into a double-arrow. Drag the bracket so that the new component appears within the brackets.

Note: ISIS/Draw does not automatically renumber the components.


To add a new component to an unordered mixture

Use this procedure to add a new component to an unordered mixture.

1.	Draw the structure(s) that you want to include in the new component.

2.	Click

3.	Draw a set of brackets around the new component.

4.	Click the Bracket type box and choose component (c).

5.	Click Apply.

6.	Click

7.	Click the outer bracket (labeled mix) and move the cursor until it changes into a double-arrow. Drag the bracket so that the new component appears within the brackets.


To delete a component from an ordered mixture

Use this procedure to delete a component from an ordered mixture.

1.	Click

2.	Select the component that you want to delete from the mixture, including the brackets surrounding the component.

3.	Choose Edit > Cut.

Note: ISIS/Draw does not automatically renumber the remaining components.


To delete a component from an unordered mixture

Use this procedure to delete a component from an unordered mixture.

1.	Click

2.	Select the component that you want to delete from the mixture, including the brackets surrounding the component.

3.	Choose Edit > Cut.


Creating and Editing Attached Data

You can use attached data to annotate an atom, a bond, a group of atoms and bonds, or set of brackets. Unlike ordinary text, attached data is stored with the structure in the database and can be used in a graphical search query.

For information on attached data in polymers, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

For information on attached data in non-polymer structures, see Drawing Mixtures: MDL Requirements for Database Searching and Registration.

Click any of the following:

*	To attach data to bonds or atoms (with or without a tag)

*	To attach data to brackets (with or without a tag)

*	To change the database field associated with attached data

*	To edit the tag for the data

*	To draw an undefined structure

To delete attached data, first select it, and then press the Delete key or choose Edit > Cut.

To edit the text of attached data, first click [image], then click the text and edit as you would normal text.

Note: If you select and then move attached data, the association between the attached data and atoms, bonds, or brackets is not changed in any way.


To attach data to atoms or bonds

Use this procedure to attach data to an atom, a bond, or to a group of atoms and bonds, with or without tags.

1.	Click

2.	Do one of the following:

*	Click one atom or bond to attach data to.

*	Press and drag the mouse to select multiple atoms and bonds to attach data to.

3.	Click the Field name box and do one of the following:

*	If you have a database open that contains substance group (Sgroup) fields, choose a field name.

*	If you don't have a database open but you know the name of the Sgroup field, enter the field name. Note

4.	Click the drawing area where you want to enter the data.

5.	Do one of the following:

*	Enter the data (such as 80)

*	(Optional) Enter a single tag character, followed by an equal sign, followed by the data (such as a = 80)

6.	(Optional) To attach data to additional atoms or bonds, repeat steps 2 to 6.

7.	Click Done.


Note

Get the name of the substance group field from your ISIS Administrator.


To attach data to brackets

Use this procedure to attach data (with or without tags) to a set of brackets.

1.	Click

2.	Click one set of brackets that surround the atoms, bonds, components, or structures that you want to attach data to.

3.	Click the Field name box and do one of the following:

*	If you have a database open that contains substance group (Sgroup) fields, choose a field name.

*	If you don't have a database open but you know the name of the Sgroup field, enter the field name. Note

4.	Click the drawing area where you want to enter the data.

5.	Do one of the following:

*	Enter the data (such as 80)

*	(Optional) Enter a single tag character, followed by an equal sign, followed by the data (such as a = 80)

6.	(Optional) To attach data to additional brackets, repeat steps 2 to 6.

7.	Click Done.


To edit the tag for the attached data

Use this procedure to edit the tag character associated with the attached data.

1.	Select the attached data.

2.	Choose Object > Edit Data.

3.	Click the Data tab.

4.	Click the Character box and enter a one-character tag.

5.	(Optional) To change the position of the tag, click the Position box and choose a different position.

6.	Click OK.


To change the database field associated with attached data

Use this procedure to change the database field that is associated with the attached data.

1.	Select the attached data.

2.	Choose Object > Edit Data.

3.	Click the Data tab.

4.	Click the Field name box and do one of the following:

*	If you have a database open that contains substance group (Sgroup) fields, choose a field name.

*	If you don't have a database open but you know the name of the Sgroup field, enter the field name. Note

5.	Click OK.


Changing Bracket Display

To change the style of a set of brackets

To change the color of a set of brackets

To change the orientation of a single bracket

To resize a single bracket

To change the label of a set of SRU brackets


Changing Bracket Display

To change the style of a set of brackets

To change the color of a set of brackets


To change the style of a set of brackets

Use this procedure to modify the style of one or more sets of brackets.

Note: Bracket style in ISIS/Draw is saved with the structure in remote databases.

1.	Click

2.	Select one or more sets of brackets.

3.	Choose Object > Edit Brackets.

4.	Click the Bracket tab.

5.	Click the Bracket style box and choose a style.

6.	Click OK.


To change the color of a set of brackets

Use this procedure to modify the color of one or more selected sets of brackets.

Note: Bracket color in ISIS/Draw is for display purposes only, has no chemical significance, and is not saved in remote databases.

1.	Click

2.	Select one or more sets of brackets.

3.	Choose Object > Edit Brackets.

4.	Click the Bracket tab.

5.	Click the Color box and choose a color.

6.	Click OK.


To change the orientation of a single bracket

1.	Click

2.	Move the cursor over the bracket whose orientation you want to change, and click it.

Note: Make sure that the cursor appears as a single arrow and not as a hand or double- arrow.

2.	Drag the bracket in the desired direction.


To resize a single bracket

1.	Click

2.	Move the cursor over the bracket that you want to resize, and click it.

Note: Make sure that the cursor appears as a single arrow and not as a hand or double- arrow.

3.	Drag the bracket and resize it.


To change the label of a set of SRU brackets

Use this procedure to change the SRU label associated with a set of SRU brackets.

1.	Click

2.	Select the set of brackets whose SRU label you want to change.

3.	Choose Object > Edit Brackets.

4.	Click the Bracket tab.

5.	Click the SRU label box.

6.	Enter a different SRU label.

7.	Click OK.


Drawing 2D Structures

A 2D structure is a molecule that is drawn without regard to its 3D spatial arrangement. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Working With Abbreviated Structures

*	Drawing Polymers: MDL Requirements for Database Searching and Registration

*	Verifying the Chemistry of Sketches


Drawing 2D Structures

A 2D structure is a molecule that is drawn without regard to its 3D spatial arrangement. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Working With Abbreviated Structures

*	Drawing an Undefined Structure

*	Drawing Mixtures: MDL Requirements for Database Searching and Registration

*	Verifying the Chemistry of Sketches


To represent a structure as a fixed number of identical units

Use this procedure to represent a structure as a fixed number of identical units (multiple group).

1.	Draw the 2D structure of the repeating unit.

2.	Click

3.	Draw a set of brackets around the structure. Make sure that each bracket overlays one of the bonds in the structure.

4.	Click the Bracket type box and choose multiple group (#).

5.	Click the Repeat count box and enter how many times you want the structure to be repeated.

6.	Click Apply.

7.	To close the Create Brackets dialog, click another tool.


To draw brackets for presentation

Use this procedure to draw brackets that are not chemically significant.

1.	Draw any structures that you want to include within the brackets.

2.	Click

3.	Draw a set of brackets around the structures.

4.	Click the Bracket type box and choose generic ( ).

5.	Click Apply.

6.	To close the Create Brackets dialog, click another tool.


To draw structures

For information on drawing structures, see the ISIS/Draw "Quick Start". The ISIS/Draw "Quick Start" is a 14-page document, written in a quick-reference style, that explains most of the basic functionality of ISIS/Draw. We strongly recommend that you print and read this document.


To create generic brackets to which you can attach data

Use this procedure to create generic brackets to which you can attach data. Such brackets are chemically significant.

1.	Draw the structure(s) that you want to include in the brackets.

2.	Click

3.	Draw a set of brackets around the structures.

4.	Click the Bracket type box and choose generic ( ).

5.	Click Apply.

6.	To close the Create Brackets dialog, click another tool.

7.	Attach data to the brackets.


To attach a text/numeric query to atoms and bonds

Use this procedure to attach a text/numeric query to an atom, a bond, or to a group of atoms and bonds.

1.	Click

2.	Do one of the following:

*	Click one atom or bond to attach the search operator and target value to.

*	Press and drag the mouse to select multiple atoms and bonds to attach the search operator and target value to.

3.	Click the Field name box and do one of the following:

*	If you have a database open that contains substance group (Sgroup) fields, choose a field name.

*	If you don't have a database open but you know the name of the Sgroup field, enter the field name. Note

4.	Click the Query box and do one of the following:

*	To retrieve solely structures in which the attached data matches your query exactly, choose none.

*	To specify a search operator for attached data, choose a search operator.

5.	Click the drawing area where you want to enter the query condition. ISIS/Draw inserts the search operator.

6.	Do one of the following:

*	If you chose none, enter a numeric value or a text string. (Do not enter quote marks.)

*	If you chose >, >=, <, <=, or <>, enter a text or numeric value.

*	If you chose between, enter a text or numeric value, a space, and then a second text or numeric value (such as Between 60 90 or Between aa cc).

*	If you chose contains or like, enter a text string. (Do not enter quote marks.)

7.	Click Done.


To attach a text or numeric query to brackets

Use this procedure to attach a text or numeric query to a set of brackets.

1.	Click

2.	Click one set of brackets that surround the atoms, bonds, components, or structures to attach the search operator and target value to.

3.	Click the Field name box and do one of the following:

*	If you have a database open that contains substance group (Sgroup) fields, choose a field name.

*	If you don't have a database open but you know the name of the Sgroup field, enter the field name. Note

4.	Click the Query box and do one of the following:

*	To retrieve solely structures in which the attached data matches your query exactly, choose none.

*	To specify a search operator for attached data, choose a search operator.

5.	Click the drawing area where you want to enter the query condition. ISIS/Draw inserts the query operator.

6.	Do one of the following:

*	If you chose none, enter a numeric value or a text string. (Do not enter quote marks.)

*	If you chose >, >=, <, <=, or <>, enter a text or numeric value.

*	If you chose between, enter a text or numeric value, a space, and then a second text or numeric value (such as Between 60 90 or Between aa cc).

*	If you chose contains or like, enter a text string. (Do not enter quote marks.)

7.	Click Done.


Specifying Attached Data

Click one of the following items:

*	For an exact search in a remote molecule database (such as MEXACT)

*	For a substructure search in a remote molecule database (such as SSS/Poly)


Specifying an exact search using attached data

Click one of the following items:

*	To attach data to bonds or atoms

*	To attach data to brackets


Specifying a substructure search using attached data

Click one of the following items:

*	To attach a text or numeric query to atoms and bonds

*	To attach a text or numeric query to brackets


To edit the structure within a polymer

You can edit any of the structures within a polymer. For example, to draw a polymer that was modified after polymerization, you edit a duplicate of the structural repeating unit (SRU):

 Caution: Do not delete any bonds that cross polymer brackets (crossing bonds). To delete crossing bonds, you must first delete the brackets, then edit the structure, then redraw the brackets.

For more information on editing structures, see Editing atoms, bonds, and structures in Section 5.7 of the "ISIS/Draw Quick Start".


To draw an undefined structure

1.	Click

2.	Click in the drawing area. You see a box with a text insertion point.

3.	Type * and press Enter (or click the down arrow and choose * from the list of atom types).

4.	To attach data to the undefined structure, click [image], and then click the * atom. You see the Attach Data to Objects dialog.

5.	Click the Field name box and do one of the following:

*	If a database is open that contains substance group (Sgroup) fields, choose a field name.

*	If a database is not open, but you know the name of the Sgroup field, enter the field name. Note

This associates the attached data with a database field for searching and registration.

For information on attached data in polymers, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

For information on attached data in non-polymer structures, see Drawing Mixtures: MDL Requirements for Database Searching and Registration.

6.	Click in the drawing area near the * atom where you want to position the data. You see a text insertion point.

7.	Type the data.

8.	Click Done.


Drawing an Unordered Mixture

Click here for step-by-step instructions

An unordered mixture is a mixture where the order in which the components are combined is not important. Use unordered mixture (mix) brackets to enclose the individual components of an ordered mixture. For example, the following is a reaction product that consists of a mixture of stereoisomers:

For information on drawing mixtures of polymers, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

For information on drawing mixtures of non-polymer structures, see Drawing Mixtures: MDL Requirements for Database Searching and Registration.


Drawing an Ordered Mixture

Click here for step-by-step instructions

An ordered mixture is a mixture where the order in which the components are combined (order of addition) is important. Use ordered mixture (f) brackets to enclose the individual components of an ordered mixture. The following structure represents the formulation of an aspirin tablet in which the acetaminophen (c1) must be added before the binder (c2) and other components (c3 and c4): Example

Note: In MACCS-II, ordered mixtures were called formulations.

For information on drawing mixtures of polymers, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

For information on drawing mixtures of non-polymer structures, see Drawing Mixtures: MDL Requirements for Database Searching and Registration.


Example


To draw an unordered mixture

1.	Draw the structures that comprise the mixture.

2.	Click

3.	To define a structure as a component in a mixture, press and drag a pair of brackets around one of the structures. Release the mouse and you see the Create Brackets dialog. You see the component definition shimmer.

Note: If you make a mistake, click Cancel. Then, draw the brackets again.

4.	Click the Bracket type box and choose component (c).

5.	(Optional) To change the style of the brackets, click the Bracket style box and choose a style.

6.	Repeat Steps 3 through 5 to define each component in the mixture.

7.	To draw the mixture brackets, drag a pair of brackets around all of the components in the mixture.

Note: SSS search queries

8.	Click the Bracket type box and choose mixture, unordered (mix).

9.	Click Apply to complete the definition of the mixture.

10.	To close the Create Brackets dialog, click another tool.

11.	(Optional) You can attach data to the component and/or mixture brackets.

12.	(Optional) Edit the mixture.


To draw an ordered mixture

1.	Draw the structures that comprise the mixture.

2.	Click

3.	To define a structure as a component in a mixture, press and drag a pair of brackets around one of the structures. Release the mouse and you see the Create Brackets dialog. You see the component definition shimmer.

Note: If you make a mistake, click Cancel. Then, draw the brackets again.

4.	Click the Bracket type box and choose component (c).

5.	If this is the first component of the mixture, click the Order box and enter 1 in place of None.

Note: ISIS/Draw automatically increments the Order box for subsequent components.

6.	(Optional) To change the style of the brackets, click the Bracket style box and choose a style.

7.	Repeat Steps 3 through 6 to define each component in the mixture.

8.	To draw the mixture brackets, drag a pair of brackets around all of the components in the mixture.

Note: SSS search queries

9.	Click the Bracket type box and choose mixture, ordered (f).

10.	Click Apply to complete the definition of the mixture.

11.	To close the Create Brackets dialog, click another tool.

12.	(Optional) You can attach data to the component and/or mixture brackets.

13.	(Optional) Edit the mixture.


Example


Drawing an Undefined Structure

Click here for step-by-step instructions

You can use *atoms with attached data to represent substances where the structure is undefined. For example, the following *atom representations represent two distinct binders of undefined structure:

In each *atom representation, the attached data is associated with the a database field, BINDER_DESCRIPTION. The attached data distinguishes Bind_16 from other binders during a search.


Drawing a Structure-Based Polymer or Copolymer

Click here for step-by-step instructions

Draw a structure-based representation of a polymer or copolymer when you know the structure of the constitutional repeating units (structural repeating units or SRUs) of the polymer. The structure-based representation is the preferred representation for polymers that you register to a database. For example:

For more information on polymer representation, see Drawing Polymers: MDL Requirements for Database Searching and Registration.


Drawing a Source-Based Polymer
Drawing a Source-Based Polymer or Copolymer

Click here for step-by-step instructions

Draw a source-based representation of a polymer or copolymer when you know the structure of the monomers, but do not know the structure of the constitutional repeating unit (structural repeating unit) of the polymer. For example:

For more information on polymer representation, see Drawing Polymers: MDL Requirements for Database Searching and Registration.


To draw a source-based polymer
To draw a source-based polymer or copolymer

1.	Draw the monomers (source materials) from which the polymer is made.

2.	Click

3.	Press and drag a pair of brackets around one or more monomers. Release the mouse and you see the Create Brackets dialog. You see the polymer definition shimmer.

Note: If you make a mistake, click Cancel. Then, draw the brackets again.

4.	Click the Bracket type box and choose monomer (mon).

5.	(Optional) To draw a copolymer, repeat Step 3 as needed to draw monomer brackets around additional monomers. Then, draw copolymer brackets around the monomer brackets.

6.	Click Apply to complete the definition of the polymer.

7.	To close the Create Brackets dialog, click another tool.

8.	(Optional) Edit the polymer.


To draw a structure-based polymer
To draw a structure-based polymer or copolymer

1.	Draw one or more structures that you will define later as polymers.

2.	Click

3.	Do one of the following:

*	Click the crossing bonds of the structural repeating unit of the polymer, then click Apply.

*	Press and drag a pair of brackets over the crossing bonds that define the structural repeating unit of the polymer, then click Apply.

*	(Ladder-type polymers only) Press the Shift key, then press and drag a bracket over the two crossing bonds at one end of the structural repeating unit. Next, press and drag another bracket over the two crossing bonds at the other end of the structural repeating unit. Then, click Apply.

Note: For information on how to include or exclude fragments in the polymer definition, click here.

4.	Click the Bracket type box and choose SRU (n).

5.	(Optional) To draw a copolymer, repeat Step 3 as needed to draw SRU brackets around additional structural repeating units. Then, draw copolymer brackets around all the SRU brackets.

6.	To close the Create Brackets dialog, click another tool.

7.	(Optional) Edit the polymer.


Note: Including and Excluding Fragments

ISIS/Draw automatically perceives salt fragments next to a structure enclosed in polymer brackets as part of the polymer definition. You can override the automatic salt perception, as follows:

*	To include an additional fragment as part of the polymer definition, press Shift and click the fragment. You see the fragment shimmer when it is included in the polymer definition.

*	To exclude a fragment that is part of the polymer definition, press Shift and click the fragment. You see the fragment stop shimmering when it is no longer included in the polymer definition.

Click Apply.


Drawing Copolymer Brackets

Click here for step-by-step instructions

Use copolymer brackets (co) to enclose multiple SRU (n) or monomer (mon) brackets within the same polymer. For example, use copolymer brackets to enclose the individual repeating units within a copolymer:

You should also use copolymer brackets for drawing polymers that are chemically altered after polymerization, such as modified polymers, cross-linked polymers, or graft polymers.

For more examples of polymer structures that use copolymer brackets, see Drawing Polymers: MDL Requirements for Database Searching and Registration.


To draw copolymer brackets

This procedure assumes that you have drawn one or more polymer structures that you want to enclose in copolymer brackets.

1.	Click

2.	Press and drag a pair of brackets around the polymer brackets that you want to enclose within copolymer brackets. Release the mouse and you see the Create Brackets dialog. You see the enclosed structures shimmer.

Note: If you make a mistake, click Cancel. Then, draw the brackets again.

3.	Click the Bracket type box and choose copolymer (co).

Note on additional polymer types

4.	Click the Polymer repeat pattern box and choose either/unknown.

5.	Click Apply to complete the definition of the polymer.

6.	To close the Create Brackets dialog, click another tool.

7.	(Optional) Edit the polymer.


Note on Additional Polymer Types

In addition to copolymer brackets (co), MDL provides additional copolymer types (random, block, and alternating). These brackets were used in earlier conventions for polymer representation that are no longer recommended. MDL provides these brackets in ISIS/Draw solely for compatibility with MACCS-II. If you are not sure whether your corporate database uses these additional copolymer types, see your ISIS Administrator.


Drawing a Modified Polymer

Click here for step-by-step instructions

Draw a polymer that was modified after polymerization as a copolymer that contains the original structural repeating unit (SRU) and the modified SRU. For example:


Drawing a Graft Polymer

Click here for step-by-step instructions

Draw a graft polymer as a copolymer that contains the both the original structural repeating unit (SRU) and a representation of the SRU after grafting. For example:


Drawing a Cross-Linked Polymer

Click here for step-by-step instructions

Draw a graft polymer as a copolymer that contains the both the original structural repeating unit (SRU) and a representation of the SRU after cross-linking. For example:


Modifying the Duplicate Polymer

Click here for step-by-step instructions

Modify the duplicate polymer by editing atoms and bonds on the duplicate polymer. For example:

For more information on polymer representation, see Drawing Polymers: MDL Requirements for Database Searching and Registration.


Adding a Graft to the Duplicate Polymer

Click here for step-by-step instructions

Add a graft to the duplicate polymer by drawing the grafted side chain on the duplicate polymer. Then, drawing SRU brackets. For example:

For more information on polymer representation, see Drawing Polymers: MDL Requirements for Database Searching and Registration.


Adding Cross-Linked Structures to the Duplicate Polymer

Click here for step-by-step instructions

Add cross-linked structures to the duplicate polymer by drawing atoms and bonds to represent the cross-linked structural repeating unit, then adding two more brackets to the SRU.

For more information on polymer representation, see Drawing Polymers: MDL Requirements for Database Searching and Registration.


To draw a graft polymer

1.	Draw a structure-based polymer.

2.	Select the polymer.

3.	Choose Edit > Duplicate.

4.	Add one or more grafts to the duplicate polymer.

5.	Click

6.	Press and drag a pair of brackets around the polymers that you drew in Steps 1 through 4. Release the mouse and you see the Create Brackets dialog. You see the definition shimmer.

Note: If you make a mistake, click Cancel. Then, draw the brackets again.

7.	Click the Bracket type box and choose copolymer (co).

8.	Click Apply to complete the definition of the polymer.

Note: While the Bracket dialog is open, you can continue to define polymers and copolymers.

9.	To close the Create Brackets dialog, click another tool.

10.	(Optional) Edit the polymer.


To draw a cross-linked polymer

1.	Draw a structure-based polymer.

2.	Select the polymer.

3.	Choose Edit > Duplicate.

4.	Add cross-linked structures to the duplicate polymer.

5.	Click

6.	Press and drag a pair of brackets around the polymers that you drew in Steps 1 through 4. Release the mouse and you see the Create Brackets dialog. You see the definition shimmer.

Note: If you make a mistake, click Cancel. Then, draw the brackets again.

7.	Click the Bracket type box and choose copolymer (co).

8.	Click Apply to complete the definition of the polymer.

Note: While the Bracket dialog is open, you can continue to define polymers and copolymers.

9.	To close the Create Brackets dialog, click another tool.

10.	(Optional) Edit the polymer.


To draw a modified polymer

1.	Draw a structure-based polymer.

2.	Select the polymer.

3.	Choose Edit > Duplicate.

4.	Modify the duplicate polymer.

5.	Click

6.	Press and drag a pair of brackets around the polymers that you drew in Steps 1 through 4. Release the mouse and you see the Create Brackets dialog.

Note: If you make a mistake, click Cancel. Then, draw the brackets again.

7.	Click the Bracket type box and choose copolymer (co).

8.	Click Apply to complete the definition of the polymer.

Note: While the Bracket dialog is open, you can continue to define polymers and copolymers.

9.	To close the Create Brackets dialog, click another tool.

10.	(Optional) Edit the polymer.


To modify the duplicate polymer

This procedure assumes that you have drawn the original structural repeating unit (SRU) of the polymer and a duplicate copy that you will edit to show how the SRU was modified.

1.	Edit the atoms and bonds in the duplicate polymer to show the modifications. If you need help on drawing atoms and bonds, click here.

2.	(Optional) Use Chem Inspector to ensure that the chemistry of the polymer correct is before you register or use the molecule to search in ISIS/Base. See Verifying the Chemistry of Sketches for more information.

3.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To add a graft to the duplicate polymer

This procedure assumes that you have drawn the original structural repeating unit (SRU) of the polymer and a duplicate copy that you will edit to show the SRU in the side-chain (graft).

1.	Draw the atoms and bonds in the side chain (graft). If you need help on drawing atoms and bonds, click here.

2.	Click

3.	Click the two crossing bonds of the structural repeating unit (SRU) of the graft.

4.	Click the Bracket type box and choose SRU (n).

5.	Click Apply to complete the definition of the SRU in the graft.

6.	To close the Create Brackets dialog, click another tool.

7.	(Optional) Use Chem Inspector to ensure that the chemistry of the polymer correct is before you register or use the molecule to search in ISIS/Base. See Verifying the Chemistry of Sketches for more information.

8.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To add cross-linked structures to the duplicate polymer

This procedure assumes that you have drawn the original structural repeating unit (SRU) of the polymer and a duplicate copy that you will edit to show how the SRUs are cross-linked.

1.	Draw the atoms and bonds that show cross-linking in the duplicate structure of the polymer. If you need help on drawing atoms and bonds, click here.

2.	Click

3.	Click a bracket in the duplicate SRU. You see the Create Brackets dialog. You also see the polymer definition shimmer.

4.	Click the two crossing bonds in the duplicate polymer that show how the two SRUs are cross-linked.

5.	Click Apply to complete the edited definition of the duplicate SRU.

6.	To close the Create Brackets dialog, click another tool.

7.	(Optional) Use Chem Inspector to ensure that the chemistry of the polymer correct is before you register or use the molecule to search in ISIS/Base. See Verifying the Chemistry of Sketches for more information.

8.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


Specifying Mixture Queries

For information on mixtures of polymers, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

For information on mixtures of non-polymeric structures, see Drawing Mixtures: MDL Requirements for Database Searching and Registration.

1.	Do one of the following:

*	Draw an Unordered Mixture

*	Draw an Ordered Mixture

3.	(Optional) Specify query features on a molecule for an SSS search.

2.	(Optional) To specify that the query contain attached data, click here.


Specifying Polymer Queries

Drawing Polymers: MDL Requirements for Database Searching and Registration.

1.	Do one of the following:

*	Draw a structure-based representation of a polymer

*	Draw a source-based representation of a polymer

*	Draw a modified polymer

*	Draw a graft polymer

*	Draw a cross-linked polymer

2.	(Optional) To specify one or more anypolymer brackets for an SSS/Poly or POLY/Sub search, select the brackets that you want to change, and then choose Object > Edit Brackets. Click the Bracket type box and choose anypolymer (anyp). Click OK.

3.	(Optional) Specify query features on a molecule for an SSS/Poly or POLY/Sub search.

4.	(Optional) Specify attached data on the query.


Mixtures, Formulations, Undefined Structures, and Attached Data
Drawing Mixtures: MDL Requirements for Database Searching and Registration

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Basics of Drawing Mixtures	8.1

*	Examples of Mixtures	8.2

We recommend that you print this 5-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

This Request-A-Document covers the basic concepts that you need to draw mixtures. Mixtures might also contain attached data and *atoms (star atoms). For step by step instructions for drawing the structures that are shown in this document, click here.

We assume that you know the basic concepts of drawing and manipulating molecules, reactions, and other objects in ISIS/Draw. For more information on these basic concepts, click here.

8.1 Basics of Drawing Mixtures

8.1.1 Unordered and Ordered Mixtures

To represent mixtures, enclose each structure within component brackets, and then enclose the components within mixture brackets. Mixtures can be unordered or ordered:

*	If the order of addition of components is not important, specify an unordered mixture (mix). Unordered mixtures contain components (c) that are not numbered:

*	If the order of addition of components of the formulation is important, use an ordered mixture (f). Ordered mixtures contain components that are numbered (c1, c2, c3, and so forth):

For examples of mixtures, see Section 8.2.

Note: In MACCS-II, ordered mixtures were called formulations.

8.1.2 Attached Data

Attached data is chemically-significant text that you can associate with an atom, a bond, a set of atoms and bonds, or with brackets. In the following example, the data that is attached to the deuterium atom specifies the percentage of deuteration at that site:

Attached data differs from chemically-insignificant text (plain text). Attached data can be exported to a molfile, stored in a molecule database, and/or used in a graphical search query in a remote molecule database.

Each piece of attached data must be associated with a special kind of database field, called a Substance group (Sgroup) field. The Sgroup field defines what the data means. For example, in the following structure, the attached data on percentage of deuteration is associated with the Sgroup field PERCENT_DEUTERATION:

In the following example, the data is associated with the asymmetric double bond, and represents the percentage of isomer that is in the trans configuration. Therefore, the data that is attached to the double bond is associated with a different Sgroup field, PERCENT_TRANS:

For numeric data, the Sgroup field can also specify the units of the data. In these examples, the PERCENT_DEUTERATION field has the associated units "% deuterated", and the PERCENT_TRANS field has the associated units “% trans”.

Your ISIS Administrator creates and maintains the Sgroup fields in your corporate database. Your ISIS Administrator also establishes guidelines that specify which Sgroup fields you must associate with specific types of data on a structure. In the previous example, the ISIS Administrator defines the Sgroup field PERCENT_TRANS in your database and assigns the units "% trans" to the Sgroup field.

 Caution: When you draw a structure for registration, you must follow the guidelines that your ISIS Administrator establishes. For example, specify the correct Sgroup field for each piece of attached data on the structure. If you do not follow these guidelines, other users might not be able to retrieve the structures that you register. For information on guidelines for using Sgroup fields at your company, see your ISIS Administrator. For guidelines on using attached data for chemical representation, see Appendix B, "Polymer Representation" in ISIS/Base Database Maintenance.

You can display attached data with a tag character that serves as a footnote. ISIS ignores tags in searching. For example, the two structures below are equivalent:

8.1.3 Undefined Structures (*Atoms)

You can use *atoms with attached data to represent substances where the structure is unknown. For example, the following *atoms represent two distinct binders of unknown structure:

In each *atom representation, the attached data is associated with the Sgroup field BINDER_DESCRIPTION.

8.2 Examples of Mixtures

8.2.1 Unordered Mixtures

Reaction Product

To draw a mixture of compounds such as a reaction product, draw a mixture with unordered components (unordered mixture). You use an unordered mixture because the order of addition is not important. The following example shows a reaction product that consists of a mixture of geometric stereoisomers:

Each component of the mixture is enclosed within component brackets (c). The numeric data that is attached to each set of component brackets specifies the mole percentage of that component of the mixture. Unordered mixture brackets (mix) enclose the component brackets.

Mixture of Optical Stereoisomers

The following example is a mixture of optical stereoisomers:

Each component bracket (c) within the mixture has two pieces of attached data associated with it:

*	Numeric data (0.74, 0.03, or 0.23) that represents the fraction of each component in the mixture. The numeric data is associated with the Sgroup field COMPONENT_FRACTION.

*	Non-numeric data (Active, Adverse, or Inert) that represents the activity of each component. This non-numeric data is associated with the Sgroup field ACTIVITY_TYPE.

Aspirin Tablet

The following mixture is the formulation of an aspirin tablet. The representation uses mixture brackets (mix), because the components (c) can be combined in any order. Each component bracket has attached data that specifies the weight percentage of each component (the associated Sgroup field is WEIGHT_PERCENT). One component (*atom with attached data Bind_46) is a binder of undetermined structure (the associated Sgroup field is BINDER_DESCRIPTION):

8.4.2 Ordered Mixture

In the following formulation, the acetaminophen (c1) must be added before the binder (c2) and other components (c3 and c4).

The attached data specifies the weight percentage of each component of the mixture (the associated Sgroup field is WEIGHT_PERCENT).


Drawing Polymers
Drawing Polymers: MDL Requirements for Database Searching and Registration

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Basics of Polymer Representation	9.1

*	Structure-Based Representation of Polymers	9.2

*	Source-Based Representation of Polymers	9.3

We recommend that you print this 24-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

 Caution: This document describes the conventions that MDL requires for drawing polymer structures that you can register to an ISIS database. You must use these conventions when you draw structures that you register. If you do not follow these conventions, other users might not be able to retrieve the structures that you register.

Your company might create structures for which no MDL conventions exist. If you are not sure how to draw a structure that you want to register, see your ISIS Administrator.

We assume that you know the basic concepts of drawing and manipulating molecules, reactions, and other objects in ISIS/Draw. For more information on these basic concepts, click here.

9.1 Basics of Polymer Representation

9.1.1 Structure-Based and Source-Based Representation of Polymers

Polymers can be drawn using either the structure-based or source-based representation. The following example shows both representations of a simple homopolymer:

Use the following guidelines when drawing polymers that you register to ISIS databases:

*	Draw a polymer structure that contains as much structural detail as possible. Consequently, use the structure-based representation whenever possible.

*	Use the source-based representation when the structural details are unknown.

Note: If your corporate database contains extremely complex polymer structures and formulations, your ISIS Administrator might specify solely source-based representation.

For information on conventions for drawing structure-based representations of polymers and copolymers, see Section 9.2. For information on conventions for drawing source-based representations of polymers and copolymers, see Section 9.3.

Note: For certain types of polymerization reactions, the source-based and structure-based representations of a polymer can find each other in a POLY/Both search. For example:

For information on POLY/Both search, click here. Alternatively, choose Help > Index and search for POLY/Both, how-to/examples. Then, click Searching Concepts/Examples.

9.1.2 Polymer Bracket Types

A polymer structure consists of a collection of structural fragments that are enclosed by polymer brackets. This section describes the types of polymer brackets that you can use to build polymer structures.

Structural Repeating Unit (SRU) Brackets (n)

Use Structural Repeating Unit (SRU) brackets to enclose the structural repeating unit (constitutional repeating unit) of the structure-based representation of a homopolymer:

SRU brackets imply that the structure within the brackets can repeat with itself. Consequently, you should enclose the structure "A" in SRU brackets solely if the sequence ...AAAAA... can occur.

Each set of SRU brackets has two or more bonds, called crossing bonds, that overlay the brackets. The crossing bonds of an SRU show how the repeating units connect to each other within the polymer (connectivity).

Note: For SRUs that have 2 or 4 crossing bonds, the repeat pattern of the SRU specifies additional information on connectivity. For more detailed information on repeat pattern, see Section 9.1.3.

For examples of polymer structures that use SRU brackets, see Section 9.2.

Monomer Brackets (mon)

Use Monomer (mon) brackets to draw the repeating unit(s) for the source-based representation of a homopolymer:

For examples of source-based representations of polymers, see Section 9.3.

Mer Brackets (mer)

For source-based representations of copolymers, use mer brackets (mer) to enclose a monomer that can not repeat with itself. For example, if you know that a diol monomer for a polyester does not homopolymerize to form polyperoxides within the copolymer, enclose the diol in mer brackets. For examples of copolymers that use mer brackets, see Section 9.3.6.

Copolymer Brackets (co)

If a structure contains more than one set of SRU, monomer, and/or mer brackets, enclose the entire structure within copolymer brackets. Always use copolymer brackets when you require more than one set of polymer brackets to represent the structure. For example, polymers that are chemically modified after polymerization are represented as copolymers. For examples of chemically-modified polymers, see Sections 9.2.7 through 9.2.9.

If the sequence of the repeating units within the copolymer is known (for example, a regular block copolymer), draw the structure-based representation with connecting bonds between the SRUs. If the sequence repeats, draw the structure so that bonds from the SRUs cross the copolymer brackets:

If the sequence of the repeating units is unknown or unspecified (for example, an irregular block copolymer, or a random copolymer), draw the structure-based representation with no connecting bonds between the SRUs:

Note: When you draw copolymer brackets with no crossing bonds, specify the either/unknown repeat pattern. The head-to-tail and head-to-head repeat patterns are meaningful solely when the copolymer brackets have crossing bonds. For more information on repeat pattern, see Section 9.1.3.

For examples of polymer structures that use copolymer brackets, see Sections 9.2.4 through 9.2.9 (structure-based representations) and Sections 9.3.4 and 9.3.5 (source-based representations).

Additional Polymer Brackets

Additional polymer and copolymer bracket types can be used to represent specific types of copolymers. These bracket types are available in ISIS/Draw, but are no longer recommended for polymer representation. If you are not sure whether your corporate database contains polymer structures that use these polymer types, see your ISIS Administrator.

The additional copolymer bracket types are: alternating (alt), block (blk), and random (ran).

The additional polymer bracket types are: cross-link (xl), modified (mod), and graft (grf).

9.1.3 Polymer Repeat Pattern

For polymer brackets that contain crossing bonds (SRUs and some copolymers), the polymer repeat pattern shows how the repeating units are joined together. The repeat patterns that you can specify depends on the number of crossing bonds in the polymer.

Polymers With Two Crossing Bonds

If the polymer bracket has one crossing bond on each bracket of the SRU or copolymer, you have three possible repeat patterns: head-to-tail (the default), head-to-head, and either/unknown. The following table shows examples of the three repeat patterns in a homopolymer:

For an example of a homopolymer that uses either/unknown repeat pattern, see Section 9.2.2.

Ladder-Type Polymers

For paired brackets with two crossing bonds on each bracket (ladder-type polymers), you must also specify how the two crossing bonds on each bracket connect to the corresponding bonds of the adjacent SRUs:

*	If the repeat pattern is head-to-tail, you must specify whether the SRU flips around the polymer backbone when it attaches to the adjacent SRU. Consequently, you have two options for connecting the corresponding bonds:

*	If the repeat pattern is head-to-head, the options for connecting the corresponding bonds are as follows:

*	If the repeat pattern is either/unknown, the connections between corresponding bonds might be unknown. Alternatively, the polymer might contain a mixture of units that are joined head-to-head, and other units that are joined head-to-tail (either).

The following table shows examples of the five repeat patterns that are possible for ladder-type polymers:

For the either/unknown repeat pattern, a structure that contains two brackets with four crossing bonds is equivalent to a structure that contains four brackets with one crossing bond on each bracket. For example, the following structures are equivalent:

Polymers With Three or More Brackets

Polymers with three or more brackets always have the either/unknown (eu) repeat pattern. The following are additional representations of polymer structures:

9.1.4 Attached Data

Attached data is chemically-significant text that you can associate with a portion of a molecule, such as an atom, a bond, a set of atoms and bonds, or a set of brackets. For example, the following structure of a statistical copolymer contains attached data on the type of copolymer (stat), the number-average molecular weight of the copolymer (20,000 Mn), and on the mass percentage of each type of repeating unit (75 mass %, 25 mass %):

Attached data differs from chemically-insignificant text (plain text). Attached data can be exported to a molfile, stored in a molecule database, and/or used in a graphical search query in a remote molecule database.

Sgroup Fields

Each piece of attached data is associated with a special kind of database field, called a Substance Group (Sgroup) field. The Sgroup field defines what the data means. The following table shows the associated Sgroup field and the meaning of each piece of attached data in the polymer structure from the previous example:

Your ISIS Administrator creates and maintains the Sgroup fields in your corporate database. Your ISIS Administrator also establishes guidelines that specify which Sgroup fields you must associate with specific types of data. In the previous example, the ISIS Administrator defines the Sgroup field POLYMER_MASS_PERCENT in your database and assigns the units "mass %" to the Sgroup field.

 Caution: When you draw a structure for registration, you must follow the guidelines that your ISIS Administrator establishes. For example, you must specify the correct Sgroup field for each piece of attached data on the structure. If you do not follow these guidelines, other users might not be able to retrieve the structures that you register. For more information on how to use the Sgroup fields that are available at your site, see your ISIS Administrator.

Specifying Tags For Attached Data

You can display attached data with a tag character that serves as a footnote. In searching, ISIS ignores tags. For example, the two structures below are equivalent:

9.1.5 Polymer End Groups

The end groups of polymers are generally unknown. Use *atoms (star atoms) to represent unknown or unspecified end groups. For example:

Note: When you draw the brackets of a polymer structure, ISIS automatically changes terminal carbon atoms to *atoms.

9.1.6 Abbreviated Structures and Multiple Groups

For complicated structures, you might want to abbreviate parts of the structure. An abbreviated structure is all or part of a molecule that has been abbreviated to a text label. Structures that you abbreviate keep their chemical significance, but the underlying structure is hidden. In this example, the phenyl ring in polystyrene is abbreviated to the text string Ph:

You can use queries that contain abbreviated structures to search a database using ISIS/Base. ISIS/Base uses the underlying chemistry and ignores the name. For more information on abbreviated structures, click here. Alternatively, choose Help > Index, and search for abbreviated structures, definition of.

You can also use multiple groups to abbreviate structures. A multiple group is a pair of brackets that represents a fixed number of replications of the structure within the brackets. For example:

Like abbreviated structures, you can use queries that contain multiple groups to search a remote molecule database using ISIS/Base. During the search, ISIS/Base uses the underlying chemistry of the multiple group. For step-by-step instructions on creating multiple groups, click here. Alternatively, choose Help > Index, and search for multiple groups, drawing.

9.1.7 Polymer Mixtures

To represent polymer mixtures, enclose each polymer structure within component brackets, and then enclose the components within mixture brackets. Mixtures can be unordered or ordered:

*	If the order of addition of components is not significant, specify an unordered mixture (mix). Unordered mixtures contain components (c) that are not numbered:

*	If the order of addition of components of the formulation is important, use an ordered mixture (f). Ordered mixtures contain components that are numbered (c1, c2, c3, and so forth):

The following example shows an unordered mixture of a copolymer and two other components:

Note: In MACCS-II, ordered mixtures were called formulations.

9.2 Structure-Based Representations of Polymers

The examples in this section show how to draw structure-based representations of different kinds of polymers and copolymers. The conventions in this section are based on standards for polymer representation that have been established by the International Union of Pure and Applied Chemistry (IUPAC). For more information on IUPAC standards, see Bareiss, R. E.; Kahovec, J.; and Cratochvil, P.; Pure Appl. Chem. 1994, 66:12, 2469-2482.

9.2.1 Regular Homopolymers

Simple Homopolymers

Stereoregular Polymers

Avoid using Up and Down stereo bonds to show stereoregularity in polymers. Instead, use Sgroup data to specify stereoregular polymers. In the following example, attached data (associated with the Sgroup field STEREO) shows tacticity in polystyrene:

Ladder-Type Polymers

To draw ladder-type polymers, use paired brackets with two crossing bonds per bracket. For example:

9.2.2 Irregular Homopolymers

For polymers that contain a mixture of SRUs joined head-to-head and head-to-tail, specify the polymer repeat pattern as either/unknown (eu). In the following example, poly(1-chloroethylene/2-chloroethylene) consists of units of chloroethylene that can be joined head-to-head (1-chloroethylene) or head-to-tail (2-chloroethylene):

9.2.3 Alternating and Periodic Copolymers

Represent alternating and other periodic copolymers as homopolymers. For example:

9.2.4 Statistical, Random, and Unspecified Copolymers

In statistical, random, and unspecified copolymers, the sequence of repeating units is irregular or unspecified. Therefore, you need to draw the copolymer with no connecting bonds between the SRUs.

Always use the either/unknown repeat pattern for copolymer brackets that do not have crossing bonds.

Unspecified Copolymers

Random Copolymers

Represent random copolymers as a combination of SRUs without connecting bonds. Attach data (ran) to the brackets to show the copolymer type. For example:

Statistical Copolymers

Represent “statistical” copolymers as random copolymers. Use attached data (stat) to specify the polymer type, and/or to specify repeating-unit probabilities. The following are examples of statistical copolymers:

9.2.5 Regular Block Copolymers

In a regular block copolymer, the sequence of repeating units is known. Therefore, you need to draw the copolymer in sequence, with connecting bonds between the SRUs.

If the copolymer brackets have crossing bonds, specify the head-to-tail or head-to-head repeat pattern as necessary. Otherwise, specify either/unknown.

Ordered Diblock

Block Copolymer With Junction Unit

A junction unit is a nonrepeating unit that joins two sequences within a polymer. Do not enclose a junction unit in SRU brackets, because SRU brackets imply that the unit can repeat with itself. For example:

Segmented Block Copolymers

If bonds cross the copolymer brackets, then the entire sequence of blocks repeats, giving a segmented block structure.

Star Block Copolymers

9.2.6 Irregular Block Copolymers

In a block copolymer that consists of irregular blocks, the sequence of repeating units is unknown. Therefore, draw the copolymer with no connecting bonds between the SRUs, and specify the either/unknown repeat pattern on the copolymer brackets:

9.2.7 Chemically-Modified Polymers

Represent a chemically-modified polymer as a copolymer that contains the original SRU and the chemically-modified SRU.

9.2.8 Graft Polymers and Copolymers

Represent a graft polymer as a copolymer that contains the original SRU and the grafted SRU.

Single Graft at a Known Site

Mixed Graft at a Known Site

9.2.9 Cross-Linked Polymers

Represent cross-linked polymers as copolymers. That is, represent the polymer as a copolymer that contains both the original and cross-linked SRU.

9.3 Source-Based Representation of Polymers

If you do not know the structural details of the structural repeating units within the polymer, you need to use the source-based representation of the polymer.

9.3.1 Guidelines for Source-Based Representation

The source-based representation of a polymer is based on the source-based name of the polymer. Use the following guidelines when you draw source-based representations of polymers:

*	If a monomer forms homopolymers, enclose the monomer within monomer (mon) brackets.

*	If you know that a monomer does not homopolymerize, enclose the monomer within mer brackets. For example, the diol and diacid monomers of a polyester generally do not react to form polyperoxides and polyanhydrides (see Section 9.3.6).

*	If the structure contains more than one set of monomer and/or mer brackets, enclose the structure within copolymer brackets (co).

*	Always use the either/unknown repeat pattern on copolymer brackets. Copolymer brackets in source-based polymers do not have bonds that overlay the brackets (crossing bonds), and therefore cannot have the head-to-head (hh) or head-to-tail (ht) repeat pattern.

The following figures show the source-based and structure-based representations of a homopolymer and a copolymer:

For more examples of source-based representation, see the following sections.

9.3.2 Homopolymers

9.3.3 Alternating and Other Periodic Copolymers

For alternating and other periodic copolymers, you generally know enough about the structure to draw the structure-based representation. Therefore, we strongly recommend that you do not register source-based representations of alternating and periodic copolymers.

9.3.4 Statistical, Random, and Unspecified Copolymers

Unspecified Copolymers

Random Copolymers

Statistical Copolymers

9.3.5 Block Copolymers

9.3.6 Copolymers From Monomers That Do Not Homopolymerize

Use mer brackets to enclose monomers that you know do not homopolymerize. For example, when you combine a diol monomer and a diacid monomer to create a polyester, you might know that the two monomers do not homopolymerize to form polyperoxides or polyanhydrides. To show this, you enclose the diol and diacid monomers in mer brackets:


Learning Basic Skills for Drawing Mixtures and Formulations

MDL provides special tools that you can use to draw mixtures and formulations that you can register to your database, or use as search queries. These tools include mixture brackets, *atoms, and attached data. To learn how to use these tools to represent mixtures and formulations, see Drawing Mixtures and Formulations: MDL Requirements for Database Searching and Registration.

 Caution: Your ISIS Administrator establishes conventions for using mixture brackets, *atoms, and attached data to represent mixtures and formulations. You must follow these conventions when you draw structures that you register to your database. If you do not follow these conventions, other users might not be able to retrieve the structures that you register. If you are not sure how to draw a structure that you want to register, see your ISIS Administrator.


Learning Basic Skills for Drawing Polymers

To draw polymer structures that you can register to a database or use as search queries, you must follow the required conventions for drawing polymer structures. If you do not follow these conventions, other users might not be able to retrieve the structures that you register. To learn the polymer drawing conventions that you need, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

 Caution: Your ISIS Administrator might establish conventions for polymer representation that are different from the conventions that MDL recommends. Also, your site might create structures for which no MDL conventions have been established. If you are not sure how to draw a structure that you want to register, see your ISIS Administrator.


Learning Basic Skills for Drawing Polymers

To draw polymer structures that you can register to a database or use as search queries, you must follow the required conventions for drawing polymer structures. If you do not follow these conventions, other users might not be able to retrieve the structures that you register. To learn the polymer drawing conventions that you need, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

 Caution: Your ISIS Administrator might establish conventions for polymer representation that are different from the conventions that MDL recommends. Also, your site might create structures for which no MDL conventions have been established. If you are not sure how to draw a structure that you want to register, see your ISIS Administrator.


Queries for Common Functional Groups

For many classes of compounds, the generic structure (for example, R-Br for alkyl bromides) can not be directly used as a query. You must add additional structural details (including query features) to ensure that you retrieve exactly the class of compounds that you want. For example:

To learn the query features and other structural details that are required to retrieve the compounds that you want, click one of the following:

Acetals and Hemiacetals

Alcohols and Phenols

Aldehydes

Alkenes and Alkynes

Alkyl Halides

Amines

Aryl Halides

Azo Compounds

Carbamates and Carbazates

Carboxylic Acids and Derivatives

Cyanates and Thiocyanates

Disulfides

Guanidines

Hydrazines and Hydrazides

Hydroxylamines

Imines

Ketones

Lactams and Lactones

Nitriles

Nitroxides (Aminoxyl Radicals)

Oximes

Phosphines

Phosphonic Acids and Derivatives

Stannanes

Sulfimides (Sulfilimines)

Sulfonic Acids and Derivatives

Sulfoxides

Thiols

Other compounds

Rings, Chains, and Other Common Structures

Note: To learn how to draw query features and other structures in ISIS/Draw, see the ISIS/Draw "Quick Start".


Queries for Common Classes of Compounds

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Acetals and Hemiacetals	150.2

*	Alcohols and Phenols	150.3

*	Aldehydes	150.4

*	Alkenes and Alkynes	150.5

*	Alkyl Halides	150.6

*	Amines	150.7

*	Aryl Halides	150.8

*	Azo Compounds	150.9

*	Carbamates and Carbazates	150.10

*	Carboxylic Acids and Derivatives	150.11

*	Cyanates and Thiocyanates	150.12

*	Disulfides	150.13

*	Guanidines	150.14

*	Hydrazines and Hydrazides	150.15

*	Hydroxylamines	150.16

*	Imines	150.17

*	Ketones	150.18

*	Lactams and Lactones	150.19

*	Nitriles	150.20

*	Nitroxides (Aminoxyl Radicals)	150.21

*	Oximes	150.22

*	Phosphines	150.23

*	Phosphonic Acids and Derivatives	150.24

*	Stannanes	150.25

*	Sulfimides (Sulfilimines)	150.26

*	Sulfonic Acids and Derivatives	150.27

*	Sulfoxides	150.28

*	Thiols	150.29

*	Other Compound Classes	150.30

*	Rings, Chains, and Other Common Structures	150.31

We recommend that you print this Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

150.2 Acetals and Hemiacetals

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

150.2.1 Acetals

The following query retrieves acetals:

The atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the central carbon atom.

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

150.2.2 Hemiacetals

The following query retrieves hemiacetals:

The hydrogen atom on the hydroxy group is drawn explicitly to prevent substitution of other atoms.

The atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the central carbon atom.

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

To retrieve both hemiacetals and salts of hemiacetals (that is, structures with either a hydroxy group or a negatively-charged oxygen atom attached to the central carbon atom), use the Substitution Count as Drawn (s*) query feature rather than drawing the hydrogen explicitly:

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

150.3 Alcohols and Phenols

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see Using ISIS/Draw.

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

150.3.1 Aliphatic Alcohols

The following query retrieves all alcohols (primary, secondary, and tertiary):

The four single bonds to the alcohol carbon ensure that the carbon will be saturated, as required by the IUPAC definition of an alcohol.

The hydrogen atom on the oxygen is drawn explicitly to prevent substitution of other atoms.

The atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the alcohol carbon.

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

Note: This query also retrieves a small number of structures such as the following:

To avoid retrieving these structures, add the Substitution Count as Drawn (s*) query feature to the oxygen atom:

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

150.3.2 Primary Alcohols

150.3.3 Secondary Alcohols

150.3.4 Tertiary Alcohols

150.3.5 Primary and Secondary Alcohols

The following query retrieves both primary and secondary alcohols:

The atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the alcohol carbon.

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

150.3.6 Phenols and Other Aromatic Alcohols

Phenols

The following query retrieves phenols:

The following are examples of the structures that you retrieve:

To avoid retrieving phenols that contain fused rings, apply the Ring Bond Count as Drawn (r*) query feature to all the atoms of the ring:

The following are examples of the structures that you retrieve:

To specify Ring Bond Count as Drawn in ISIS/Draw, select the ring atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Ring bond count box and choose *.

Aromatic and Heteroaromatic Alcohols

To retrieve all aromatic alcohols, including those with heteroatoms in the ring, use the Any atom (A) query feature and the Aromatic query bond. For example:

The following are examples of the structures that you retrieve:

To specify an Any Atom in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose A.

To specify an Aromatic query bond in ISIS/Draw, select the bond and double-click it. In the Edit Bond dialog, click the Bond tab, then click the Bond type box and choose Aromatic.

150.3.7 Salts of Alcohols and Phenols

To retrieve both phenols and salts of phenols, use the Substitution Count as Drawn (s*) query feature rather than drawing the hydrogen explicitly:

The following are examples of the structures that you retrieve:

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

To retrieve only salts of phenols, specify a charge of -1 on the oxygen:

To specify a charge of -1 in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Atom tab, then click the Charge box and choose -1.

The following are examples of the structures that you retrieve:

The same principles apply to other aromatic and aliphatic alcohols. For example, the following query retrieves both aliphatic alcohols and alkoxides:

The following query retrieves both aromatic and heteroaromatic alcohols:

150.4 Aldehydes

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

The following query retrieves aldehydes:

The hydrogen atom on the carbonyl group is drawn explicitly to prevent substitution of other atoms.

150.5 Alkenes and Alkynes

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

150.5.1 Alkenes

The following query retrieves alkenes:

The Chain bond query feature specifies acyclic double bonds, as required by the IUPAC definition of an alkene.

The open valences at the two carbon atoms allow any substituent at those positions. Consequently, this query retrieves all compounds that contain at least one acyclic carbon-carbon double bond.

The following query retrieves only structures with either hydrogen or carbon atoms attached to the acyclic double bond:

The atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the double bond.

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

To specify a Chain bond in ISIS/Draw, select the bond and double-click it. In the Edit Bond dialog, click the Bond tab, then click the Topology box and choose Chain.

150.5.2 Alkynes

The following query retrieves alkynes:

The Chain bond query feature specifies acyclic triple bonds, as required by the IUPAC definition of an alkyne.

The open valences at the two carbon atoms allow any substituent at those positions. Consequently, this query retrieves all compounds that contain at least one acyclic carbon-carbon triple bond.

The following query retrieves only structures with either hydrogen or carbon atoms attached to the acyclic triple bond:

The atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the double bond.

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

To specify a Chain bond in ISIS/Draw, select the bond and double-click it. In the Edit Bond dialog, click the Bond tab, then click the Topology box and choose Chain.

150.6 Alkyl halides

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

The following query retrieves alkyl halides:

The four single bonds to the central carbon atom ensure that this carbon is saturated.

The atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the central carbon atom.

The atom list query feature [F,Cl,Br,I] specifies halogens.

The following structures are retrieved:

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

To eliminate structures with rings at the alpha carbon, add the Chain bond query feature (Ch) to the bonds to the central carbon atom:

The following structures are retrieved:

To specify a Chain bond in ISIS/Draw, select the bond and double-click it. In the Edit Bond dialog, click the Bond tab, then click the Topology box and choose Chain.

You can edit the atom list of halides to include only the halogens that you want. For example, to eliminate fluorides and iodides, use one of the following:

Note: The queries shown in this section also retrieve structures such as the following:

To avoid retrieving structures such as these, add the Substitution Count as Drawn query feature (s*) to the atom list of halides:

Alternatively, you can specify an explicit valence of 1 on the halide atom list:

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

To specify explicit valence in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Atom tab, then click the Valence box and choose 1.

If you want, you can extend the definition of an alkyl halide to allow additional atom types to attach to the central carbon atom. For example, the following query retrieves structures with either carbon, hydrogen, nitrogen, oxygen, or sulfur attached to the central carbon atom:

150.7 Amines

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

150.7.1 Primary Aliphatic Amines

The following query retrieves primary aliphatic amines, but not amides, thioamides, or enamines:

The four single bonds to the carbon that is attached to the amine nitrogen ensure that the carbon is saturated. This avoids the retrieval of compounds such as amides and enamines.

The hydrogen atoms on the nitrogen are drawn explicitly to prevent substitution of other atoms.

The Atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the carbon at the amine.

The following are examples of the structures that you retrieve:

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

Note1: This query also retrieves a small number of secondary ammonium salts such as the following:

To avoid retrieving these structures, add the Substitution Count as Drawn (s*) query feature to the nitrogen atom:

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

The following query uses Rgroup query features to specify a primary aliphatic amine:

The query retrieves primary aliphatic amines. It does not retrieve aromatic amines, carboxamides, thioamides, enamines, or nitrogen compounds with imino (-C=N) substituents, such as guanidines.

The root structure of the Rgroup specifies a single nitrogen atom with the Rgroup labels R1 and R2 attached by a single bond. Together, the two Rgroups specify the substituents that can attach to the nitrogen.

The Rgroup condition R1=1 specifies that the nitrogen atom must have exactly one attachment (Rgroup member) from R1. The (Rest H) Rgroup condition specifies that all other substituents of the nitrogen must be hydrogen atoms. R1 contains one member, a single carbon atom. Thus, R1 specifies primary amines, but not compounds such as hydrazines or hydroxylamines.

The Rgroup condition R2=0 specifies that none of the Rgroup members in the definition of R2 can attach to the nitrogen atom. Thus, R2 specifies the groups that are not retrieved by the query, as follows:

*	The first Rgroup member in R2 contains a carbon atom attached to an Any atom (A) query feature through an Aromatic query bond. This specifies aromatic amines, so the query does not retrieve aromatic amines.

*	The second Rgroup member in R2 contains a carbon atom attached to the Atom list query feature [O,S,N,C] through a double bond. This specifies carboxamides, thioamides, structures that contains imino groups, and enamines, so the query does not retrieve these structures.

For additional information and examples of Rgroup query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

150.7.2 Anilines and Other Primary Aromatic Amines

Anilines

The following query retrieves anilines:

The hydrogen atoms on the nitrogen are drawn explicitly to prevent substitution of other atoms.

The following are examples of the structures that you retrieve:

To avoid retrieving anilines that contain fused rings, apply the Ring Bond Count as Drawn (r*) query feature to all the atoms of the ring:

The following are examples of the structures that you retrieve:

To specify Ring Bond Count as Drawn in ISIS/Draw, select the ring atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Ring bond count box and choose *.

Note: To avoid retrieving secondary ammonium salts, add the Substitution Count as Drawn (s*) query feature to the nitrogen atom:

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

See also section 150.7.6, Additional Queries for Aromatic Primary, Secondary, and Tertiary Amines.

Aromatic and Heteroaromatic Primary Amines

To retrieve all aromatic primary amines, including those with heteroatoms in the ring, use the Any atom (A) query feature and the Aromatic query bond. For example:

The following are examples of the structures that you retrieve:

To specify an Any Atom in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose A.

To specify an Aromatic query bond in ISIS/Draw, select the bond and double-click it. In the Edit Bond dialog, click the Bond tab, then click the Bond type box and choose Aromatic.

Note1: To avoid retrieving secondary ammonium salts, add the Substitution Count as Drawn (s*) query feature to the nitrogen atom:

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

For comprehensive reference information on all available query features, including Rgroup query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

150.7.3 Secondary Amines

Use the same principles to construct queries for secondary amines as for primary amines.

Secondary Aliphatic Amines

The following query retrieves secondary aliphatic amines:

The four single bonds to the carbons that are attached to the amine nitrogen ensure that the carbon atoms are saturated. This avoids the retrieval of compounds such as amides and enamines.

The hydrogen atom on the nitrogen is drawn explicitly to prevent substitution of other atoms.

The Atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the carbon atoms.

Note: This query also retrieves a small number of tertiary ammonium salts:

To avoid retrieving these structures, add the Substitution Count as Drawn (s*) query feature to the nitrogen atom:

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

The following query for secondary aliphatic amines uses the same Rgroups as the query for primary aliphatic amines. The only difference is that the Rgroup condition for R1 has changed to R1 = 2 (RestH), so that the query retrieves only secondary amines. The query does not retrieve aromatic amines, carboxamides, thioamides, enamines, or nitrogen compounds with imino (-C=N) substituents, such as guanidines.

The root structure of the Rgroup specifies a single nitrogen atom with the Rgroup labels R1 and R2 attached by a single bond. Together, the two Rgroups specify the substituents that can attach to the nitrogen.

The Rgroup condition R1=2 specifies that the nitrogen atom must have exactly two attachments (Rgroup members) from R1. The (Rest H) Rgroup condition specifies that all other substituents of the nitrogen must be hydrogen atoms. The definition of R1 contains one member, a single carbon atom. Thus, R1 specifies secondary amines, but not compounds such as hydrazines or hydroxylamines.

The Rgroup condition R2=0 specifies that none of the Rgroup members in the definition of R2 can attach to the nitrogen atom. Thus, R2 specifies the groups that are not retrieved by the query, as follows:

*	The first Rgroup member in R2 contains a carbon atom attached to an Any atom (A) query feature through an Aromatic query bond. This specifies aromatic amines, so the query does not retrieve aromatic amines.

*	The second Rgroup member in R2 contains a carbon atom attached to the Atom list query feature [O,S,N,C] through a double bond. This specifies carboxamides, thioamides, structures that contains imino groups, and enamines, so the query does not retrieve these structures.

For additional information and examples of Rgroup query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

Secondary Aromatic Amines

The following query retrieves secondary aromatic amines (one aromatic substituent):

To retrieve all aromatic secondary amines, including those with heteroatoms in the ring, use the Any atom (A) query feature and the Aromatic query bond on the aromatic substituent. For example:

To avoid retrieving tertiary ammonium salts, add the Substitution Count as Drawn (s*) query feature to the nitrogen atom:

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

For comprehensive reference information on all available query features, including Rgroup query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

See also section 150.7.6, Additional Queries for Aromatic Primary, Secondary, and Tertiary Amines.

150.7.4 Tertiary Amines

Use the same principles to construct queries for tertiary amines as for primary and secondary amines.

Tertiary Aliphatic Amines

The following query retrieves tertiary aliphatic amines:

The four single bonds to the carbons that are attached to the amine nitrogen ensure that the carbon atom is saturated. This avoids the retrieval of compounds such as enamines.

The Atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the carbon atoms.

The Substitution Count as Drawn (s*) query feature specifies that only three nonhydrogen atoms can attach to the nitrogen atom. Using s* prevents the retrieval of quaternary amines such as the following:

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

The following query for tertiary aliphatic amines uses the same Rgroups as the Rgroup query for primary aliphatic amines. The only difference is that the Rgroup condition for R1 has changed to R1 = 3 (RestH), so that the query specifies only tertiary amines. The query does not retrieve aromatic amines, carboxamides, thioamides, enamines, or nitrogen compounds with imino (-C=N) substituents, such as guanidines.

The root structure of the Rgroup specifies a single nitrogen atom with the Rgroup labels R1 and R2 attached by a single bond. Together, the two Rgroups specify the substituents that can attach to the nitrogen.

The Rgroup condition R1=3 specifies that the nitrogen atom must have exactly three attachments (Rgroup members) from R1. The (Rest H) Rgroup condition specifies that all other substituents of the nitrogen must be hydrogen atoms. R1 contains one member, a single carbon atom. Thus, R1 specifies tertiary amines, but not compounds such as hydrazines or hydroxylamines.

The Rgroup condition R2=0 specifies that none of the Rgroup members in R2 can attach to the nitrogen atom. Thus, R2 specifies the groups that are not retrieved by the query, as follows:

*	The first Rgroup member in R2 contains a carbon atom attached to an Any atom (A) query feature through an Aromatic query bond. This specifies aromatic amines, so the query does not retrieve aromatic amines.

*	The second Rgroup member in R2 contains a carbon atom attached to the Atom list query feature [O,S,N,C] through a double bond. This specifies carboxamides, thioamides, structures that contains imino groups, and enamines, so the query does not retrieve these structures.

For additional information and examples of Rgroup query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

Tertiary Aromatic Amines

The following query retrieves tertiary aromatic amines (one aromatic substituent):

As with tertiary aliphatic amines, the Substitution Count as Drawn (s*) query feature prevents the retrieval of quaternary amines.

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

To retrieve all aromatic tertiary amines, including those with heteroatoms in the ring, use the Any atom (A) query feature and the Aromatic query bond on the aromatic substituent. For example:

For comprehensive reference information on all available query features, including Rgroup query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

See also section 150.7.6, Additional Queries for Aromatic Primary, Secondary, and Tertiary Amines.

150.7.5 Quaternary Amines

The following query retrieves all quaternary amines, both aliphatic and aromatic:

Quaternary Aliphatic Amines

The following query retrieves quaternary aliphatic amines:

Quaternary Aromatic Amines

To retrieve all aromatic quaternary amines, including those with heteroatoms in the ring, use the Any atom (A) query feature and the Aromatic query bond on the aromatic substituent amines (the Available Chemicals Directory contains fewer than 100 quaternary aromatic amines):

150.7.6 Additional Queries for Aromatic Primary, Secondary, and Tertiary Amines

The following query retrieves primary, secondary, and tertiary amines that contain at least one aromatic substituent. The query does not retrieve carboxamides, thioamides, enamines, or nitrogen compounds with imino (-C=N) substituents, such as guanidines.

The root structure of the Rgroup specifies a single nitrogen atom with the Rgroup labels R1, R2, and R3 attached by a single bond. Together, the three Rgroups specify the substituents that can attach to the nitrogen.

The Rgroup condition R1<4 specifies that the nitrogen atom can have one, two, or three attachments (Rgroup members) from R1. The (Rest H) Rgroup condition specifies that all other substituents of the nitrogen must be hydrogen atoms. R1 contains one Rgroup member, a single carbon atom. Thus, R1 specifies primary, secondary, and tertiary amines, but not compounds such as hydrazines or hydroxylamines.

The Rgroup condition R2>0 specifies that at least one of the attachments specified by R2 must be attached to the nitrogen atom. R2 contains one Rgroup member, a carbon atom attached to an Any atom (A) query feature through an Aromatic query bond. This combination of query features specifies any aromatic group. Thus, R2 specifies that at least one attachment of the nitrogen must be aromatic.

The Rgroup condition R3=0 specifies that none of the attachments specified by R3 can attach to the nitrogen atom. Thus, R3 specifies the groups that the query does not retrieve. R3 contains one Rgroup member, a carbon atom attached to the Atom list query feature [O,S,N,C] through a double bond. This member specifies carboxamides, thioamides, structures that contains imino groups, and enamines. Therefore, the query does not (R3=0) retrieve these structures.

For additional information and examples of Rgroup query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

150.7.7 Primary, Secondary, and Tertiary Ammonium Salts

In the Available Chemicals Directory (ACD) and other MDL databases, primary, secondary, and tertiary ammonium salts are drawn so as to minimize charges on the molecule. If necessary, hydrogen atoms are moved to minimize charges. The following figure compares the representation of these salts in the chemical literature to their representation in ACD:

A small number of primary, secondary, and tertiary ammonium salts in ACD use a positive charge on the nitrogen. To retrieve a primary or secondary amine and its ammonium salts, draw the query without explicit hydrogen atom and add the Substitution Count as Drawn (s*) query feature to the nitrogen atom. For example, the following query retrieves both primary aliphatic amines and primary ammonium salts:

The following are examples of the structures that you retrieve:

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

150.7.8 Amino Groups

The following queries retrieve all compounds that contain amino groups, including aliphatic amines, aromatic amines, enamines, amides, and so forth:

For all three queries, the Substitution Count as Drawn (s*) query feature and explicitly drawn hydrogen atoms on the nitrogen atom ensure that no additional substitution can occur at the nitrogen.

150.8 Aryl Halides

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

The following query retrieves aryl halides:

The atom list query feature [F,Cl,Br,I] specifies halogens.

The following structures are retrieved:

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

To avoid retrieving structures that contain fused rings, add the Ring Bond Count as Drawn (r*) query feature to all the atoms of the ring:

The following are examples of the structures that you retrieve:

To specify Ring Bond Count as Drawn in ISIS/Draw, select the ring atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Ring bond count box and choose *.

To retrieve both aryl and heteroaryl halides, use the Any atom (A) query feature and the Aromatic query bond:

By drawing only one bond of the ring, you retrieve aromatic rings of any size. The following are examples of the structures that you retrieve:

To specify an Any Atom in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose A.

To specify an Aromatic query bond in ISIS/Draw, select the bond and double-click it. In the Edit Bond dialog, click the Bond tab, then click the Bond type box and choose Aromatic.

Note: The queries shown previously also retrieve structures like the following:

To eliminate structures such as these, add the Substitution Count as Drawn query feature (s*) to the list of halides:

Alternatively, you can specify an explicit valence of 1 on the halide atom list:

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

To specify explicit valence in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Atom tab, then click the Valence box and choose 1.

150.9 Azo Compounds

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

The following query retrieves azo compounds:

Note: This query retrieves a small number of structures such as the following:

To avoid retrieving these structures, draw the query with Substitution Count as Drawn (s*) query feature on the nitrogen:

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

150.10 Carbamates and Carbazates

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

150.10.1 Carbamates

The following query retrieves carbamates:

The atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the carbonyl carbon, or to the amine nitrogen. This avoids the retrieval of carbamates and carbazates.

The open (unspecified) valence on the oxygen atom allows any atom (including hydrogen) to attach at that site. Consequently, this query retrieves both acids and esters.

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

150.10.2 Carbazic Acid and Carbazates

The following query retrieves carbazic acid and its esters:

The atom list query feature [C,H] on the oxygen atom specifies that only carbon or hydrogen can be attached to the oxygen.

The hydrogen atoms are drawn explicitly to avoid retrieving N-substituted compounds.

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

To retrieve both unsubstituted and N-substituted derivatives of carbazates, use the Atom list query feature [C,H] instead of explicit hydrogens on the nitrogen atoms:

150.11 Carboxylic Acids and Derivatives

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

150.11.1 Acids

The following query retrieves carboxylic acids:

The hydrogen atom on the oxygen is drawn explicitly to prevent substitution of other atoms.

150.11.2 Salts of Carboxylic Acids

To retrieve only salts of carboxylic acids, draw a charge of -1 on the oxygen:

To specify a charge of -1 in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Atom tab, then click the Charge box and choose -1.

To retrieve both carboxylic acids and salts, use the Substitution Count as Drawn (s*) query feature on the oxygen atom:

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

150.11.3 Acid Halides

The following query retrieves acid halides:

The atom list query feature [F,Cl,Br,I] specifies halogens.

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

150.11.4 Amides

The following query retrieves amides of carboxylic acids:

The atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the carbonyl carbon, or to the amine nitrogen. This avoids the retrieval of carbamates and carbazates.

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

Note: To specify lactams, add the Ring bond query feature to the single bonds:

To specify a Ring bond in ISIS/Draw, select the bond and double-click it. In the Edit Bond dialog, click the Bond tab, then click the Topology box and choose Ring.

For more information on queries for lactams, see 150.19 Lactams and Lactones.

150.11.5 Anhydrides

The following query retrieves anhydrides of carboxylic acids:

150.11.6 Esters

The following query retrieves esters of carboxylic acids:

Note: To specify lactones, add the Ring bond query feature to the single bonds:

To specify a Ring bond in ISIS/Draw, select the bond and double-click it. In the Edit Bond dialog, click the Bond tab, then click the Topology box and choose Ring.

For more information on queries for lactones, see 150.19 Lactams and Lactones.

150.12 Cyanates and Thiocyanates

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

150.12.1 Cyanates

The following query retrieves cyanates:

150.12.2 Thiocyanates

The following query retrieves thiocyanates:

Note: The [C,H] atom list on the sulfur atom ensures that you retrieve structures such as the following:

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

150.13 Disulfides

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

The following query retrieves all structures that contain a single bond between two sulfur atoms that have a valence of 2:

To retrieve only structures with carbon attached to the sulfur atoms (as required for the IUPAC definition of sulfides and disulfides), use the following query:

150.14 Guanidines

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

The following query retrieves guanidines:

The Chain bond query feature (Ch) specifies that the bond can not be part of a ring.

The following are examples of the structures that you retrieve:

To specify a Chain bond in ISIS/Draw, select the bond and double-click it. In the Edit Bond dialog, click the Bond tab, then click the Topology box and choose Chain.

To retrieve both cyclic and acyclic structures, use the following query:

150.15 Hydrazines and Hydrazides

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

The following query retrieves hydrazines and hydrazides:

The atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the nitrogen atoms.

The following are examples of the structures that you retrieve:

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

To retrieve only hydrazides, specify an acyl group on one of the nitrogen atoms:

The following are examples of the structures that you retrieve:

You can further refine your list of hydrazines by adding structural details and other query features. For example, to avoid retrieving structures in which the two nitrogen atoms are part of a ring, add the Chain bond query feature (Ch) to the bond between the nitrogen atoms:

To specify a Chain bond in ISIS/Draw, select the bond and double-click it. In the Edit Bond dialog, click the Bond tab, then click the Topology box and choose Chain.

To ensure that at least one substituent of the nitrogens is not aromatic, attach a saturated carbon to one of the nitrogen atoms, as shown:

150.16 Hydroxylamines

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

The following query retrieves hydroxylamines:

The atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the nitrogen and oxygen atoms.

The following are examples of the structures that you retrieve:

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

150.17 Imines

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

The following query retrieves imines:

The atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the nitrogen atom.

The following are examples of the structures that you retrieve:

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

150.18 Ketones

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

The following query retrieves ketones:

Note: This query also retrieves a small number of structures such as the following:

To avoid retrieving these structures, add the Substitution Count as Drawn (s*) query feature to the oxygen atom on the query:

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

In the following query, the Chain bond (Ch) query feature specifies acyclic ketones:

In the following query, the Ring bond (Rn) query feature specifies cyclic ketones:

To specify a Chain bond in ISIS/Draw, select the bond and double-click it. In the Edit Bond dialog, click the Bond tab, then click the Topology box and choose Chain.

To specify a Ring bond in ISIS/Draw, select the bond and double-click it. In the Edit Bond dialog, click the Bond tab, then click the Topology box and choose Ring.

150.19 Lactams and Lactones

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

150.19.1 Structures With Rings of Any Size

The following query retrieves lactams of any ring size:

The following query retrieves lactones of any ring size:

For both lactones and lactams:

*	The Atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the atom.

*	The Ring bond query feature (Rn) specifies that the amide or ester group must be part of a ring.

The following are examples of the lactams that are retrieved:

The following are examples of the lactones that are retrieved:

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

To specify a Ring bond in ISIS/Draw, select the bond and double-click it. In the Edit Bond dialog, click the Bond tab, then click the Topology box and choose Ring.

150.19.2 Structures With a Range of Ring Sizes

Saturated Rings

To specify lactams with a saturated ring with a range of sizes, draw the query as a four-membered ring, and use the Link atom query feature to specify a variable-length chain of carbon atoms. For example:

The following are examples of the structures that you retrieve:

To specify a link atom in ISIS/Draw, select an atom and its two adjacent ring or chain bonds. Choose Chemistry > Link Node and enter the maximum number of repeating atoms allowed (this must be 2 or greater). Click OK.

Both Saturated and Unsaturated Rings

To retrieve lactams in a range of sizes with either a saturated or unsaturated ring, use the Any bond query feature on the bonds that are attached to the carbon with the link atom query feature:

The following are examples of the structures that you retrieve:

The following is the equivalent query for lactones:

The following are examples of the structures that you retrieve:

To specify an Any bond in ISIS/Draw, select the bond and double-click it. In the Edit Bond dialog, click the Bond tab, then click the Bond type box and choose Any.

150.19.3 Additional Queries For Lactams and Lactones

The following query retrieves both unsubstituted and N-substituted lactams:

The open (unspecified) valence on the nitrogen atom allows this query to retrieve lactams with either hydrogen or any other atom attached to the nitrogen atom.

The following query for lactones uses Rgroup query features to avoid retrieving structures such as anhydrides.

The ring bond query feature (Rn) in the root structure specifies that the ester group must be part of a ring. A double bond attaches the Rgroup label R1 to the ester carbon in the ring.

Rgroup R1 contains one member, an oxygen atom. The Rgroup condition (R1 = 0) specifies that this oxygen atom can not be present at the R1 site on the root structure. Thus, the Rgroup condition specifies that the query does not retrieve compounds with a carbonyl group at this position (that is, anhydrides).

150.20 Nitriles

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

The following query retrieves nitriles:

Note: This query retrieves a small number of structures such as the following:

To avoid retrieving these structures, draw the query with Substitution Count as Drawn (s*) query feature on the nitrogen:

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

150.21 Nitroxides (Aminoxyl Radicals)

Note 1: Nitroxides are called aminoxyl radicals in IUPAC nomenclature.

Note 2: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note 2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

The following query retrieves nitroxides:

The radical on the oxygen atom (a doublet monoradical) ensures that you retrieve only structures that have an unpaired electron on the oxygen. The following are examples of the structures that you retrieve:

To specify a doublet monoradical in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Atom tab, then click the Radical box and choose .

150.22 Oximes

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

The following query retrieves oximes:

The hydrogen atom on the hydroxyl group is drawn explicitly to prevent substitution of other atoms.

The atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the carbon atom.

The following are examples of the structures that you retrieve:

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

150.23 Phosphines

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

The following query retrieves phosphines:

The hydrogen atom on the hydroxyl group is drawn explicitly to prevent substitution of other atoms.

The atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the phosphorus atom.

The valence (III) of the phosphorus atom is drawn explicitly to avoid retrieving compounds that contain other substituents (such as P=O) at the phosphorus atom.

The following are examples of the structures that you retrieve:

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

To specify explicit valence in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Atom tab, then click the Valence box and choose 1.

150.24 Phosphonic Acids and Derivatives

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

The following query retrieves phosphonic acid, its esters, and its P-substituted derivatives:

The atom list query feature [C,H] attached to the oxygen atoms retrieves both esters and acids.

The atom list query feature [C,H] attached to the phosphorus specifies that only carbon or hydrogen can be attached to the phosphorus atom, as required by the IUPAC definition of a phosphonate.

The following are examples of the structures that you retrieve:

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

To retrieve structures in which any atom (including hydrogen) can attach to the oxygen atom, use open (unspecified) valences on the oxygen atoms:

The following query retrieves phosphonamides:

The atom list query feature [C,H] specifies that only carbon or hydrogen can attach to the phosphorus atom.

150.25 Stannanes

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the example in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

The following query retrieves stannanes:

The Atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the tin atom.

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

150.26 Sulfimides (Sulfilimines)

Note: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".  For reference information on query features (including Rgroup query features), see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

The following query retrieves sulfimide (sulfilimine) and its derivatives:

The atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the sulfur atom.

The valence (IV) of the sulfur atom is drawn explicitly to avoid retrieving compounds that contain other substituents on the sulfur, such as sulfoximides (S=O).

The following are examples of the structures that you retrieve:

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

To specify explicit valence in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Atom tab, then click the Valence box and choose 1.

To retrieve structures in which any atom (including hydrogen) can attach to the sulfur and nitrogen atoms, use open (unspecified) valences on these atoms:

150.27 Sulfonic Acids and Derivatives

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

150.27.1 Sulfonic Acids

The following query retrieves sulfonic acids, but not salts or esters:

The hydrogen atom on the oxygen is drawn explicitly to prevent substitution of other atoms.

150.27.2 Sulfonates

The following query retrieves both sulfonic acids and esters of sulfonic acids:

The atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the oxygen atom.

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

150.27.3 Sulfonamides

The following query retrieves amides of sulfonic acids:

The atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the carbonyl carbon, or to the amine nitrogen.

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

To retrieve structures in which any atom (including hydrogen) can attach to the nitrogen atom, use open (unspecified) valences on the nitrogen:

150.27.4 Sulfonyl Halides

The following query retrieves sulfonyl halides:

The atom list query feature [C,H] specifies that only carbon or hydrogen can be attached to the oxygen atom.

To specify an atom list on one or more atoms in ISIS/Draw, select the atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose List.... In the Periodic Table dialog, click the atom symbols to build your list of allowed atoms.

150.28 Sulfoxides

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

The following query retrieves sulfoxides:

The valence (IV) of the sulfur atom is specified explicitly to avoid retrieving compounds that contain other substituents on the sulfur, such as sulfones.

The following are examples of the structures that you retrieve:

To specify explicit valence in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Atom tab, then click the Valence box and choose 1.

150.29 Thiols

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

Use any of the following queries to retrieve thiols:

Using explicit valence (II) or Substitution Count as Drawn (s*) on the sulfur atom allows you to avoid retrieving molecules such as the following:

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

To specify explicit valence in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Atom tab, then click the Valence box and choose 1.

150.30 Other Compound Classes

Note1: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".

Note2: Use the examples in this section as a starting point for creating your own queries. You can use other query features, including Rgroup query features, in your queries. For comprehensive reference information on all available query features, see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

This section shows queries for common classes of compounds that generally do not require query features.

150.30.1 Azides

150.30.2 Boronic Acids

The hydrogens on the oxygen atoms are drawn explicitly to prevent substitution of other atoms.

Note: To retrieve both boronic acids and their salts, use the Substitution Count as Drawn (s*) query feature on the oxygen atoms instead of explicit hydrogens:

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

150.30.3 Epoxides

150.30.4 Isocyanates

150.30.5 Isonitriles

150.30.6 Isothiocyanates

150.30.7 Nitrates

150.30.8 Nitrites

The Substitution Count as Drawn (s*) query feature on the nitrogen atom ensures that the query retrieves organic nitrites but not organic nitrates.

To specify Substitution Count as Drawn in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Substitution count box and choose *.

To retrieve both organic nitrates and nitrites, remove the Substitution Count as Drawn query feature:

150.30.9 Peroxides

Note: To retrieve only structures with carbon substituents on the oxygen atoms, use the following:

150.30.10 Sulfoxamides (Sulfoximines)

150.31 Rings, Chains, and Other Common Structures

This section provides examples of common structural motifs (functional groups and other structures) that require query features in the query. Use these with any of the functional groups in the preceding section. For example, if you want to find acid chlorides that contain a phenyl ring that has no other rings fused to it, draw the query as follows:

Note: For information on how to draw atoms, bonds, and query features in ISIS/Draw, see ISIS/Draw "Quick Start".  For reference information on query features (including Rgroup query features), see the Request-A-Document, Remote RGROUP: Searching Concepts/Examples. For information on how to draw Rgroup query features, see Specifying Rgroup query features.

150.31.1 Alkyl Groups and Aliphatic Carbons

To specify a saturated carbon atom, draw four single bonds to the carbon:

To specify any aliphatic substituent, draw a saturated carbon atom, then draw a [C,H] atom list at the ends of three of the bonds:

To specify an alkyl group (that is, a hydrocarbyl group with no rings at the alpha carbon), draw an aliphatic substituent, then add the Chain bond query feature to the three single bonds:

To specify a Chain bond in ISIS/Draw, select the bond and double-click it. In the Edit Bond dialog, click the Bond tab, then click the Topology box and choose Chain.

150.31.2 Rings

To specify a ring in a range of sizes, use the Link atom query feature:

To allow heteroatoms in the ring, use the Any atom query feature at the link atom:

To specify aromatic and heteroaromatic rings of any size, use the Aromatic bond and the Any atom query features. For example, the following query retrieves aryl and heteroaryl bromides:

To specify an Any Atom in ISIS/Draw, select an atom and double-click it. In the Edit Atom dialog, click the Query Atom tab, then click the Symbol box and choose A.

To specify an Aromatic query bond in ISIS/Draw, select the bond and double-click it. In the Edit Bond dialog, click the Bond tab, then click the Bond type box and choose Aromatic.

To specify an arene ring with no other rings fused to it (an isolated ring), draw the ring, and apply the Ring Bond Count as Drawn (r*) query feature:

To specify Ring Bond Count as Drawn in ISIS/Draw, select the ring atoms and choose Object > Edit Atom. In the Edit Atom dialog, click the Query Atom tab, then click the Ring bond count box and choose *.


Query Features

A query feature is a restriction on an atom or bond in the query that allows you to retrieve solely those molecules from the database that adhere to your restriction. Add query features to ensure that you retrieve all the structures, and only the structures, that you want. The following example shows how the atom list query feature [C,H] allows you to retrieve only alkyl bromides:

Many common functional groups require query features. For information on query features for common classes of compounds, click here.


ISIS/Draw Dialog Boxes

Alignment Options

Attach Data to Objects

Beilstein Generic

Change Settings to Match the Sketch?

Chem Inspector

Choose Sequence Type

Click on Attachment Atom

Create 3D Object

Create Brackets

Create No-Structure

Create Rgroup

Create R-Logic

Customize Sequence Menu

Edit -- 3D

Edit -- Arrow

Edit -- Atom

Edit -- Bond

Edit -- Bracket

Edit -- Data

Edit -- Font

Edit -- No-Structure

Edit -- Query Atom

Edit -- Rgroup

Edit -- R-Logic

Edit -- Sequence

Edit -- Style

Grid Coordinates

Insert New Object

Link Node

Lose original coordinates

Lost original coordinates

Molecular Calculation Settings

Open/Insert/Import

Periodic Table

Point to Rgroup

Rquery Attachment

Save As

Save Name/Comments

Save Residue Changes

Settings -- 3D

Settings -- Bracket

Settings -- Chem Inspector

Settings -- Chemical Drawing

Settings -- Font

Settings -- General

Settings -- Line/Fill/Arrow

Settings -- Ruler/Grid

Settings -- Sequence

Template Menu

Template Tools

Transfer Options


Create No-Structure

Use this dialog to:

*	Create a no-structure to register into a local or remote database.

Click any of the following items:

Label

Remote internal regno

Thickness

Color

For information on how to register and retrieve no-structures, see the ISIS/Base Database Maintenance 2.0 manual.


Label

Enter a label for the no-structure only if you plan to register the no-structure into a local database.

To enter a label for the no-structure, click the Label box and enter a label. The label is for display purposes only and has no significance for searching.


Remote internal regno

Enter a remote regno number for the no-structure only if you plan to register the no-structure into a remote database. The regno should be a positive integer.

To enter the regno of a no-structure that already exists in a remote database, click the box and enter a regno.

If you are creating a new no-structure, the regno that you enter here will be registered if you later register the no-structure into a remote database.


Thickness

To specify a line thickness for the no-structure, click the Thickness box, then enter or choose a line thickness. Then, choose the unit of measure.


Color

To specify a color for the no-structure, click the Color box and choose a color. To specify a new color, choose Other. You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on how to use this feature.

Note: Specify a color for the no-structure only if you plan to export the no-structure into a local database.


Edit -- No-Structure

Use this dialog to:

*	Edit all selected no-structures.

Click any of the following items:

Label

Remote internal regno

Thickness

Color

OK, Cancel

For information on how to register and retrieve no-structures, see the ISIS/Base Database Maintenance 2.0 manual.


Thickness

To specify a line thickness for selected object(s), click the Thickness box, then enter or choose a line thickness. Then, choose the unit of measure.

Thickness applies to all selected objects except atoms, 3D atom data, and text objects.


Color

To choose a color for selected object(s), click the Color box and choose a color. Color applies to all types of selected objects. To specify a new color, click the box and choose Other. You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on how to use this feature.


OK, Cancel

OK

To apply the current settings to the appropriate selected object(s), click OK. All of the changes that you have made in the Edit tabs to the selected object(s) are applied.

Cancel

To close the dialog box without applying the settings, click Cancel. None of the changes that you have made in the Edit tabs to the selected object(s) are applied.


Edit -- Arrow

Use this dialog to:

*	Edit all of the selected arrows.

Click any of the following items:

Arrow Style

Position Arrowhead at

Measurements

Thickness

Color

OK, Cancel


Arrow Style

To choose an arrow style for the selected arrow(s), click the Arrow Style box and choose a style.


Position Arrowhead at

Start

To have the arrowhead display at the location where you started to draw a line, set [image] Start.

Finish

To have the arrowhead display at the location where you finished drawing a line, set [image] Finish.

To have arrowheads display at the location where you started drawing a line and at the location where you finished drawing the line, set [image] Start and [image] Finish.


Measurements

Arrowhead length

To specify the length of the arrowhead, click the Arrowhead length box and enter or choose a length. Then, choose the unit of measure.

Arrowhead width

To specify the width of the arrowhead, click the Arrowhead width box and enter or choose a width. Then, choose the unit of measure.

Arrow-shaft spacing

To specify the distance between the two arrow-shaft lines, click the Arrow-shaft spacing box and enter or choose a value. Then, choose the unit of measure. Arrow-shaft spacing applies only to equilibrium, bi-directional, block, and straight filled arrows.


Edit -- Atom

Use this dialog to:

*	Create a new atom.

*	Edit all of the selected atoms.

*	Allow or exclude specific atoms (A, Q, List, NOT List atom query features).

*	Specify an Rgroup label on the root structure of an Rgroup query.

*	Specify atom properties, such as isotope, charge, and valence, that are significant in searching.

*	Control the display of implicit hydrogens, atom numbers, atom values, and other display attributes of atoms.

Query features are required on queries for certain common functional groups, such as alcohols, amines, alkyl halides, and others. For information on how to draw these functional groups, see Queries for Common Functional Groups.

Click any of the following items:

Isotope

Charge

Radical

Valence

Symbol

Hydrogens

Atom number

Number position

Value

Thickness

Color

OK, Cancel

For complete information on how to draw or edit atoms, see the ISIS/Draw "Quick Start".


Isotope

To change the neutron-to-proton ratio within the selected atom(s), click the Isotope box, then enter or choose a value.

See also:

To add isotopes using the keyboard


Charge

To change the charge of the selected atom(s), click the Charge box and enter or choose a value. To remove all charges on an atom, choose 0.

See also:

To add atom charges using the keyboard


Radical

To apply a radical notation to the selected atom(s), click the Radical box and choose one of these values:

:	(singlet diradical)

.	(doublet monoradical)

^^	(triplet diradical).

To remove radical notation, choose Off.


Valence

To add a non-standard (explicit) valence symbol to the selected atom(s), click the Valence box and enter or choose a value. To remove a non-standard valence, choose Off.


Symbol

To enter a different atom symbol for a selected atom or to add to the existing atom symbol, click the Symbol box and enter the symbols of your choice. For example, you can enter N, C, CN, PO4, and Na+.

Note: If you enter the symbol H with another, non-hydrogen atom (such as OH), you have a query that is for display purposes only. To create explicit hydrogens that are chemically significant in ISIS/Base, click here.

You can also use the Symbol box to enter *Atoms (star atoms) and the following atom query features:

*	A (allow any atom except H)

*	Q (allow any atom except C or H)

*	List (allow one atom from a list of allowed atoms)

*	Not List (list of prohibited atoms)

*	Rgroup label on the root structure of an Rgroup query.

*	Beilstein atom generics and group generics. These query features are for Beilstein databases only.

*	Periodic Table (list of allowed atoms). To specify standard Periodic Table abbreviations (such as Na), click the Symbol box and choose Periodic table.

There are multiple ways to draw and edit atom symbols. For complete information on these methods, see the ISIS/Draw "Quick Start".

See also:

To add atom symbols using the keyboard


Value

To specify an atom value for the selected atom(s), click the Value box and enter a value. The value can be a real number or a range of real numbers (including exponential notation).

Note: Atom values on a structure can be registered in local databases only.

See also:

To add an atom value to an existing atom

To edit or delete existing atom values


Hydrogens

To change the way that hydrogens are displayed on a selected atom, click the Hydrogens box and enter or choose an option.

Note: This option is for display only, and is not for searching purposes. To create explicit hydrogens that are chemically significant in ISIS/Base, click here.

See also:

To display hydrogens for all carbon atoms or all heteroatoms in a sketch


Atom number

To edit the atom number for a selected atom, click the Atom number box and enter a new value.

To display an atom number next to the selected atom at a position that you specify, click the Number position box and choose a value.


Number position

ISIS/Draw automatically assigns an atom number to each atom in a structure as it is drawn.

To display an atom number next to the selected atom(s) at a position that you specify, click the Number position box and choose a value.

To edit the atom number for the selected atom(s), click the Atom number box and enter a new value.


Edit -- Bond

Use this dialog to:

*	Edit all of the selected bonds.

*	Allow solely ring bonds or chain bonds in your query.

*	Specify an aromatic bond in your query.

*	Specify bond variations in a query (Single/Double, Single/Aromatic, Double/Aromatic, Any).

*	Specify bond stereochemistry (Up, Down, Either, Dbl Either).

*	Specify a bond as a reacting center in a reaction query.

*	Specify stereo boxes on cis or trans configurations.

Query features are required on queries for certain common functional groups, such as alcohols, amines, alkyl halides, and others. For information on how to draw these functional groups, see Queries for Common Functional Groups.

Click any of the following items:

Bond type

Bond length

Alternate stereo bond

Standard

Crossed bond

Reacting center

Topology

Stereo search

Thickness

Color

OK, Cancel

For complete information on how to draw or edit bonds, see the ISIS/Draw "Quick Start".

For information on how to remove query bond features, click here.


Bond type

To convert selected bond(s) to a different bond type, click the Bond type box and choose a bond type.

Use the following bond types to add bond query features: Any, Aromatic, Single/Double, Double/Aromatic, Single/Aromatic. For information on how to use these bond types, see To allow a specific bond type.

There are multiple ways to draw bonds and change their types. For complete information on these methods, see the ISIS/Draw "Quick Start".


Bond length

To set the length of selected bond(s), click the Bond length box and enter or choose a bond length. Then, choose the unit of measure.

To set the default standard bond length, choose Options > Settings and click the Chemical Drawing tab. Click the Standard bond/grid length box and enter or choose a bond length. Then, choose the unit of measure.


Standard

To set the selected bond(s) to the standard bond length, click [image].

To set the default standard bond length, choose Options > Settings and click the Chemical Drawing tab. Click the Standard bond/grid length box and enter or choose a bond length. Then, choose the unit of measure.


Alternate stereo bond

To replace a selected stereo bond with the alternative type, set [image] Alternate stereo bond.

Alternate stereo bond is available only when you choose an up or down bond from Bond type.


Crossed bond

To mark the lower bond as a crossed bond (broken bond) when bonds overlap each other without joining, set [image] Crossed bond.


Reacting center

To mark selected bond(s) to show a reacting center, click the Reacting center box and choose one of the following values:

None

Removes all existing reaction center markings.

Center

Places a pound sign (#) to mark a bond that changes in the reaction without being specific about the change.

Make/Break

Places a double bar (//) to mark a bond that is formed or broken in the reaction.

Change

Places a single bar (/) to mark a bond that changes order.

Make and Change

Places a triple bar (///) to mark a bond that is formed or changes in the reaction and changes bond order.

Not Center

Places an X to mark a bond that does not change in the reaction

For more information, see To specify reacting center query features.


Topology

To specify the topology markings for selected bond(s), click the Topology box and choose a value.

None

Removes the Rn or Ch designation

Ring

Marks a bond with Rn to indicate it is part of a ring

Chain

Marks a bond with Ch to show it is part of a chain

For more information, see To allow solely chain bonds and To allow solely ring bonds.


Stereo search

To place a small rectangular stereo box on a selected asymmetric double bond to mark the adjacent bonds as drawn (either the cis or trans stereoconfiguration), set [image] Stereo search.

For more information, see To specify stereo boxes on cis or trans configurations.


Edit -- Font

Use this dialog to:

*	Set the appearance of all of the selected text.

Click any of the following items:

Font

Size

Style

Alignment

Thickness

Color

OK, Cancel


Font

To specify a font for the selected text, click the Font box and enter or choose the name of a font.


Size

To specify a font size for the selected text, click the Size box and enter or choose a size in points.


Subscript/Superscript

To specify that selected text be subscripted or superscripted, click the Subscript/Superscript box and choose a display method. To display text normally, choose None.


Offset

To specify how many points above or below the base line selected text will display, click the Offset box and enter or choose a value.


% of point size

To specify the size of subscripted or superscripted text, click the % of point size box and enter or choose a percentage.

For example, if you use 12 point text and choose 75%, subscripted or superscripted text will display at 8 points.


Style

To specify a style to apply to selected text, set [image]. You can specify multiple styles for the selected text.

To display unstyled text, make sure that all styles are set to [image].


Alignment

To position a selected text paragraph in one of nine possible positions, click one text alignment option from the Horizontal column and one from the Vertical column.

Horizontal Left

To align selected text on the left side of the selection box, click [image] Left.

Horizontal Center

To center selected text in the selection box, click [image] Center.

Horizontal Right

To align selected text on the right side of the selection box, click [image] Right.

Vertical Top

To align selected text at the top of the selection box, click [image] Top.

Vertical Center

To center selected text in the selection box, click [image] Center.

Vertical Bottom

To align selected text at the bottom of the selection box, click [image] Bottom.


Edit -- Query Atom

Use this dialog to:

*	Allow a specific number of attachments to an atom (s*, s1, s2, s3, s4, s6 atom query features).

*	Allow a specific number of ring bond attachments to an atom (r*, r2, r3, r4 atom query features).

*	Allow or exclude specific atoms (A, Q, List, NOT List atom query features).

*	Specify an Rgroup label on the root structure of an Rgroup query.

*	Specify whether the stereochemistry at an atom is inverted or retained in a reaction query.

*	Specify that the characteristics of an atom must change exactly as shown in a reaction query.

*	Prohibit substitution of hydrogens at an atom.

Query features are required on queries for certain common functional groups, such as alcohols, amines, alkyl halides, and others. For information on how to draw these functional groups, see Queries for Common Functional Groups.

Click any of the following items:

Symbol

Substitution count

Ring bond count

Reaction stereo

No implicit hydrogens

Unsaturated atoms

Exact change [reaction]

Thickness

Color

OK, Cancel

For information on how to remove atom query features, click here.


Symbol

To specify that a selected atom be included or excluded from a search at a specified position, click the Symbol box and choose an option.

Note: If you enter the symbol H with another, non-hydrogen atom (such as OH), you have a query that is for display purposes only. To create explicit hydrogens that are chemically significant in ISIS/Base, click here.

Use the Symbol box to enter *Atoms (star atoms) and the following atom query features:

*	A (allow any atom except H)

*	Q (allow any atom except C or H)

*	List (allow one atom from a list of allowed atoms)

*	Not List (list of prohibited atoms)

*	Rgroup label on the root structure of an Rgroup query.

*	Periodic Table (list of allowed atoms). To specify standard Periodic Table abbreviations (such as Na), click the Symbol box and choose Periodic table.


Substitution count

To specify the number of substituents permitted on a selected atom, click the Substitution count box and choose a value. A substituent is a non-hydrogen attachment on an atom.

For more information, see To allow a specific number of attachments.


Ring bond count

To specify the number of permitted ring bonds on a selected atom, click the Ring bond count box and choose a value.

For more information, see To allow a specific number of ring bond attachments.


Reaction stereo

To specify whether a stereo bond is inverted or retained in a reaction, click the Reaction stereo box and choose an option.

To specify that a stereo bond must change its stereoconfiguration in the reaction, choose Inversion.

To specify that the bond must not change its stereoconfiguration in the reaction, choose Retention.

To delete the .inv. or .ret. markings, choose Off.


No implicit hydrogens

To add the prohibition-of-hydrogens symbol "H0" to a selected atom, set [image] No implicit hydrogens.


Unsaturated atoms

To add the [u] symbol to mark the atom as being connected to at least one multiple bond, set [image] Unsaturated atoms. The bond can be double, triple, or aromatic.

For more information, see To allow an unsaturated atom.


Exact change [reaction]

To specify that the characteristics of selected atom(s) must change exactly as shown in the reaction query, set [image] Exact change [reaction]. (The reaction query must be atom-atom mapped.)


Edit -- Style

Use this dialog to:

*	Specify the appearance of all selected lines, circles, squares, polygons, brackets, polylines, splines, arcs, and ellipses.

Click any of the following items:

Line style

Fill

Thickness

Color

OK, Cancel


Fill

Pattern

Color

Opaque/Transparent


Fill Pattern

To choose the pattern used when filling selected enclosed object(s), click the Pattern box and choose a pattern.

You must choose both a fill pattern and a fill color to fill an enclosed object.

Note: Fill pattern applies only to boxes, ellipses, and polygons.


Fill Color

To choose the color of the fill pattern for selected enclosed object(s), click the Color box and choose a fill color. To specify a new color, click the box and choose Other. You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on how to use this feature.

You must choose both a fill pattern and a fill color to fill an enclosed object.

Note: Fill color applies only to boxes, ellipses, and polygons.


Opaque/Transparent

When objects overlap and the top object is opaque, objects below cannot be seen. When the top object is transparent, objects underneath are visible. Objects in solid colors are always opaque - you cannot make them transparent.

Opaque

To make selected object(s) opaque, click [image] Opaque.

Transparent

To make selected object(s) transparent, click [image] Transparent.


Line style

To choose a line style for the selected object(s), click the Line style box and choose a line style.


OK, Cancel

OK

To use the dialog box settings for the current ISIS/Draw work session, click OK. The settings that you change in the dialog box are not saved in the settings file when you exit ISIS/Draw. To save the current settings, click Save before you exit ISIS/Draw.

Cancel

To cancel all modifications to settings, including modifications made by reading in a new settings file and modifications that you made in other Settings tabs, click Cancel. This also closes the Settings dialog.


Settings -- Chem Inspector

Use this dialog to:

*	Set defaults to specify the problems that Chem Inspector looks for.

For information on Chem Inspector and how to use it, click here.

Atoms are overlapped

Atom symbol is not an element

Please verify reaction

Possible reaction in molecule context

Atom-map warnings

Non-query reaction missing reactants

Non-query reaction missing products

Non-chemical objects

Text labels

Display-hydrogens not searchable

Valence exceeded

Unsupported in remote database, molfile, rxnfile

OK, Cancel

Save, Save As, Read

For more information on how to work with ISIS/Draw settings, click here.


Atoms are overlapped

To have Chem Inspector warn you when it detects atoms that overlap, set [image].


Atom symbol is not an element

To have Chem Inspector warn you when it detects atom symbol(s) that it does not recognize, set [image].


Please verify reaction

To have Chem Inspector warn you when your reaction is not interpreted as a reaction by ISIS/Draw, set [image].


Atom-map warnings

To have Chem Inspector warn you when it detects problems with atom-atom maps, set [image]. Chem Inspector can warn you about the following problems:

*	Unpaired atom-maps.

*	Atom-maps between atoms that do not have the same atom symbol.

*	Atom-maps between hydrogens. These are not supported by ISIS/Base.

*	Atom-maps between atoms that are inside a link node.

*	Atom-maps used when searching or registering to local reaction databases.


Non-query reaction missing reactants

To have Chem Inspector warn you when it detects a reaction that is not a query because it is missing reactants, set [image].


Non-query reaction missing products

To have Chem Inspector warn you when it detects a reaction that is not a query because it is missing products, set [image].


Non-chemical objects

To have Chem Inspector warn you when it detects objects that are not chemically significant, such as lines or circles, set [image].


Text labels

To have Chem Inspector warn you when it detects text labels rather than atoms, set [image]. ISIS/Base ignores text labels when searching databases.


Display-hydrogens not searchable

To have Chem Inspector warn you when it detects displayed hydrogens that are not drawn appropriately for searching purposes, set [image]. ISIS/Base ignores display hydrogens when it searches databases.

Note: To create explicit hydrogens that are chemically significant in ISIS/Base, click here.


Valence exceeded

To have Chem Inspector warn you when it detects atoms whose normal valences are exceeded, set [image].


Unsupported in remote database, molfile, rxnfile

To have Chem Inspector warn you about sketch features that will be lost or ignored when you export to a molfile or rxnfile, or when you transfer the sketch to a remote database, set [image].

Chem Inspector warns you if it detects two or more occurrences of the following sketch features:

*	Pen colors and pen thickness

*	Fonts

*	Line and arrow styles

*	Bond spacing and hash spacing

*	Crossed bonds

*	Alternate stereo bond styles

*	Hydrogen styles

*	Atom number and atom value styles

*	Atom values (valid for molfiles and rxnfiles, but not for host databases)

*	Valence styles

Chem Inspector warns you if it detects any occurrence of the following sketch features:

*	Dot or circle notation used to indicate some hydrogen atoms

*	Explicit carbon atom styles

*	Double bonds that are manually positioned

*	Objects that are not chemically significant, such as lines and circles

*	Objects that are grouped together


Possible reaction in molecule context

To have Chem Inspector warn you that detects a possible reaction where it expects a molecule, set [image].


Settings -- Chemical Drawing

Use this dialog to:

*	Set defaults for the appearance of atoms, bonds, and chemical structures.

Click any of the following items:

Show hydrogen labels

Atom number/map size

Atom label margin (width)

Standard bond/grid length

Stereo bond width

Spacing

OK, Cancel

Save, Save As, Read

For more information on how to work with ISIS/Draw settings, click here.

For information on how to draw and edit atoms, bonds, and chemical structures, see the ISIS/Draw "Quick Start".


Show hydrogen labels

To specify the default for how you want hydrogens to be displayed on a selected atom, click the Show Hydrogen labels box and choose an option.

Note: This setting controls how hydrogens are displayed in ISIS/Draw only. To create explicit hydrogens that are chemically significant in ISIS/Base, click here.


Atom number/map size

To set the default size for atom numbers and atom-atom maps, click the Atom number/map size box. Then enter or choose a size in points.


Atom label margin (width)

To specify the default distance for the white space between an atom label (atom value) and a bond, click the Atom label margin (width) box. Enter or choose a value, then choose the unit of measure.


Standard bond/grid length

To set the default length for standard bonds, click the Standard bond/grid length box and enter or choose a bond length. Then, choose the unit of measure.

Note: This setting also affects the spacing of the dots on the grid.


Stereo bond width

To control the default width of wedge stereo up and stereo down bonds, and of regular stereo up bonds, click the Stereo bond width box. Enter or choose a value, then choose the unit of measure.


Spacing

Double/triple bond (% of length)

Down bond hashes


Double/triple bond (% of length)

To control the default spacing between double and triple bonds and the width of stereo bonds, click the Double/triple bond box. Then, enter or choose a percent value.


Down bond hashes

To set the default distance for the white space between hash marks on a stereo bond, click the Down bond hashes box and enter or choose a distance. Then, choose the unit of measure.


Settings -- Font

Use this dialog to:

*	Set defaults for the appearance of text.

Click any of the following items:

Font

Size

Style

Alignment

OK, Cancel

Save, Save As, Read

For more information on how to work with ISIS/Draw settings, click here.


Font

To choose a default text font, click the Font box and enter or choose the name of a font.


Size

To choose a default font size, click the Size box and enter or choose a size in points.


Style

To specify a default text style, set [image]. You can specify multiple default styles.

To specify default unstyled text, make sure that all styles are set to [image].


Alignment

To specify one of nine possible ways to align text paragraphs as the default, click one text alignment option from the Horizontal column and one from the Vertical column.

Horizontal Left

To align text on the left side of the selection box, click [image] Left.

Horizontal Center

To center text in the selection box, click [image] Center.

Horizontal Right

To align text on the right side of the selection box, click [image] Right.

Vertical Top

To align text at the top of the selection box, click [image] Top.

Vertical Center

To center text in the selection box, click [image] Center.

Vertical Bottom

To align text at the bottom of the selection box, click [image] Bottom.


Superscript Options

% of point size

To specify the default size of superscripted text, click the % of point size box and enter or choose a percentage. For example, if you use 12 point text and choose 75%, superscripted text will display at 8 points.

Offset

To specify the default for how many points above the base line superscripted text will display, click the Offset box and enter or choose a value.


Subscript Options

% of point size

To specify the default size of subscripted text, click the % of point size box and enter or choose a percentage. For example, if you use 12 point text and choose 75%, subscripted text will display at 8 points.

Offset

To specify the default for how many points below the base line subscripted text will display, click the Offset box and enter or choose a value.


OK, Cancel

OK

To apply the current settings, click OK.

For new sketches, this applies the current settings to any new objects you draw.

For a sketch with existing objects, a dialog asks if you want to apply the new settings to the existing objects. Your options are Yes, No, or Cancel. To apply new settings to the existing objects, click Yes. To apply new settings only to new objects you create, click No. To cancel the operation and return to the Settings dialog, click Cancel.

Cancel

To cancel all changes to settings, including changes made by reading in a new settings file and changes made in other Settings tabs, click Cancel. This also closes the Settings dialog.


Save, Save As, Read

Save

To save the current settings in the currently-opened settings file, click Save.

Save As

To specify a name and location for a new settings file, click Save As.

Read

To read in MDL-defined and user-defined settings files, click Read.


Settings -- General

Use this dialog to:

*	Set defaults for miscellaneous ISIS/Draw functions.

Click any of the following items:

Draw bonds using

Abbreviate typed-in templates

Show "Valence exceeded" message

Prompt before fusing overlapping atoms

Delete atom when deleting all its bonds

Highlight last drawn atoms and bonds

Adjust single and double bonds in aromatic rings

Use open stereo wedge

Reset to Select tool after using another tool

Highlight buttons with reverse video

Adjust text display to match printed appearance (PC only)

Show toolbar help messages

Copy Mol/Rxnfile to the Clipboard

Snap to object

OK, Cancel

Save, Save As, Read

For more information on how to work with ISIS/Draw settings, click here.


Draw bonds using

To specify how to draw bonds, click the Draw bonds using box, then choose one of the following options:

*	To draw bonds using the default standard bond length: choose Standard length. ISIS snaps the bond angle in 15 degree increments.

*	To draw bonds of any length: choose Snap to standard. ISIS snaps the bond angle in 15 degree increments.

*	To draw bonds of any length or angle: choose Any length/angle.

To set the default standard bond length, choose Options > Settings and click the Chemical Drawing tab. Click the Standard bond/grid length box and enter or choose a bond length. Then, choose the unit of measure.


Abbreviate typed-in templates

When you draw structures, you can enter an abbreviation and ISIS/Draw will draw the corresponding template (if one exists).

To draw the template (if one exists) by entering an abbreviation, set [image].

To simply type the abbreviation you entered, set [image].

To see tips for correctly entering structures and a list of substituents included with ISIS/Draw 2.0, click here.


Show "Valence exceeded" message

To display a warning message when the normal valence on an atom is exceeded, set [image].


Prompt before fusing overlapping atoms

To display a warning message when your actions cause atoms to overlap, set [image]. This helps to prevent fusion when you attach a new template or bond to a structure.


Delete atom when deleting all its bonds

To automatically delete any isolated terminal atoms when you delete a bond, set [image].


Highlight last drawn atoms and bonds

To automatically select the last atoms and bonds that you drew, set [image].


Adjust single and double bonds in aromatic rings

To automatically adjust bond order in aromatic rings as you add bonds to the structure, set [image].


Use open stereo wedge

To specify that stereo bonds be displayed open (unfilled), set [image].

To specify that stereo bonds be displayed closed (filled), set [image].


Reset to Select tool after using another tool

To automatically choose the Select tool after using any other tool, set [image].


Highlight buttons with reverse video

To have the currently-selected tool button highlighted in reverse-video, set [image].

Use this setting if your monitor makes it hard to see which button is depressed when you use the default 3D look.


Adjust text display to match printed appearance (PC only)

When you create detailed sketches that contain text, the screen text might not match the printed text. The width and position of the text and the space between the letters that you see on the screen might be different.

Note: This setting does not affect the printed text. It only affects how the text appears on the screen.

To adjust the screen text to more closely resemble the printed text, set [image].

To adjust the screen text so that it is easier to read, set [image]. This is useful when you project an ISIS/Draw sketch from your computer screen to an audience.


Show toolbar help messages

To view help messages when you use the tools on the vertical and horizontal tool bars, set [image].


Copy Mol/Rxnfile to the Clipboard

To copy structures and reactions to the Clipboard in the Molfile or the Rxnfile format, set [image]. You can then paste the structures or reactions into any application that recognizes these formats. For information on how to paste molfiles and rxnfiles into other applications, click here.

To copy molecules or reactions into applications that do not understand the formats, set [image].


Snap to object

To show a highlight dot when you draw lines, boxes, and polygons to see the point where the objects can snap together, set [image].


Settings -- Line/Fill/Arrow

Use this dialog to:

*	Set defaults for the appearance of boxes, polygons, lines, polylines, arcs, ellipses, and arrows.

Click any of the following items:

Line Style

Fill Pattern

Arrow length

OK, Cancel

Save, Save As, Read

For more information on how to work with ISIS/Draw settings, click here.


Fill Pattern

Pattern

Color

Opaque/Transparent


Pattern

To choose the default pattern used when filling enclosed objects, click the Pattern box and choose a pattern.

You must choose both a fill pattern and a fill color to fill an enclosed object.

Note: Fill pattern applies only to boxes, ellipses, and polygons.


Color

To choose the default color of the fill pattern for enclosed objects, click the Color box and choose a fill color. To specify a new color, click the box and choose Other. You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on how to use this feature.

You must choose both a fill pattern and a fill color to fill an enclosed object.

Note: Fill color applies only to boxes, ellipses, and polygons.


Opaque/Transparent

When objects overlap and the top object is opaque, objects below cannot be seen. When the top object is transparent, objects underneath are visible. Objects in solid colors are always opaque - you cannot make them transparent.

Opaque

To make objects opaque by default, click [image] Opaque.

Transparent

To make objects transparent by default, click [image] Transparent.


Line Style

Thickness

To choose a default line thickness, click the Thickness box and enter or choose a thickness. Then, choose the unit of measure. Thickness applies to bonds, lines, arrows, brackets, and borders of filled objects.

Style

To choose a default line style, click the Style box and choose a style.

Color

To choose a default line color, click the Color box and choose a color. Choose Other to see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on how to use this feature.

Color applies to bonds, lines, arrows, brackets, and borders of filled objects.


Arrow length

To choose a default arrow length, click the Arrow length box and enter or choose a length. Then, choose the unit of measure.


Settings -- Ruler/Grid

Use this dialog to:

*	Set defaults for the ruler and grid. For information on how to set up the grid, click here.

Click any of the following items:

Ruler Settings

Show/snap grid

Grid type

Standard bond/grid length

Grid Orientation

OK, Cancel

Save, Save As, Read

For more information on how to work with ISIS/Draw settings, click here.


Ruler Settings

Show ruler

To display the ruler by default, set [image] Show ruler.

Snap to ruler

To specify by default that any object that you draw is sized using the increments marked on the current ruler, set [image] Snap to ruler.

Divisions

To specify the default for the number of divisions displayed on the ruler, click the Divisions box and choose a value.

Show Ruler in Inches

To specify that, by default, the ruler displays in inches, click [image] Show ruler in Inches.

Show Ruler in Centimeters

To specify that, by default, the ruler displays in centimeters, click [image] Show ruler in Centimeters.

Note: Due to device resolution issues, you will not see the correct number of divisions if you specify that the ruler display in centimeters with 10 divisions. To see the correct number of divisions, choose Options > Zoom > 200%.


Show/snap grid

To display the grid and have any object that you draw attempt to snap to the grid, set [image] Show/snap grid.


Grid type

Hexagonal

To use a hexagonal grid pattern, click [image] Hexagonal.

Square.

To use a square grid pattern, click [image] Square.


Standard bond/grid length

To enter a default length for the grid, click the Standard bond/grid length box and enter or choose a value. Then, choose the unit of measure.

Note: This setting also sets the default bond length.


Grid Orientation

Horizontal

To use a horizontal grid, click [image] Horizontal.

Vertical

To use a vertical grid, click [image] Vertical.

Other

You can define a grid by entering X and Y values for the line origin and vector values. To do so, click [image] Other. You see a dialog box where you can enter the coordinates.

Note: When you define a grid by entering coordinates, this changes the standard bond length.


Template Menu

Use this dialog to:

*	Add, remove, or rename template pages on the Templates menu.

Click any of the following items:

Insert

Rename

Remove

Template file

OK, Cancel

For information on how to create a template page and add it to the Templates menu, click here.


Insert

To add a template page to the Templates menu, click Insert, then select a sketch file.


Rename

To rename a template on the Templates menu, select the template name, then click Rename.


Remove

To remove a template from the Templates menu, select the template name, then click Remove.


Template File

Displays the full name of the sketch file associated with the name you selected in the list box.


Template Tools

Use this dialog to:

*	Add or remove template tools from the horizontal tool bar.

Click any of the following items:

Templates area

Template tools area

Remove

OK, Cancel

For information on how to create a template tool and add it to the horizontal tool bar, click here.


Templates area

This area displays all the available template tools.

To add an available template to the template toolbar, first click the template you want to add. Then, in the template tools area, click the location where you want the new template to appear.


Template tools area

This area displays the template tools currently available on the template toolbar.


Remove

To remove a template from the template toolbar, first click the template tool that you want to remove in the Template tools area. Then, click Remove.


OK, Cancel

OK

To apply the changes you made to the Templates Menu or to the horizontal toolbar, click OK. All of the changes that you have made in both tabs are applied.

Cancel

To close the dialog box without applying the changes you made to the Templates Menu or to the horizontal toolbar, click Cancel. None of the changes that you have made in either tabs are applied.


Alignment Options

Use this dialog to:

*	Align selected objects, entire reactions, or molecules. For information on the different ways that you can align objects, click here.

Click the following items:

Vertical

Horizontal

Space Evenly

Align to a Line


Step-By-Step Instructions

To align objects horizontally or vertically

To align objects to a line

To align molecules by individual atoms


Horizontal

None

To align multiple objects vertically, click [image] None.

Tops

To align the tops of multiple objects, click [image] Tops.

Tops/Bottom Centers

To align the centers of multiple objects, click [image] Tops/Bottom Centers.

Bottoms

To align the bottoms of multiple objects, click [image] Bottoms.


Vertical

None

To align multiple objects horizontally, click [image] None.

Left Sides

To align the left sides of multiple objects, click [image] Left Sides.

Left/Right Centers

To align the centers of multiple objects, click [image] Left/Right Centers.

Right Sides

To align the right sides of multiple objects, click [image] Right Sides.


Align to a Line

To align objects to a line that you draw or to a particular point, click [image] Align to a line.


Space Evenly

To evenly space selected objects within the window, click [image] Space Evenly.


Periodic Table

Use this dialog to:

*	Replace an existing atom symbol with one that you selected from the standard or extended Periodic Table.

Click any of the following items:

Standard

Extended


Standard

To display the standard Periodic Table of the Elements, click [image] Standard.

Note: The standard Periodic Table contains solely natural elements.


Extended

To display additional choices including pseudoatoms in the extended Periodic Table (X and R) and lone pairs (LP), click [image] Extended.

Note: This dialog also displays any additional atom symbols that your ISIS Administrator may have defined in the file ptable.dat.


Save Name/Comments

Use this dialog to:

*	Specify a name and/or comment that you can save with an ISIS/Draw sketch.

Click any of the following items:

Name

Comments

Windows 95/NT users only: You can use the Name box to specify a name to display when you move the mouse over a custom tool on the horizontal tool bar.


Name

To specify a name to be saved with the file, click the Name box and enter a name. The name can be up to 66 characters long.


Comments

To specify a comment to be saved with the file, click the Comments box and enter a comment.


Transfer Options

Use this dialog to:

*	Specify how structures are transferred from ISIS/Draw back to ISIS/Base when you use the ISIS/Draw Transfer window.

For information on how to transfer a structure back to ISIS/Base, click here.

Click any of the following items:

Automatic Transfer

Use Auto-Zoom on Transfer

Cancel Transfer

Update Now


Automatic Transfer

To automatically replace the structure in the ISIS/Draw transfer window with the current structure in the ISIS/Base Structure box (or column), set [image].


Use Auto-Zoom on Transfer

To automatically resize current and future structures in the ISIS/Draw transfer window, set [image].


Cancel Transfer

To stop the ability of the Draw transfer window to transfer structures, click Cancel Transfer. The ISIS/Draw transfer window will act just as any other ISIS/Draw window.


Update Now

To replace the structure in the ISIS/Draw transfer window with the current structure in the ISIS/Base Structure box (or column), click Update Now.


Scale Percent

Enter percent to scale drawing

To scale selected objects by a specific percentage, enter a number between 10 and 1000. For example, 50 reduces the object to half size and 200 doubles it. Do not enter "%".

OK

To scale the selected objects by the percentage you specified, click OK.

Cancel

To cancel the scaling operation, click Cancel.


Link Node

Use this dialog to:

*	Specify the addition of a variable member of repeating units to a chain or ring in a search query.

 Requirements to use this dialog

Click the following item:

Enter the maximum repeat count (2 or more)


Requirements to Use This Dialog

You can only use this dialog to create a search query for a specific subset of remote chemical searches.


Enter the Maximum Repeat Count (2 or More)

To specify the addition of a maximum number of repeating units to a chain or ring in a search query, enter a number between 2 and 32,000.

Examples: Rings or Chains


Open/Insert/Import

Use this dialog to:

*	Open an ISIS/Draw sketch file.

*	Insert the contents of a sketch file directly into the active window.

*	Import data into ISIS/Draw.

Click any of the following items:

Read Name/Comments

Use Settings

Consult your system documentation for information about the other items in this dialog box.


Open/Insert/Import

Use this dialog to:

*	Open an ISIS/Draw sketch file.

*	Insert the contents of a sketch file directly into the active window.

*	Import data into ISIS/Draw.

Click any of the following items:

Read Name/Comments

Use Settings

Consult your system documentation for information about the other items in this dialog box.


Read Name/Comments

To display any names and comments that may have been saved with the selected ISIS/Draw sketch file, click Read Name/Comments.


Use Settings

To display the selected ISIS/Draw sketch file using the default settings the file had when it was saved, set [image] Use Settings.


Save As

Use this dialog to:

*	Save a new ISIS/Draw sketch file.

*	Save an existing ISIS/Draw sketch file under a different name.

For information on how to export data from ISIS/Draw, click here.

Click any of the following items:

Save Name/Comments

Save Settings

Consult your system documentation for information about the other items in this dialog box.


Save As

Use this dialog to:

*	Save a new ISIS/Draw sketch file.

*	Save an existing ISIS/Draw sketch file under a different name.

For information on how to export data from ISIS/Draw, click here.

Click any of the following items:

Save Name/Comments

Save Settings

Consult your system documentation for information about the other items in this dialog box.


Save Name/Comments

To enter a name and comments that will be saved with the ISIS/Draw sketch file, click Save Name/Comments. Then, enter a name and comment.


Save Settings

To save the ISIS/Draw sketch file using the current default settings, set [image] Save Settings.


Grid Coordinates

Use this dialog to:

*	Specify custom grid coordinates. For information on how to set up the grid, click here.

Click any of the following items:

Origin: x

Origin: y

Vector: x

Vector: y

Note: When you enter coordinates to define a grid, the standard bond length is modified.


Origin: x

To set the X coordinate for the starting point for the grid, click the box and enter a value.


Origin: y

To set the Y coordinate for the starting point for the grid, click the box and enter a value.


Vector: x

To set the X coordinate of the line direction in relation to the origin, click the box and enter a value.


Vector: y

To set the Y coordinate of the line direction in relation to the origin, click the box and enter a value.


Click on Attachment Atom

To attach a bond to an atom of a contracted residue, click the atom of the residue to which the bond attaches.

OK

To attach the new bonds and close the dialog box, click OK.

Cancel

To close the dialog box without attaching any new bonds, click Cancel.


Edit -- Sequence

Use this dialog to:

*	Improve the readability of a sequence. You can change the default settings and group residues into suitably sized blocks, limit the number of residues per line, or change the spacing between blocks or residues. Example

Click any of the following items:

Spacing Between

Grouping

Thickness

Color

OK, Cancel


Grouping

Wrap After

Block Size


Settings -- Sequence

Use this dialog to:

*	Set defaults to group residues into suitably sized blocks, limit the number of residues per line, or change the spacing between blocks or residues. Example

Click any of the following items:

Spacing Between

Grouping

Show

Delimiter

Save, Save As, Read

For more information on how to work with ISIS/Draw settings, click here.


Example


Spacing Between

Residues

Blocks

Lines


Residues

To specify the spacing between individual residue codes, click the Residues box, and then enter or choose a value. Then, choose the unit of measure. The default setting is 0.125 cm.

To insert one character between residue codes, set [image] Plus character width. (This is the default setting.)


Blocks

To specify the spacing between blocks of residue codes, click the Blocks box, and then enter or choose a value. Then, choose the unit of measure. The default setting is 0.125 cm.

To insert one character between blocks of sequence codes, set [image] Plus character width. (This is the default setting.)


Lines

To specify the spacing between lines of residue codes, click the Lines box, and then enter or choose a value. Then, choose the unit of measure. The default setting is 0.00 cm.

To position lines of sequence code as close together as possible, set [image] Plus character height. (This is the default setting.)


Wrap after

To specify the default number of residues per line of residues, click the Wrap after box and enter a value between 0 and 999. [The default setting of 0 (zero) specifies that there are is solely a single line of residues.] Example

Caution: If you do not specify the number of residues per line, all the residue codes that you type will remain on a single line that might extend past the drawing window. However, you can insert a line break anywhere if you press the Return key.


Example

If you enter a value of 15, you specify 15 residues per line:


Block size

To improve the readability of a sequence, you can group residues into suitably sized blocks. By default, each block contains the same number of residues. Example

To specify the default number of residues in a block, click the Blocksize box and enter or choose a value between 0 and 999. [The default setting of 0 (zero) specifies that there are no blocks of residues (zero residues per block).]


Example

The following sequence contains 5 residues per block:


Show

Sequence Bonds

Crosslink Bonds

Residue Brackets

Leaving Groups


Sequence Bonds

To show sequence bonds by default, set [image] Sequence Bonds.


Crosslink Bonds

You can either display or hide crosslink bonds on contracted residues in the ISIS/Draw window.

To show the crosslink bonds by default, set [image] Crosslink Bonds.

Note: If you hide the crosslink bonds, you see markers, such as x1 or x2, that designate those pairs of residues that are crosslinked. Example


Residue Brackets

You can either display or hide residue brackets on expanded residues in the ISIS/Draw window. (You do not see brackets on a contracted residue.)

To show the residue brackets by default, set [image] Residue Brackets.


Leaving Groups

You can either display or hide leaving groups on contracted residues in the ISIS/Draw window.

To show residue leaving groups by default, set [image] Leaving Groups.


Customize Sequence Menu

Use this dialog to:

*	Specify the name of the list of residue codes that you want to use.

*	Specify the letter characters for the list that you want to use. For example, you might want to use the set of 3-letter residue codes (that includes Arg for arginine) or the set of 1-letter residue codes (that includes R for arginine).

*	Specify the delimiter between each residue code.

Click any of the following items:

Insert

Rename

Remove

Residue Map File

Code Length

Delimiter

If you are not sure which list of residue codes to use, see your ISIS Administrator.


Insert

To add a new Residue Map file to the Sequence menu, click Insert, and then select a file.


Rename

To rename a Residue Map file on the Sequence menu, select the file in the list box, then click Rename.


Remove

To remove a Residue Map file from the Sequence menu, select the file in the list box, then click Remove.


Residue Map File

Displays the name of the Residue Map file that is highlighted in the list box.


Code Length

To specify different letter characters for the list that you want to use, click a code length in the Code Length list box. For example, to change the current 1-letter code to 3 letters, click 3-letter.


Delimiter

To specify a different delimiter between each residue code of variable length, click the delimiter of your choice in the Delimiter list box. The default delimiter is a hyphen.


Save Residue Changes

Use this dialog to:

*	Specify a name for any new or modified residues.

New Name

To create a new name for the residue, click the box and enter a new name.

Yes

To accept the structural changes in the Edit window and accept the name in the New Name box, click OK.

No

To reject the changes in the Edit window, click No.

Cancel

To close the dialog box and return to the Edit window, click Cancel.


Chem Inspector

Use this dialog to:

*	Check for problems that might keep a structure or reaction from being registered in ISIS/Base, or from being used in searching a database.

*	Check for problems that might keep you from manually atom-atom mapping a reaction. For more information, see To atom-atom map manually.

*	Check for problems that might keep you from exporting a reaction as a rxnfile.

Click any of the following items:

Results

Intended Use

Check entire sketch, Check selected objects

Explanation

Recheck

For step-by-step instructions on how to check molecules and reactions, click here. You must fix any errors that Chem Inspector finds to successfully:

*	Register a structure or reaction

*	Use a structure or reaction to search a database

*	Export a reaction as a rxnfile

*	Manually atom-atom map a reaction.

For information on how to turn individual Chem Inspector warnings on or off, click here.

For information on how to draw and edit reactions, see the ISIS/Draw "Quick Start".


Results

To see error, warning, and Informational messages about the selected objects or the entire sketch, click the box and choose a result.

Note: ISIS/Draw displays informational messages even if it finds no errors or warning.


Intended Use

To specify the type of problems that Chem Inspector looks for, click the Intended Use box and choose an option.

For example, if you want to register a reaction into a remote database, choose Host Database > Reaction > Registration as the intended use. Chem Inspector can then look for features (such as fonts or pen size) that are not supported by remote databases.


Check entire sketch, Check selected objects

To check the entire sketch, set [image] Check entire sketch.

To check only selected object(s) in the sketch, set [image] Check selected objects.

Note: When you click [image] to transfer a sketch to ISIS/Base, Chem Inspector always verifies the entire sketch.


Explanation

To see an explanation for a specific result in the Results box, click the Results box, choose the result, and then click [image].


Recheck

To recheck the sketch after you have made changes to it in the drawing area, click [image].


Change Settings to Match the Sketch?

When you resize or scale all the molecules in a sketch, ISIS/Draw can change the settings to reflect the new molecule size. The next time you draw a molecule, it will be drawn using the new settings. The settings affected are:

*	Atom number size

*	Atom label margin (width)

*	Standard bond length

*	Hash spacing

*	Stereo bond width

*	Font size

*	Arrow length

1.	Do one of the following:

*	To leave all settings as they are, click No.

*	To have all new molecules drawn at the new size, click Yes. The settings are changed only for the current session.

2.	(Optional) To permanently save the new settings, choose Options > Settings and click Save.


Insert New Object

Use this dialog to:

*	Embed an object that was created by an application that supports object linking and embedding into an ISIS/Draw sketch.

See your Windows documentation for more information on this feature.


Choose Sequence Type

To specify the type of sequence (such as DNA instead of amino acids) and the type of residue code that you want to use (such as 1-letter instead of 3-letter), click the file of your choice.

Notes: (1) When you import a sequence, you see a question mark on the list of residue codes for each residue code that was not on the list prior to importing the sequence. You also see a specific character, such as a hyphen, in place of any letter characters in the residue codes that are not chemically significant. Also, a blank line in the sequence file that you import translates into the start of a new sequence.

(2) Before you import a sequence, be certain that the list of residue codes that is current contains the matching residues for the sequence that you want to import. First, choose Chemistry > Sequence, and then choose the list of residue codes that you want. Then, import your sequence.


Create Rgroup

Use this dialog to:

*	Specify the Rgroup label that you want to associate with the Rgroup substituents that you selected.

 Requirements to use this dialog

Click any of the following items:

R1-R32

Thickness

Color

For information on Rgroup searching, see Searching Concepts/Examples


Requirements to use the Create Rgroup dialog

To use this dialog, you must have previously completed the following tasks, in this order:

1.	Draw the root structure of the Rgroup.

2.	Draw Rgroup substituents.

3.	Specify attachment points for Rgroup substituents.

4.	Select the Rgroup substituents that you want to include in the Rgroup.


Edit -- Rgroup

Use this dialog to:

*	Edit the Rgroup that is associated with the set of Rgroup substituents that you selected.

 Requirements to use this dialog

R1-R32

Thickness

Color

OK, Cancel

For information on Rgroup searching, see Searching Concepts/Examples


R1-R32

To specify the Rgroup that is associated with the set of Rgroup substituents that you selected, click a button that represents the Rgroup label (R1 through R32).


Requirements to Use The Edit - Rgroup Dialog
Requirements to use the Edit -- Rgroup dialog

To use this dialog, you must have selected the Rgroup that you want to edit.

Note: To create an Rgroup query, you need to create the components of the query in a specific order.


Create R-Logic

Use this dialog to:

*	Specify Rgroup conditions. If you do not specify Rgroup conditions for your Rgroup query, ISIS assigns the default Rgroup conditions.

 Requirements to use this dialog

Click any of the following items:

Rgroup # (i)

Occurrence range

Rest H

If R(i) then

Up/Down

Thickness

Color

For information on Rgroup searching, see Searching Concepts/Examples


Requirements to use the Create R-Logic dialog

To use this dialog, you must have previously completed the following tasks, in this order:

1.	Draw the root structure of the Rgroup.

2.	Draw Rgroup substituents.

3.	Specify attachment points for Rgroup substituents.

4.	Specify the members of each Rgroup.


Edit -- R-Logic

Use this dialog to:

*	Edit Rgroup conditions on an existing Rgroup query.

 Requirements to use this dialog

Click any of the following items:

Rgroup #(i)

Occurrence range

Rest H

If R(i) then

Up/Down

Thickness

Color

OK, Cancel

For information on Rgroup searching, see Searching Concepts/Examples


Requirements to use the Edit R-Logic dialog

To use this dialog, you must have previously created an Rgroup query and selected the Rgroup conditions that you want to edit.

Note: To create an Rgroup query, you need to create the components of the query in a specific order. For more information on creating Rgroup queries, click here.

For information on Rgroup searching, see Searching Concepts/Examples


Rgroup #(i)

To specify the Rgroup for which you want to define Rgroup conditions, enter the number (1 to 32).


Occurrence range

To specify how many times the Rgroup can occur in the query, enter a value.


Rest H

To specify that only hydrogens can occur at unsaturated Rgroup-labeled sites, set [image] Rest H.

To specify that any fragment can occur, set [image] Rest H.


If R(i) then

To specify logical conditions, click the box and enter the number of the dependent Rgroup. Use the Rgroup condition If R(I) Then to specify whether the presence of one Rgroup is dependent on the presence of another Rgroup. To specify conditions, click the box and enter the number of the dependent Rgroup.


Up/Down

To view more Rgroup conditions, click Up or Down.


Point to Rgroup

Use this dialog to:

*	Specify Rgroup labels on the root structure of an Rgroup query.

 Requirements to use this dialog

Click the following item:

R1-R32

For information on Rgroup searching, see Searching Concepts/Examples


Requirements to use the Point to Rgroup dialog

To use this dialog, you must have already drawn the portion of your Rgroup query that must not vary, drawn bonds to the atoms that you want to represent Rgroups, and have selected the atom that you want to change to an Rgroup label. Example

Note: To create an Rgroup query, you need to create the components of the query in a specific order. For more information on creating Rgroup queries, click here.

For information on Rgroup searching, see Searching Concepts/Examples


Example


R1-R32

To label selected atoms(s) as Rgroup sites, click a button representing the label to apply (R1 through R32).


Rquery Attachment

Use this dialog to:

*	Specify attachment points for Rgroup substituents.

 Requirements to use this dialog

Click the following item:

Enter attachment point

For information on Rgroup searching, see Searching Concepts/Examples


Requirements to use the Rquery Attachment dialog

To use this dialog, you must have previously completed the following tasks, in this order:

1.	Draw the root structure of the Rgroup.

2.	Draw Rgroup substituents.

3.	Select the atom(s) on the Rgroup substituents that you want to specify as attachment point(s).


Enter Attachment Point

To specify 1 or 2 attachment points, enter 1 or 2. To remove any existing attachment points, enter 0.


Explicit and Implicit Hydrogens

An explicit hydrogen is a hydrogen that is visible at a specific position on a structure (You see an atom with a bond that is attached to a hydrogen). An implicit hydrogen is a hydrogen that you know to be present at a specific position in a structure (implied), but it is not visible. You can control the display of implicit hydrogens in ISIS/Draw and ISIS/Base:


Create 3D Object

Use this dialog to:

*	Add 3D objects and 3D constraints to queries for the following searches: CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly.

 Requirements to use this dialog

Click any of the following items:

Type

Measured Value

Radius, Field, Range, Distance, RMS Deviation

Name, Query

Allow nonquery atoms within exclusion sphere

For information on drawing 3D objects and constraints, see the step-by-step instructions for the search of your choice.


Requirements to use the Create 3D Object dialog

To use this dialog, you must have previously completed the following tasks, in this order:

1.	(Optional) Create the submodel components of the query.

2.	(Optional) Identify the 3D atom fields and/or 3D atom-pair fields that are associated with any 3D data constraints that you want to create. (To identify the fields, you can print or view a list of database fields.)

3.	(Optional) Draw any 3D objects that comprise the 3D object or constraint that you want to create.

4.	Select the reference positions (atoms, points, or centroids) and/or 3D objects that you want to use to create the 3D object or constraint.

For information on creating queries for 3D searching, see the step-by-step instructions for any of the following searches: CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly.


Why Identify Database Fields?

When you create a 3D data constraint, you must specify the database field with which the data is associated. In the following example, atom data on partial charges is associated with a field called charge:

To identify the atom or atom-pair field that is associated with the 3D data constraint that you want to create, print or view a list of database fields.


Printing or Viewing a List of Your Database Fields

Click here for step-by-step instructions

Before you create a 3D data constraint, print or view a list of database fields to obtain the name of the atom or atom-pair field that is associated with that constraint.

It is important that you print or view a list of your database fields to understand the database structure. Do not make assumptions about your database structure based on experience with other MDL programs. For example, a flat database in MACCS-II is hierarchical in ISIS.

We recommend that you print a list of database fields, because it is difficult to see the relationship of fields when scrolling through a list box.


Type

Use this option to choose the type of 3D object or 3D constraint that you want to select.

Angle

To specify an angle constraint, click Angle. This choice is available solely if you select three reference positions (atoms, points, or centroids) or two lines, planes or normals.

Atom

To specify an atom data constraint, click Atom. This choice is available solely if you select one atom.

Atom-Pair

To specify an atom-pair data constraint, click Atom-Pair. This choice is available solely if you select two atoms.

Centroid

To specify a centroid, click Centroid. This choice is available solely if you select two or more reference positions (atoms, points, or other centroids).

Dihedral

To specify a dihedral angle constraint, click Dihedral. This choice is available solely if you select four reference positions (atoms, points, or centroids).

Distance

To specify a distance constraint, click Distance. This choice is available solely if you select two reference positions (atoms, points, or centroids).

Exclusion Sphere

To specify an exclusion sphere, click Exclusion Sphere. This choice is available solely if you select one reference position (atom, point, or centroid).

Line

To specify a line or linearity constraint, click Line. This choice is available solely if you select two or more reference positions (atoms, points, or centroids).

Normal

To specify a normal, click Normal. This choice is available solely if you select a plane and one reference positions (atom, point, or centroid).

Plane

To specify a plane or planarity constraint, click Plane. This choice is available solely if you select three or more reference positions (atoms, points, or centroids).

Point

To specify a point, click Point. This choice is available solely if you select two reference positions (atoms, points, or centroids), or if you select a reference position and a normal.


Measured Value

Displays the measured value (if applicable) for the type of 3D geometric constraint that you are creating. The value is in Angstroms or degrees.

Constraint values and measured values are defined as follows:


Radius, Field, Range, Distance, RMS Deviation

Use these options to specify the value (if any) that is associated with a 3D object or 3D constraint. The value that you see depends on the type of 3D object or constraint that you create.

ISIS provides default values for some types of 3D objects and constraints. ISIS calculates the default value from values that you specify in ISIS/Draw Settings. To change the default constraint value, change the corresponding value in Settings. For more information on how to change Settings to get different default values, click here.

Value restrictions apply to some types of 3D objects.

Radius

To enter the radius for an exclusion sphere, click the box (if not already selected) and enter a value.

Range

If you specify a distance, you see the default distance constraint in the box. If you specify an angle or dihedral angle, you see a default angle constraint. To specify a different range, highlight the default range (if not already selected) and enter a new range.

RMS Deviation

If you specify a best-fit line or best-fit plane, you see a default value (default RMS Deviation) for the associated linearity or planarity constraint. To specify a different value for the linearity or planarity constraint, highlight the default RMS deviation (if not already selected) and enter a new value. To specify a best-fit line or best-fit plane without an RMS deviation constraint, highlight the RMS deviation and press the Delete key.

Distance

To specify the distance between two reference positions (atoms, points, or centroids), enter a distance.


Name
Name, Query

Name

To name the 3D object or 3D geometric constraint, click the box and enter a name.

Query

To specify the constraint for an atom or atom-pair data constraint, click the box and enter a value or a text/numeric query.


Allow nonquery atoms within exclusion sphere

To allow unconnected atoms that are not part of the query (for example, salt ions) to lie within the exclusion sphere, in the 3D structures that you retrieve, set [image] Allow nonquery atoms within exclusion sphere.

This choice is available solely if you select one atom, point, or centroid.

Note: You can allow atoms that are part of the query, but are not connected to the atom at the center, to lie within the exclusion sphere. To do this, you add atoms to the basis of the exclusion sphere. For step-by-step instructions on allowing atoms within an exclusion sphere, click here.


3D Objects -- Value Restrictions

Angle

For angle defined using lines or planes, value must be between 0 and 90 degrees. For angle defined using three reference points, value must be between 0 and 180 degrees.

Atom

Enter a database field name (up to 30 characters long) and the data constraint (up to 60 characters long).

Atom-Pair

Enter a database field name (up to 30 characters long) and the data constraint (up to 60 characters long).

Centroid

None

Dihedral

Range must be between -180 and +180 degrees.

Distance

Both values in the range must be greater than 0 and equal or less than 1000.

Exclusion Sphere

Radius must be between 0.1 and 20 Angstroms.

Line

Value must be greater than 0 and equal or less than 1000.

Normal

You can change the direction of normal by redefining the plane. To reverse the direction of the normal, reverse the order in which you define the reference positions (atoms, points, or centroids) that comprise the plane.

Plane

Value must be greater than zero and equal or less than 1,000.

Point

Distance can be less than 0 or greater than the distance between reference points A and B. (Point need not be between A and B.) Linear distance must be between -100 and +100 Angstroms. Percentage distance must be between -1000% and +1000% and must include the % sign.


Edit -- 3D

Use this dialog to:

*	Edit one selected 3D object or 3D constraint.

 Requirements to use this dialog

Click any of the following items:

Type

Measured Value

Radius, Field, Range, Distance, RMS Deviation

Name, Query

Allow nonquery atoms within exclusion sphere

Thickness

Color

OK, Cancel

For information on creating queries for 3D searching, see the step-by-step instructions for any of the following searches: CFS, CFS/Biopoly, SSS3D, SSS3D/Biopoly.


Requirements to use the Edit -- 3D dialog

To use this dialog:

*	You must have previously created a 3D object or 3D constraint in your search query.

For information on creating queries for 3D searching, see the step-by-step instructions for any of the following searches: CFS, CFS/Biopoly, SSS3D, SSS3D/Biopoly.


Type

Displays the type of 3D object or 3D constraint that you selected.


Measured Value

Displays the measured value (if applicable) for the type of 3D geometric constraint that you are creating. The value is in Angstroms or degrees.

Constraint values and measured values are defined as follows:


Radius, Field, Range, Distance, RMS Deviation

Displays the value (if any) that is associated with a 3D object or 3D constraint. The value that you see depends on the type of 3D object or constraint that you create.

Value restrictions apply to some types of 3D objects.

Radius

To specify the radius of an exclusion sphere, click the box (if not already selected) and enter a value.

Range

To specify the range of the distance, angle, or dihedral angle constraint that you selected, highlight the range (if not already selected) and enter the range.

RMS Deviation

To specify the linearity or planarity constraint for the best-fit line or best-fit plane that you selected, highlight the RMS deviation (if not already selected) and enter a value. To specify a best-fit line or best-fit plane without a linearity or planarity constraint, highlight the RMS deviation and press the Delete key.

Distance

To specify the distance for the point that you selected, click the box (if not already selected) and enter a distance.


Distance

To edit the distance from a reference position for a point, click the Distance box and edit the distance.


Name
Name, Query

To edit the name of the 3D object or 3D geometric constraint, click the Name box and edit the name.

To edit the value or text/numeric query of a 3D data constraint, click the Query box and edit the value or query.


Allow nonquery atoms within exclusion sphere

To allow atoms that are not part of the query, and that are not connected to the atom at the center of the exclusion sphere, (for example, salt ions) to lie within the exclusion sphere in the 3D structures that you retrieve, set [image] Allow nonquery atoms within exclusion sphere.

Note: You can allow atoms that are part of the query, but are not connected to the atom at the center, to lie within the exclusion sphere. To do this, you add atoms to the basis of the exclusion sphere. For step-by-step instructions on allowing atoms within an exclusion sphere, click here.


Settings -- 3D

Use this dialog to:

*	Set defaults for drawing 3D queries for searching remote databases.

 Requirements to use this dialog

Click any of the following items:

3D rotation increment

Display measured values

Allow nonquery atoms within exclusion sphere

Default Constraint Ranges

OK, Cancel

Save, Save As, Read

For more information on drawing 3D queries, click here.


Requirements to use the Settings -- 3D dialog

To use this dialog, you need to understand how to create a 3D query to search a remote database for 3D structures. The 3D query that you use depends entirely on the type of 3D search that you want to conduct. For more information on 3D searching, click one of the following search types.

3D Structure Records (Remote Searches):

3DEXACT    ALL    CFS    CFS/Biopoly    ID    MSim    QB    SBF    SSS3D    SSS3D/Biopoly


3D rotation increment

To specify the increment by which the 3D Rotate tool rotates a structure, click the box and enter or choose a value between 0 and 180 degrees.


Display measured values

To display the measured values of 3D objects and geometric constraints that you see in the ISIS/Draw window, set [image] Display measured values. To display the constraint values, set [image] Display measured values.

Constraint values and measured values are defined as follows:


Allow nonquery atoms within exclusion sphere

Use this option specify the default setting for allowing unconnected nonquery atoms within exclusion spheres in the Create 3D Object dialog box, and in the Edit tab of the Edit Object dialog box.

Note: To create an exclusion sphere, you select the reference position atom, point, or centroid that you want at the center of the sphere, then choose Chemistry > 3D > Create. You see the Create 3D Object dialog box. The default setting for Allow nonquery atoms within exclusion sphere is the same as that in the 3D tab of Settings.


Default constraint ranges

Use these options to specify values that ISIS uses to calculate default values for 3D geometric constraints that you create.

Distances

ISIS uses the Distances value to calculate default distance constraints. To specify the Distances value, click the box and enter or choose a value between 0 and 1,000 Angstroms, or between 1 and 100%. Then, choose the unit of measure.

For information on how ISIS calculates default distance constraints from the Distances value, click here.

Angles, dihedral angles

ISIS uses the Angles value to calculate default constraints for angles and dihedral angles. To specify the Angles value, click the box and enter or choose a value between 0 and 180 degrees, or between 1 and 100%. Then, choose the unit of measure.

For information on how ISIS calculates default angle and dihedral angle constraints from the Angles value, click here.

Lines, planes (RMS)

ISIS uses the RMS Deviation value to calculate the default constraint value for linearity and planarity constraints. To specify the RMS Deviation value, click the box and enter or choose a value between 0 and 1,000 Angstroms, or between 1 and 10,000%. Then, choose the unit of measure.

For information on how ISIS calculates default linearity and planarity constraints from the RMS Deviation value, click here.


Lose Original Coordinates

Caution: The command that you chose will change the coordinates of the atoms of the model (3D structure) that you selected. Changing the coordinates changes the 3D spatial relationships among the atoms in the structure. If you change the 3D spatial relationship among atoms in the structure, the following searches give incorrect results:

*	A 3DEXACT search in a remote database. that uses the 3D structure as a query

*	A CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search that uses a submodel query that you create from the 3D structure with lost coordinates

OK

Executes the command and changes the original coordinates of the structure.

Cancel

Cancels the command and preserves the original 3D coordinates of the structure.


Lost Original Coordinates

Caution: The last command that you chose has changed the coordinates of the atoms of the model (3D structure) that you selected. Changing the coordinates changes the 3D spatial relationships among the atoms in the structure. If you change the 3D spatial relationship among atoms in the structure, the following searches give incorrect results:

*	A 3DEXACT search in a remote database. that uses the 3D structure as a query

*	A CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search that uses a submodel query that you create from the 3D structure with lost coordinates

OK

Keeps the changes that were made by the command. The original 3D spatial relationships among the atoms in the structure are lost.

Undo

Reverses the action of the command, and preserves the original 3D spatial relationships among atoms in the structure.


Create Brackets

Use this dialog to:

*	Create polymers

*	Edit the definition of a polymer (the definition is the set of atoms, bonds, and brackets that comprise the polymer)

*	Create and edit ordered and unordered mixtures.

*	Create structures that contain a fixed number of identical repeating units (multiple groups).

*	Create generic brackets to which you want to attach data.

*	Draw brackets for presentation graphics that are not chemically significant.

Note: You can attach data to brackets. For more information, see Creating and Editing Attached Data.

 Requirements to use this dialog

Click any of the following item:

Bracket type

Polymer repeat pattern

SRU label

Bracket style

Apply

Cancel


Requirements to Use This Dialog

If you want to draw polymers and mixtures that you can register to a molecule database, you must understand and use the correct conventions for drawing these structures. If you do not use these conventions, other users might not be able to find your structures when they search the database. For information on these conventions, see the following:

*	For information on drawing polymers and mixtures of polymers, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

*	For information on drawing non-polymer mixtures, see Drawing Mixtures: MDL Requirements for Database Searching and Registration.

Caution: Your ISIS Administrator might establish conventions for representation of polymers and/or mixtures that are different from the conventions that MDL requires. Also, your site might create structures for which no MDL conventions exist. If you are not sure how to draw a structure that you want to register, see your ISIS Administrator.


Bracket type

To specify a bracket type, click the Bracket type box and choose a type. The following bracket types are available:

anypolymer (anyp)

component (c)

copolymer (co)

copolymer, alternating (alt)

copolymer, block (blk)

copolymer, random (ran)

crosslink (xl)

generic ( )

graft (grf)

mer (mer)

mixture, ordered (f)

mixture, unordered (mix)

modification (mod)

monomer (mon)

multiple group (#)

SRU (n)


Bracket Types

anypolymer (anyp)

component (c)

copolymer (co)

copolymer, alternating (alt)

copolymer, block (blk)

copolymer, random (ran)

crosslink (xl)

generic ( )

graft (grf)

mer (mer)

mixture, ordered (f)

mixture, unordered (mix)

modification (mod)

monomer (mon)

multiple group (#)

SRU (n)


SRU (n)

Use Structural Repeating Unit (SRU) (n) brackets to enclose the structural repeating unit (constitutional repeating unit) of the structure-based representation of a homopolymer:

Using SRU brackets implies that the structure within the brackets can repeat with itself an indefinite number of times. That is, enclosing the structure "A" in SRU brackets implies that the sequence ...AAAAA... can occur.

For examples of polymer structures that use SRU brackets, see Drawing Polymers: MDL Requirements for Database Searching and Registration.


monomer (mon)

Use Monomer (mon) brackets to draw the repeating unit(s) for the source-based representation of a homopolymer:

For examples of polymer structures that use monomer brackets, see Drawing Polymers: MDL Requirements for Database Searching and Registration.


mer (mer)

For source-based representations of copolymers, use mer brackets (mer) to enclose a monomer that can not repeat with itself. For more information and examples of structures that use mer brackets, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

 Caution: MDL recommends that you not use mer brackets in structure-based representations of polymers that you register to databases. Mer brackets were specified in certain earlier conventions for structure-based polymer representation that were used in MACCS-II. These earlier conventions are no longer recommended.


Example

For more information on MDL recommendations for polymer representation, see Drawing Polymers: MDL Requirements for Database Searching and Registration. For more information on the polymer representations that your company uses, see your ISIS Administrator.


Example

For more information on MDL recommendations for polymer representation, see Drawing Polymers: MDL Requirements for Database Searching and Registration. For more information on the polymer representations that your company uses, see your ISIS Administrator.


copolymer (co)

Use copolymer brackets (co) to enclose multiple SRU or monomer (n) brackets within the same polymer. For example, use copolymer brackets to enclose the individual repeating units within a copolymer:

You should also use copolymer brackets for drawing polymers that are chemically altered after polymerization, such as modified polymers, cross-linked polymers, or graft polymers:

For more examples of polymer structures that use copolymer brackets, see Drawing Polymers: MDL Requirements for Database Searching and Registration.


copolymer, alternating (alt)

Alternating copolymer (alt) brackets were used in the earlier conventions for polymer representation that were available in MACCS-II. MDL provides alternating copolymer brackets in ISIS/Draw solely for compatibility with MACCS-II.

 Caution: MDL recommends that you not use alternating copolymer brackets for polymers that you register to databases. Instead, represent alternating and other periodic copolymers as homopolymers. For more information on MDL recommendations for polymer representation, see Drawing Polymers: MDL Requirements for Database Searching and Registration.


copolymer, random (ran)

Random copolymer (ran) brackets were used in the earlier conventions for polymer representation that were available in MACCS-II. MDL provides random copolymer brackets in ISIS/Draw solely for compatibility with MACCS-II.

 Caution: MDL recommends that you not use random copolymer brackets for polymers that you register to databases. Instead, attach data on polymer type to the copolymer brackets. For more information on MDL recommendations for polymer representation, see Drawing Polymers: MDL Requirements for Database Searching and Registration.


copolymer, block (blk)

Block copolymer (blk) brackets were used in earlier conventions for polymer representation that were available in MACCS-II. MDL provides block copolymer brackets in ISIS/Draw solely for compatibility with MACCS-II.

 Caution: MDL recommends that you not use block copolymer brackets for polymers that you register to databases. Instead, attach data on polymer type to the copolymer brackets. For more information on MDL recommendations for polymer representation, see Drawing Polymers: MDL Requirements for Database Searching and Registration. For more information on the polymer representations that your company uses, see your ISIS Administrator.


crosslink (xl)

Crosslink (xl) brackets were used to specify the modified structural repeating unit in earlier conventions for polymer representation that were available in MACCS-II. MDL provides crosslink brackets in ISIS/Draw solely for compatibility with MACCS-II.

 Caution: MDL recommends that you not use crosslink brackets for cross-linked polymers that you register to databases. Instead, attach data on polymer type to the polymer brackets that contain the modified structural repeating unit. For more information on MDL recommendations for polymer representation, see Drawing Polymers: MDL Requirements for Database Searching and Registration.


graft (grf)

Graft (grf) brackets were used to specify the modified structural repeating unit in earlier conventions for polymer representation that were available in MACCS-II. MDL provides graft brackets in ISIS/Draw solely for compatibility with MACCS-II.

 Caution: MDL recommends that you not use graft brackets for graft polymers that you register to databases. Instead, attach data on polymer type to the polymer brackets that contain the modified structural repeating unit. For more information on MDL recommendations for polymer representation, see Drawing Polymers: MDL Requirements for Database Searching and Registration.


modification (mod)

Modification (mod) brackets were used to specify the modified structural repeating unit in earlier conventions for polymer representation that were available in MACCS-II. MDL provides modification brackets in ISIS/Draw solely for compatibility with MACCS-II.

 Caution: MDL recommends that you not use modification brackets for modified polymers that you register to databases. Instead, attach data on polymer type to the polymer brackets that specify the modified structural repeating unit. For more information on MDL recommendations for polymer representation, see Drawing Polymers: MDL Requirements for Database Searching and Registration.


component (c)

Use component brackets (c) to enclose the individual components of a mixture:

*	To specify an ordered mixture, use numbered components (c1, c2, c3, ...).

*	To specify an unordered mixture, use components without numbers (c).

For information on drawing mixtures of polymers, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

For information on drawing mixtures of non-polymer structures, see Drawing Mixtures: MDL Requirements for Database Searching and Registration.


mixture, unordered (mix)

Use unordered mixture (mix) brackets to enclose the individual components of an unordered mixture. An unordered mixture is a mixture where the order in which the components are combined is not important. For example, the following is a reaction products that consists of a mixture of stereoisomers:


mixture, ordered (f)

Use ordered mixture (f) brackets to enclose the individual components of an ordered mixture. An ordered mixture is a mixture where the order in which the components are combined (order of addition) is important. For example, the following structure represents the formulation of an aspirin tablet in which the acetaminophen (c1) must be added before the binder (c2) and other components (c3 and c4):

Note: In MACCS-II, ordered mixtures were called formulations.


multiple group (#)

Use multiple group (#) brackets to draw a fixed number(#) of identical repeating units in condensed form. For example:

Note: To represent an unspecified number of identical repeating units within a polymer, use SRU brackets (n).


generic ( )

Use generic ( ) brackets for the following purposes:

*	To draw chemically-insignificant brackets for presentation graphics.

*	To associate attached data with a set of atoms and bonds. In the following example "antioxidant" is attached data:


anypolymer (anyp)

Use anypolymer (anyp) brackets to create a search query for an SSS/Poly search. A structure with anyp brackets finds any polymer bracket (SRU, monomer, copolymer, block copolymer, random copolymer, mer, crosslink, modification, or graft) that contains your query embedded within it. For example:

You can not register a structure with anyp brackets to a database. For information on drawing polymer structures for registration, see Drawing Polymers: MDL Requirements for Database Searching and Registration.


Polymer repeat pattern

To specify the polymer repeat pattern, click the Polymer repeat pattern box and choose a pattern.

Note: The repeat patterns that are available for a set of polymer brackets depend on the number of brackets, and the number of crossing bonds. For a full discussion of polymer repeat pattern, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

Head-to-tail/Head-to-head

For polymers with two crossing bonds, you can specify a repeat pattern of head-to tail (the default), head-to-head, in addition to the either/unknown repeat pattern. Examples

Head-to-tail, flip/Head-to-tail, no flip

For ladder-type polymers with the head-to-tail repeat pattern, you must specify whether the SRU flips around the polymer backbone when it attaches to the adjacent SRU. Consequently, you have two options for connecting the bonds on each bracket to the adjacent SRU. Examples

Head-to-head, flip/Head-to-head, no flip

For ladder-type polymers with the head-to-head repeat pattern, you must specify whether the SRU flips around the polymer backbone when it attaches to the adjacent SRU. Consequently, you have two options for connecting the bonds on each bracket to the adjacent SRU. Examples

Either/unknown

For polymers with two crossing bonds, use the either/unknown repeat pattern when the repeat pattern is unknown, or when either of the other two repeat patterns (head-to-tail, head-to-head) repeat patterns might be present. Example

For ladder-type polymers, use the either/unknown repeat pattern when the repeat pattern is unknown, or when any of the other four repeat patterns might be present.

Polymers with three or more brackets always have the either/unknown repeat pattern.


Examples


Examples


Examples


Example

In this example, poly(1-chloroethylene/2-chloroethylene) consists of units of chloroethylene that can be joined head-to-head (1-chloroethylene) or head-to-tail (2-chloroethylene).


SRU label

To specify the SRU label, click the SRU label box and enter a label.

An SRU label is a single alphabetic character that appears on the bracket of a structure-based homopolymer. The default SRU label is n, but you can change it to a different letter to show different multiplicities of polymeric or oligomeric sequences. For example:

Note: The SRU label box is available solely when you click the Bracket type box and choose SRU (n).


Bracket style

To specify a style for the bracket, click the Bracket style box and choose a style.

The following polymer contains both squared and curved bracket styles:

Bracket style is stored with the structure in the database. However, bracket style affects solely how brackets are displayed; bracket style does not affect searching.

Note: In the polymer shown here, the subscripts p, q, and r are SRU labels.


Apply

To save any changes that you have made to one selected set of brackets, click Apply.

Note: To close the Create Brackets dialog, click another tool.


Cancel

To undo any changes that you have made to one selected set of brackets, click Cancel.

Note: To close the Create Brackets dialog, click another tool.


Edit -- Bracket

Use this dialog to:

*	Change the bracket type, SRU label, and polymer repeat pattern of selected polymers, ordered mixtures, and unordered mixtures.

*	Change the display of selected sets of brackets.

Note: You can attach data to brackets. For more information, see Creating and Editing Attached Data.

Click any of the following items:

Bracket type

SRU label

Polymer repeat pattern

Bracket style

Bracket height

Bracket width

Thickness

Color

OK, Cancel


Bracket type

To specify the type of the selected bracket, click the Bracket type box and choose a type. The following bracket types are available:

anypolymer (anyp)

component (c)

copolymer (co)

copolymer, alternating (alt)

copolymer, block (blk)

copolymer, random (ran)

crosslink (xl)

generic ( )

graft (grf)

mer (mer)

mixture, ordered (f)

mixture, unordered (mix)

modification (mod)

monomer (mon)

multiple group (#)

SRU (n)


SRU label

To specify the SRU label for the selected brackets, click the SRU label box and enter a label.

An SRU label is a single alphabetic character that appears on the bracket of a structure-based homopolymer. The default SRU label is n, but you can change it to a different letter to show different multiplicities of polymeric or oligomeric sequences. For example:

Note: The SRU label box is available solely when you click the Bracket type box and choose SRU (n).


Bracket style

To specify the style of the selected brackets, click [image] Square [ ] or [image] Curved ( ).

The following polymer contains both squared and curved bracket styles:

Bracket style is stored with the structure in the database. However, bracket style affects solely how brackets are displayed; bracket style does not affect searching.

Note: In the polymer shown here, the subscripts p, q, and r are SRU labels.


Bracket height

To specify the height of the selected brackets, click the Bracket height box. Enter or choose a value, then choose the unit of measure.


Bracket width

To specify the width of the selected brackets, click the Bracket width box. Then, enter or choose a percent value.


Edit -- Data

Use this dialog to:

*	Change the database field associated with attached data.

*	Edit the tag character associated with attached data (including changing the tag position)

Click any of the following items:

Field name

Field type/Field format

Query

Tag character

Tag position

Thickness

Color

OK, Cancel

For more information and examples of attached data, see Drawing Mixtures: MDL Requirements for Database Searching and Registration.


Field name

To specify a substance group (Sgroup) database field to associate with the attached data that you selected, click the Field name box and enter or choose a field name.


Query

To edit a text/numeric query associated with the attached data that you selected, click the Query box and choose a search operator.


Tag character

To edit the tag character associated with the attached data that you selected, click the Character box and enter a one-character tag.


Tag position

To change the position of the tag character associated with the attached data that you selected, click the Position box and choose a position.


Settings -- Bracket

Use this dialog to:

*	Set defaults for the appearance of brackets.

Click any of the following items:

Bracket height

Bracket width

Automatically add * atoms

OK, Cancel

Save, Save As, Read

For more information on how to work with ISIS/Draw settings, click here.


Bracket height

To specify the default height for brackets, click the Bracket height box. Enter or choose a value, then choose the unit of measure.


Bracket width

To specify the default width for brackets, click the Bracket width box. Then, enter or choose a percent value.


Automatically add *atoms

To specify that *atoms be added when you create brackets on terminal bonds with implicit carbon end groups, set [image] Automatically add * atoms.


Attach Data to Objects

Use this dialog to:

*	Attach data (with or without tags) to brackets, or to atoms or bonds.

*	Attach a text or numeric query to brackets or to atoms and bonds for an SSS/Poly search.

*	Edit attached data, tags, and queries: Click [image], then click the item and edit it as you would normal text.

Click any of the following items:

Field name

Field type/Field format

Query

Show instructions

Done

Cancel

For information and examples of attached data in polymers, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

For information and examples of attached data in non-polymer structures, see Drawing Mixtures: MDL Requirements for Database Searching and Registration.


Field name

To specify a Substance group (Sgroup) database field that you want associated with the attached data, click the Field name box and enter or choose a field name.


Field type/Format string

Displays the type of data stored in the field listed in the Field name box.

If the database field is a formatted text field, additionally displays the field format.


Query

To specify a text/numeric query for attached data in an SSS/Poly search, click the Query box and choose a search operator, then click in the drawing area enter the target value for the data.


Text/Numeric Queries For Attached Data

In an SSS/Poly search, you can specify a text/numeric query that specifies the retrieval of structures in which the attached data meets the conditions that are specified by the text/numeric query. A text/numeric query contains a search operator (such as <) and a text or numeric target value (such as 25% mole fraction) that you want to find. For example, to find copolymers that contain less than 25% polystyrene, attach the text/numeric query < 25 to the monomer brackets of polystyrene:


Show Instructions

To view instruction on how to use the Attach Data to Objects dialog, set [image] Show instructions.


Done

To close the dialog and save the association between the database field that you selected and the data that you entered, click Done.


Cancel

To close the dialog without saving the last change that you made, click Cancel.


Molecular Calculations Settings

Use this dialog to:

*	Set defaults for the Chemistry > Calculate Mol Value command.

Click any of the following items:

Default Display

Edit Labels...

Use Custom table for Exact mass

Number of decimals places displayed


Default Display

To specify that calculated values be automatically pasted into the sketch when you choose Chemistry > Calculate Mol Value, set [image] Paste into sketch.

To specify that the Molecular Values dialog displays when you choose Chemistry > Calculate Mol Value, set [image] Prompt.


Edit Labels

To edit the field labels that are pasted along with the calculated values into the sketch, click Edit labels...

In the Edit Labels dialog, edit the labels and click OK.


Use Custom Table for Exact Mass

Use this procedure to specify the values that ISIS/Draw uses when it calculates the exact mass:

1.	Set [image] Use Custom table for exact mass.

2.	Do one of the following:

*	Enter the full path of the mass table file that you want to use.

*	Click Browse... and navigate to the location of the mass table file that you want to use. Then, click Open.

3.	Click OK.

Note: MDL provides the file molmass.tbl, which is a text file that contains standard molecular mass values. To create your own custom mass table, make a copy of molmass.tbl and edit it as needed.


Number of decimal places displayed

To specify the number of decimal places displayed when you paste calculated values into a sketch, enter a number from 0 to 6.


Beilstein Generic

Use this dialog to:

*	Include specific types of atoms (atom generics) at specified positions on your structure query. Use this dialog only when you are using ISIS/Draw to create a structure query for a Beilstein database.

*	Include specific types of functional groups (group generics), such as alkyl groups (ALK), heterocyclics (CHC), or aryl groups (ARY) at specified positions on your structure query. Use this dialog only when you are using ISIS/Draw to create a structure query for a Beilstein database.

Notes for ISIS Users:

*	The atom generics A and Q are equivalent to the ISIS query atoms A and Q, and can be used in queries for MDL databases. Other atom generics (for example AH, X, XH) nave no equivalents in ISIS, and can not be used in queries for MDL databases.

*	You can not use any Beilstein group generics in queries for MDL databases.

Notes for Beilstein Users:

*	You can not use this dialog to exclude Beilstein atom generics (for example, ~X, ~M, and so forth). Instead, you must use the ISIS atom query feature Not List to specify the atoms that you want to exclude. For more information on the Not List atom query feature, click here.

*	To define your own list of atoms to include (that is, to draw a user-defined generic atom), use the ISIS atom query feature List. For more information on the List atom query feature, click here.

*	To define your own generic groups to include at specified positions on your query (that is, to draw a user-defined generic group), use the Rgroup query features. For more information on Rgroup query features, click here.

*	Asterisks on atom generics G* and GH* extend search results for these groups to include structures with ring closure.

Click any of the following items:

Atom Generics

Group Generics


Atom Generics

Use atom generics to retrieve molecules that include or exclude atoms at specified positions. The following atom generics are available for searching the Beilstein database:

A	Any atom except hydrogen

AH	Any atom, including hydrogen

Q	Any atom except C or H

QH	Any atom except C

M	Any metal

MH	Any metal or hydrogen

X	Any halogen

XH	Any halogen or hydrogen


Group Generics

Click [image] to print, or click [image] to close this Request-A-Document.

Use group generics to retrieve structures with specific types of functional groups at specific positions on a molecule. Use group generics only on queries that you draw for Beilstein databases.

Group names that end in H allow either the group or hydrogen at that position. For example, ALK represents an alkyl group, while ALH represents an alkyl group or hydrogen.

On the Beilstein Generic dialog, the groups are arranged with the most generic groups at the top of the dialog, and the least generic at the bottom. The following figure shows this (for clarity, we omit groups whose symbols end in H):

Group names that are marked with an asterisk (G*, GH*) retrieve additional structures in which an atom in the group can be linked with an atom in the rest of the structure to form a ring (ring closure). For examples of searches with and without ring closure, click here.


Ring Closure

The following examples illustrate the difference in search results between the generic group (G) and the generic group (G*) that allows ring closure between the group and the rest of the structure:

Exclude structures with ring closure

Include structures with ring closure


Beilstein Databases

The following databases are available from Beilstein Informationsysteme GmbH:

*	CrossFire plusReactions

*	CrossFire Abstracts

*	CrossFire EcoPharm

*	CrossFire Gmelin

Beilstein Data: Copyright (c) 1990-1999, Beilstein Institut fuer Literatur der Organischen Chemie and is licensed to Beilstein Chemiedaten und Software GmbH and Beilstein Informationsysteme GmbH. All rights reserved.

Gmelin Data: Copyright by Gmelin Institut fuer Anorganische Chemie und Grenzgebiete der Max-Planck-Gesellschaft zur Foerderung der Wissenschaften.


Beilstein Atom and Group Generics

Use Beilstein atom and group generics on your structure query for Beilstein databases only:

*	Beilstein atom generics allow you to include specific types of atoms at specified positions on your structure query. For more information on Beilstein atom generics, click here.

*	Beilstein group generics allow you to include specific functional groups, such as alkyl groups (ALK), heterocyclics (CHC), or aryl groups (ARY) at specified positions on your structure query. For more information on Beilstein group generics, click here.

For information on how to specify a Beilstein atom or group generic to your query, click here.


To specify a Beilstein generic atom or group on a query

Use the following procedure to specify Beilstein atom and group generics on your structure query for Beilstein databases only:

1.	Select an atom.

2.	Double-click the selected atom.

3.	Click the Query Atom tab.

4.	Click the Symbol box.

5.	Choose Beilstein Generics.

6.	Click the Beilstein generic atom or group that you want to add to your query.

7.	Click OK.


Creating and Editing Forms

What is a form and why do I need one?

Differences Between ISIS and Other MDL Products

What are my alternatives?

*	Open a form

*	Import a form

*	Create a new form

*	Edit an existing form

*	Save a form

*	Export a form

What is new in forms in ISIS/Base?


To create a new form

Do these steps in the order shown:

(This procedure assumes that a database is already open).

1.	Clear the screen of an existing form.

2.	Print or view a list of your database fields.

3.	Determine the type of form that you need.

4.	(Optional) Use the ruler for precise measurements.

5.	Do one of the following:

*	Create a box

*	Create a table

6.	(Optional) Add text, graphics, or lines to the form.

7.	(Optional) Edit the form.

8.	Save the form.


To create a box

Box Creation Exercise

Do these steps in the order shown:

1.	You can create boxes using the following alternatives:

*	Draw a box outline

*	Duplicate a box

*	Make multiple copies of a box

*	Divide a box into smaller boxes of equal size

2.	Do one of the following:

*	Connect the boxes to database fields

*	Set boxes to use default data (form calculation, today's date, sketch, or text string)

3.	(Optional) Edit a box (set chemical or text data display, change the label and data fonts, and so on).


To create a table

Table Creation Exercise

Do these steps in the order shown:

1.	Determine the type of table that you need (simple, layered, or uncoupled table)

2.	Draw one or more table outlines

3.	Do one of the following:

*	Add and connect columns to database fields

*	Set columns to use default data (form calculation, today's date, sketch, or text string)

4.	(Optional) Edit a table (set chemical and text data display, change the heading and data fonts, and so on).


What is a form and why do I need one?

A form is a set of boxes and/or tables.

You need a form to:

*	Hold a search query

*	Display search results

*	Print search results

*	Register/update database records


Importing a Form

Click here for step-by-step instructions

You import a form to retrieve a form that was saved as a form file on disk. If there is a form already open on the screen, ISIS/Base will close it before importing the form.

If you need more information on the type of form to import, see Determine the type of form that you need.


Exporting a Form

Click here for step-by-step instructions

You export a form to save it as a form file on your disk instead of as an object inside of the database. Form files can be shared between databases and transferred across PC and Macintosh platforms.


Creating a New Form

Click here for step-by-step instructions

To create a new form, you draw boxes and/or tables. Then, you connect the boxes and/or tables to the database fields that are associated with the data that you want to view or register.


Editing an Existing Form

Click here for step-by-step instructions

To edit a form, you make changes to a form that already exists. There are many options that allow you to edit a form. For example, you can change a field that is connected to a box or column, change the font and color of labels and data, or change the display of structures.


Printing or Viewing a List of Your Database Fields

Click here for step-by-step instructions

Before you create a new form, it is important that you print or view a list of your database fields to understand the database definition. Do not make assumptions about your database definition based on experience with other MDL programs. For example, a flat database in MACCS-II is hierarchical in ISIS.

We recommend that you print a list of database fields, because it is difficult to see the relationship of fields when scrolling through a list box.


Adding Text or Titles to a Form

Click here for step-by-step instructions

You can add unattached text to a form to create titles or captions. This text is usually located at the top, bottom, or sides of the overall form. This type of text is not to be confused with the text that appears inside of a box or column. The text inside of a box or column is the label or the field name to which the box or column is connected.


Adding Lines to a Form

Click here for step-by-step instructions

You can add unattached lines to a form, for example, to emphasize part of the form or to underline titles.


Adding Graphics to a Form

Click here for step-by-step instructions

ISIS/Base accepts many types of graphics that you can add to a form and save as part of the form. For example, you could include a company logo as part of the form.

The following list shows the valid graphic types on the PC and Macintosh.

On the PC:

ISIS/Draw sketch

Metafile

OLE object

On the Macintosh:

ISIS/Draw sketch

PICT


Creating a Box

Click here for step-by-step instructions

To create a box, you draw one or more box outlines. Then, you connect each box to a field in the database to view or register data.


Labeling and Connecting Boxes to Database Fields

Click here for step-by-step instructions

After you create a box outline, you must connect it to a field in the database to register, search, or view data inside of the box. When you connect a box to a field, you instruct ISIS/Base to fill the box with data for that field only.

You can also provide a label for a box to identify what type of data the box will hold. Use any label that you think will be meaningful for viewing or registering data.


Creating a Table

Click here for step-by-step instructions

To create a table, you draw a table outline first. Then, you add and connect columns to database fields.


Adding and Connecting Columns to Database Fields

Click here for step-by-step instructions

After you create a table outline, you can add and connect columns to database fields. When you connect a column to a database field, you instruct ISIS/Base to fill the column with data for that field only.

You can also provide column headings to identify what type of data each column will hold. Use any headings that you think will be meaningful for viewing or registering data.


To open a form

Use this procedure to open a form that is saved inside of the database or remote-access file. If there is an existing form on the screen, ISIS/Base closes the form before it opens another form. This procedure assumes that a database is already open.

Note: If you need more information on the type of form to open, see Determine the type of form that you need.

1.	Choose File > Open Form.

2.	Select the name of the form that you want to open. (If there are no forms listed, you can create a new form.)

3.	(Optional) To make this form the default form that appears on the screen whenever you open the database, click Set Default.

4.	Click OK.


To import a form

This procedure assumes that a database is already open.

1.	Choose File > Import > Form. (To retrieve a PC-form file on the Macintosh, press and hold the Option key while you complete this step.)

2.	Navigate to where the form is located on your disk, and then click the form name in the Files list box.

3.	Click OK. The form appears in the ISIS/Base window.

4.	To save the form in the current database, choose File > Save Form. Enter a name for the form, and then click OK.


To save a form

Use this procedure to save the current form inside the database.

1.	Click the Forms button.

2.	Do one of the following:

*	To save a new form or an existing form under the same name, choose File > Save Form. For new forms only, enter a name and an optional description for the form.

*	To save an existing form under a new name, choose File > Save Form As. Enter a name and an optional description for the form.

3.	Click OK. The form is saved inside the database and you will not see it as a separate form file on disk.


To export a form as an ISIS form file

1.	Choose File > Export > Form. (Mac: To save a form that will be opened on the PC, press and hold the Option key while you complete this step.)

2.	Enter a name for the form in the File Name box.

3.	Click OK (Mac=Save).


To transfer PC files created in ISIS to the Macintosh

1.	Copy the PC ISIS-file that you exported as a file on your hard disk to a disk that you can access from Apple File Exchange on the Macintosh.

2.	Start Apple File Exchange, and choose the drive that contains the form file to transfer.

3.	Uncheck all of the options in the top half of the Mac to Mac menu.

4.	Choose Mac to Mac > Text Translation.

5.	You require the following settings:

*	 MS-DOS to Mac.

*	Activate the Replace CR with CR/LF.

*	Special Characters:  Neither.

*	Tab Characters:  Neither.

9.	Click OK.

10.	Select the ISIS file, and then click Transfer.

11.	Exit Apple File Exchange.

12.	Start ISIS on the Macintosh and import the file holding down the Option key while you choose the File > Import type.


To open a database

1.	Choose File > Open Database.

2.	Change to the appropriate directory (Mac=folder) if necessary.

3.	Click the name of the database or remote-access file that you want to open.

4.	Click OK (Mac=Open). If a password is required, you see a prompt to enter it.

If you are opening a remote-access file, enter the network connectivity information that you received from your ISIS Administrator.


To clear the screen of an existing form

Use this procedure to close an existing form on the screen. You can then open, import, or create a new form.

1.	Click the Forms button.

2.	Choose File > New Form. ISIS/Base will prompt you to save the form changes, if needed, before closing the form.


To use the ruler for precise measurement

Use the ruler to precisely measure the overall size of a form. For example, you might want to use the ruler to create a form that fits on 8 1/2 x 11 inch paper.

1.	Click the Forms button.

2.	Choose Options > Show Ruler. You see the horizontal and vertical rulers.

3.	(Optional) You can also do the following:

*	To make boxes and tables align to specific points on the ruler, choose Options > Snap to Ruler.

*	To change the units of measurement or reset the divisions, 	choose Options > Ruler Settings. Choose Inches or Centimeters for the unit of measurement. If required, choose a new ruler division from the Divisions box. Click OK.


To print or view a list of database fields

1.	Choose Database > View Definition. You see a list of the database fields.

2.	To print a list of the fields with their field information, click Save As Text File.

3.	Enter a filename to save the list of database fields. (PC=Use the .TXT default file extension.)

4.	Click OK. By default, ISIS/Base creates the ASCII file in the same directory (Mac=folder) in which the current database is located.

5.	Click Close.

6.	Open a word-processing program, and then open the ISIS file.

7.	Select the entire document and change the font to a fixed-width font, such as Courier. If you do not use a fixed-width font, the fields will not align properly. The field alignment shows how the fields are related.

8.	Print the file, and then return to the ISIS/Base program.


To draw a box outline

Use this procedure to draw one or more box outlines of any size and shape in your form.

1.	Click the Forms button.

2.	Click [image].

3.	Position the mouse where you want to begin drawing the box outline. For example, where you want to position the top-left corner of the box.

4.	Click and drag the mouse in an outwards direction. You see a box outline appear.

5.	Release the mouse when you have drawn a box at the desired size and shape.

6.	(Optional) Repeat these steps to draw additional boxes of any size and shape. To overlap boxes so that they appear to be connected, position the mouse over the corner of an existing box before you draw a new box.


To duplicate a box

Use this procedure to duplicate a box to make multiple boxes of the same size. (This procedures assumes that you have already drawn at least one box outline.)

1.	Click the Forms button.

2.	Click [image].

3.	Select the box that you want to duplicate.

4.	Choose Edit > Duplicate.

5.	Move the duplicate box to a new position.

6.	(Optional) Repeat these steps to make additional duplicate boxes.


To create multiple copies of a box

Use this procedure to make rows and/or columns of boxes that are of equal size and distance apart. (This procedures assumes that you have already drawn at least one box outline.)

1.	Click the Forms button.

2.	Click [image].

3.	Select the box that you want to copy.

4.	Choose Object > Multiply Box.

5.	Do at least one of the following:

*	To repeat a box across or down the form, enter a number in the Horizontal Repeats box or the Vertical Repeats box, respectively.

*	To allow spacing between each box across or down the form, enter a number in the Horizontal Spacing box or the Vertical Spacing box, respectively.

6.	Click OK. The new boxes are arranged in rows and columns as specified.


To divide a box into multiple boxes

Use this procedure to divide an existing box into two or more smaller boxes of equal size. (This procedures assumes that you have already drawn at least one box outline.)

1.	Click the Forms button.

2.	Click [image].

3.	Select the box that you want to divide.

4.	Choose Object > Partition Box.

5.	Do one of the following:

*	To divide a box horizontally into two or more boxes, enter the number of new boxes in the Horizontal Partition box.

*	To divide a box vertically into two or more boxes, enter the number of new boxes in the Vertical Partition box.

6.	Click OK. The original box is divided into the specified number of new boxes.


To label and connect boxes to database fields

1.	Click the Forms button.

2.	Click [image].

3.	Select a box.

4.	Choose Object > Box Properties, and then click the Field Name tab.

5.	To connect to a database field, select a field name from the Database fields list box. You see the selected field in the Field name box.

6.	(Optional) Enter a label in the Label box to identify the type of data the box will hold.

7.	(Optional) Click Next or Previous to move to the next or previous box in the form to label and connect to a field.

8.	Click OK.

Alternative method to label a box


Alternative method

Close the Box Properties dialog box if it is open. Click [image]. Then, click in the box and enter the text for the label.


To locate fields in a database listing

Use this procedure to locate a field name in a long database listing instead of scrolling through the list of fields.

1.	Click in the Field Name box.

2.	Enter the name of the field that you want ISIS/Base to locate. If you enter a path to a field, use a '>' after each parent field. For example: RXN>VARIATION>LITREF>journal.

If the field exists, the Database fields list box scrolls to highlight the appropriate path in the database hierarchy.

3.	Click Back (at the top of the screen) to return to the previous screen and continue at Step 6.


To draw one or more table outlines

1.	Click the Forms button.

2.	Click [image].

3.	Press and drag the mouse to draw a table outline.

4.	Release the mouse to fix the size and shape of the table outline. The table outline has one column and a horizontal bar called the header bar. Later, when you view data, you see that the header bar separates the column headings from the data that displays in the table.

5.	(Optional) To add another table to the form, do one of the following:

*	To add another table of a different size or shape, repeat this procedure.

*	To make an exact copy of the existing table, click [image]. Select the perimeter of the table outline, and then choose Edit > Duplicate. Drag the duplicate table outline to a new position.


To add and connect columns to database fields

1.	Click the Forms button.

2.	Click [image].

3.	Select the perimeter of the table.

4.	Choose Object > Table Properties, and then click the Field Name tab.

5.	Do one of the following:

*	Connect a column to one field at a time

*	Connect columns to multiple fields at one-level of the database hierarchy

*	Add a blank column with no field connection

6.	(Optional) To provide column headings, select a field name in the Columns list box. Click in the Column label box, and enter a label. Press Enter. Repeat this step to label all of the headings.

7.	(Optional) You can also replace, delete, or reorder columns in the table.

8.	Click OK.


To connect a column to one field at a time

1.	Select a field name in the Database fields list box.

2.	Click Add. ISIS/Base adds a column for the selected field and creates a simple table.

3.	(Optional) Repeat these steps to add another column to the table. If you have a hierarchical database, you can create a layered or uncoupled table depending on the fields that you select.

4.	Click Back (at the top of the screen) to return to the previous screen and continue at Step 5.


To connect columns to multiple fields at one level of the database hierarchy

1.	Select a parent field name in the Database fields list box.

2.	Click Add. ISIS/Base creates a columns for each field below the selected parent field.

3.	Click Back (at the top of the screen) to return to the previous screen and continue at Step 5.


To add a blank column

1.	Highlight the name of the field in the Columns list box that will precede the blank column.

2.	Select No Field in the Database fields list box.

3.	Click Add.

4.	Click Back (at the top of the screen) to return to the previous screen and continue at Step 5.


To remove a field from a box or column

1.	Click the Forms button.

2.	Click [image].

3.	Select the box or column that you want to change. (To select a column, you must select the field name inside of the column.)

4.	Choose Object > Box Properties or Object > Column Properties.

5.	Click the Field Name tab.

6. In the Database fields list box, double-click No Field to select it.

7. Click OK. You see "(no field)" appear inside of the box or column in place of a field name.


To replace a field that is connected to a column

1.	Select the name of the field in the Columns list box that you want to replace.

2.	Select a new field in the Database fields list box.

3.	Click Replace.

4.	Click Back (at the top of the screen) to return to the previous screen and continue at Step 7.


To reorder columns in the table

1.	Select the name of the field in the Columns list box that you want to reorder.

2.	Do one of the following:

*	To move the column to the left, click the down arrow under Reorder columns

*	To move the column to the right, click the up arrow under Reorder columns

3.	 (Optional) Repeat these steps to reorder additional columns.

4.	Click Back (at the top of the screen) to return to the previous screen and continue at Step 7.


To delete a column

1.	Select the name of the field in the Columns list box that you want to delete.

2.	Click Delete to remove the column.

3.	Click Back (at the top of the screen) to return to the previous screen and continue at Step 7.


To add unattached text to the form

1.	Click the Forms button.

2.	Click [image].

3.	Do one of the following:

*	Create a single line of text. Click in the form-drawing area, and then type a line of text.

*	Create a paragraph of text. Click in the form-drawing area, and then drag a paragraph text-box of any size. Release the mouse to fix the size, and then type the text.

4.	Click another tool or in the drawing area to end the text.


To add unattached lines to a form

1.	Click the Forms button.

2.	Click [image].

3.	Press and drag the mouse in any direction to draw a line.

4.	Release the mouse button to fix the end of the line.


To add graphics to a form

1.	Click the Forms button.

2.	Start an application and create or retrieve a graphic.

3.	Cut or copy the graphic onto the Clipboard.

4.	Return to ISIS/Base, and click the Forms button.

5.	Paste the graphic into the drawing area. You can then position the graphic in the blank drawing area, over a box or table, or overlapping any part of the form.


To edit an existing form

This procedure assumes that you already have a database and form open.

Note: You can Undo many of the changes that you make when you edit a form.

1.	(Optional) Create a new box, create a new table, or create a new column in an existing table.

2.	(Optional) Change the field that is connected to a box or column.

3.	(Optional) Edit one of the following:

*	Boxes, or Columns, or Tables

*	Box labels or column headings

*	Chemical display of structures

*	Text or numeric data display

*	Lines or Text

*	Entire form

4.	Save the form.


To undo a change

Use this procedure to immediately reverse a change that has just been made to a form.

1.	In the Forms mode, choose Edit > Undo immediately to reverse a change to your form. If the menu command is not available, then the change cannot be reversed.


Changing the Field that is Connected to a Box or Column

To change the data that displays in a box or column, you change the field name that is connected to the box or column. Choose one of the following options for step-by-step instructions:

*	To change a field that is connected to a box

*	To change a field that connected to a column


Creating a New Column in an Existing Table

Click here for step-by-step instructions

To add a column to an existing table, you have the choice of connecting the column to a field in the database or creating a blank column to separate columns of data.


To create a new column in an existing table

1.	Click the Forms button.

2.	Click [image].

3.	Select the perimeter of the table.

4.	Choose Object > Table Properties, and then click the Field Name tab.

5.	View the Columns list box to decide where you want to add the new column in relation to the other columns in the table. Highlight the field that will precede the new column.

6.	Do one of the following:

*	To add a column that is connected to a database field, select the field in the Database fields list box.

*	To add a blank column, select No Field in the Database fields list box.

7.	Click Add.

8.	(Optional) To create a column heading, enter a title in the Column label box.

9.	Repeat Steps 4 through 7 to add additional columns to the table.

10.	Click OK.


To change a field that is connected to a box

1.	Click the Forms button.

2.	Click [image].

3.	Select a box.

4.	Choose Object > Box Properties, and then click the Field Name tab.

5.	To change the field to which the box is connected, select a field in the Database fields list box.

6.	(Optional) To change the box label, enter a name in the Label box.

7.	Click OK.


To replace a field that is connected to a column

1.	Click the Forms button.

2.	Click [image].

3.	Select a field name or label inside of a column.

4.	Choose Object > Column Properties, and then click the Field Name tab.

5.	To change the field to which the column is connected, select a field in the Database fields list box.

6.	Click Replace.

7.	(Optional) To change the column heading, enter a name in the Column label box.

8.	Click OK.


Editing Boxes

To edit boxes in a form, you have the following options:

Adjusting:  Resize,  Move,  Align,  Delete

Styling:  Show or hide borders,  Change the color, width, or style of borders,  Change the fill pattern or fill color

Changing the data display:  Change the display of chemical data,  Change the display of text/numeric data,  Hide a box and its data,  Change the label that identifies the data,  Change a field connected to a box,  Remove a field that is connected to a box,  Display default data (today's date, sketch, text string)

Adding functionality:  Create a form calculation,  Attach a PL function


Showing or Hiding the Borders of a Box

Click here for step-by-step instructions

You can hide the borders of one or more boxes to simplify or change the appearance of a form.

Here, you see the borders for all of the boxes:

Now, you see the same form with some of the box borders hidden:


To show or hide the borders of a box

1	Click [image].

2.	Select the box.

3.	Choose Object > Box Properties, and then click the Border/Pattern tab.

4.	Do one of the following:

*	To hide the borders of a box, for example to hide the right border of the box, you require this setting: right.

*	To show the borders of a box, for example to show the right border of the box, you require this setting: right.

6.	Click OK.


To change the color, width, or line style of box borders

1.	Click [image].

2.	Select one or more boxes.

3.	Choose Object > Box Properties, and then click the Border/Pattern tab.

4.	You have the following alternatives:

*	To change the color of the box border, click the Style Border Color box, and choose a color.

*	To change the width of the box border, click the Style Border Width box, and choose a width.

*	To change the line style of the box border, click the Style Border Style box, and choose a line style.

5.	Click OK.


To fill the inside of a box or column with a color or pattern

1.	Click [image].

2.	Do one of the following:

*	To use a pattern or color inside of a box, select the box, and then choose Object > Box Properties.

*	To use a pattern or color inside of a single column, select the column, and then choose Object > Column Properties.

*	To use a pattern or color inside all of the columns in a table, select the perimeter of the table, and then choose Object > Table Properties.

3.	Click the Border/Pattern tab.

4.	(Optional) Click in the Fill Color box and choose a color.

5.	(Optional) Click in the Fill Pattern box and choose a pattern style.

6.	Click OK.


Making a Box Invisible

Click here for step-by-step instructions

You can instruct ISIS/Base to make one or more boxes in a form completely invisible while searching, browsing, or updating a database. An invisible box completely hides the data contents. For example, you might want to make a box invisible to hide confidential data, the results of a calculation, or a Procedural Language function.


To make a box invisible

1.	Click the Forms button.

2.	Select the box you want to make invisible.

3.	Choose Object > Box Properties, and then click the Function tab.

4.	(Optional) To make a box invisible, you require this setting: Invisible box.

5.	Click OK. To make the box visible again, click the Forms button. You see the contents of the box.


Editing Columns and Tables

To edit a table, you have the following options:

Adjusting tables:  Resize the table header,  Resize the table,  Move,  Align,  Delete

Adjusting columns:  Reorder,  Resize,  Delete

Styling:  Fill column with color or pattern,  Change the color, width, or style of borders  Show/hide table header-bar,  Show/hide column dividers,  Show/hide row dividers,  Show/hide table borders

Changing the data display:  Change the display of chemical data,  Change the display of text/numeric data,   Show/hide repeating data,  Add new columns to display data,  Change a field connected to a column,  Display default data (today's date, sketch, text string)

Adding functionality:  Create a form calculation,  Attach a PL function


To resize the height of the table header

A table header is the area at the top of the table that contains the column headings for each column. You can resize the width of the table header, for example to accommodate a column heading that wraps onto multiple lines.

1.	Click [image].

2.	Select the table header-bar. You see selection handles on both ends of the header-bar.

3.	 Click in the middle of the header bar and drag your mouse up or down to resize the header.

4.	Release the mouse to fix the new height.


To show or hide row dividers

Use this procedure to show or hide the horizontal lines that separate each record in a table.

1.	Click [image].

2.	Select the perimeter of a table.

3.	Choose Object > Table Properties, and then click the Border/Pattern tab.

4.	Do one of the following;

*	To hide row dividers, you require this setting: Show Style Row dividers.

*	To show row dividers, you require this setting: Show Style Row dividers.

5.	Click OK.


Showing or hiding column dividers

Column dividers are the vertical lines that separate the columns in a table. Each column has a column divider, located to the right of the column that you can show or hide. Choose one of the following procedures for step-by-step instructions:

*	To show or hide all of the column dividers

*	To select specific column dividers to show or hide


To show or hide all column dividers in a table

1.	Click [image].

2.	Select the perimeter of a table.

3.	Choose Object > Table Properties, and then click the Border/Pattern tab.

4.	Do one of the following:

*	To hide column dividers, you require this setting: Show column divider(s).

*	To show column dividers, you require this setting: Show column divider(s).

5.	Click OK.


Showing or hiding the table header-bar

Click here for step-by-step instructions

A table header is the area at the top of the table that contains headings for each column. The column headings are separated from the data in the table by a header bar.


To hide or show the table header-bar

1.	Click [image].

2. Select the perimeter of a table.

3. Choose Object > Table Properties, and then click the Border/Pattern tab.

4. Do one of the following;

*	To hide the header bar, you require this setting: Show Style Header bar.

*	To show the header bar, you require this setting: Show Style Header bar.

5. Click OK.


Showing or hiding the borders of a table

Click here for step-by-step instructions

You can hide one or more sides of a table to simplify or change the appearance of the form.


To hide or show the borders of a table

1.	Click [image].

2.	Select the perimeter of a table.

3.	Choose Object > Table Properties, and then click the Border/Pattern tab.

4.	Do one of the following:

*	To hide the borders of a table, for example to hide the right border, you require this setting: Show Borders right.

* 	To show the borders of a table, for example to show the right border, you require this setting: Show Borders right.

5.	Click OK.


Showing or hiding repeating data in a table

Click here for step-by-step instructions

Repeating data occurs in tables that combine fields from different but sequential levels of a database. For any one record, the data for one level repeats itself in the table until all of the next level data displays.


To show or hide repeating data in a table

1.	Click [image].

2.	Select the perimeter of a table.

3.	Choose Object > Table Properties, and then click the Field Name tab.

4.	Do one of the following:

*	To show repeating data in a table, you require this setting: Show repeating data.

*	To hide repeating data in a table, you require this setting: Show repeating data.

5.	Click OK.


To change the color, width, or line style of borders/dividers in a table

1.	 Click [image].

2.	Select the perimeter of a table.

3.	Choose Object > Table Properties, and then click the Border/Pattern tab.

4.	You have the following alternatives:

*	To change the table border, click in the Color, Width, or Style boxes under Style Borders, and choose a new option.

*	To change the table-header bar, click in the Color, Width, or Style boxes under Header Bar boxes, and choose a new option.

*	To change the row dividers, click in the Color, Width, or Style boxes under Row Dividers, and choose a new option.

5.	Click OK.


To resize a column

Use this procedure to resize a column without changing the size of the overall table.

1.	Click the Forms button.

2.	Click [image].

3.	Click on the column divider that is located to the right of the column you want to resize. You see a <- l -> cursor.

4.	Drag the column divider to the left or right to decrease or increase the size of the column to match the size of the data.

5.	Release the mouse to fix the new width.

Alternative method


Alternative method

To resize a single column and preserve the width of all the other columns in the table, press and hold the Ctrl key (Mac: Command key) as you drag the column divider. The table size increases or decreases to accommodate the change in the column width.


To reorder columns in a table

1.	Click the Forms button.

2.	Click [image].

3.	Select the perimeter of a table.

4.	Choose Object > Table Properties, and then click the Field Name tab.

5.	Select the column to reorder in the Columns list box.

6.	Click the up or down Reorder columns arrow as many times as you require to move the column into a new order.

7.	 (Optional) Repeat Steps 4 and 5 to reorder additional columns.

8.	Click OK.


To delete a column

1.	Click the Forms button.

2. Click [image].

3.	Select the perimeter of a table.

4.	Choose Object > Table Properties, and then click the Field Name tab.

5.	Select the field name in the Columns list box that is connected to the column that you want to delete.

6.	Click Delete.

7. Click OK.

Alternative method


Alternative method

Click on the field name inside of a column. Choose Edit > Cut, or press the Delete key.


To select column dividers to show or hide in a table

1.	Click the Forms button.

2.	Click [image].

3.	Select a field name inside of a column.

4.	Choose Object > Column Properties, and then click the Border/Pattern tab.

5.	Do one of the following:

*	To hide the right column divider, you require this setting: Show column dividers.

*	To show the right column divider, you require this setting: Show column dividers.

6.	Click OK.


Editing Box Labels or Column Headings

Use this option to change the display of box labels or column headings. A box label or column heading is text that you assign to a box or column to identify the data contents.

You have the following options:

*	Change the position

*	Change the color

*	Change the font, font size, or style

*	Change the wording


To change the wording of a box label or column heading

1.	Click the Forms button.

2.	Click [image].

3.	Select the part of the label/column heading that you want to change.

4.	Enter new text to replace the selected text.

5.	Click outside of the label to complete the change.

6.	(Optional) To change the font properties, select the part of the text that you want to change. Choose Object > Font. Select the font properties that you want, and then click OK.


To change the font of box labels and column headings

Use this procedure to change the font, font size, and font style of labels in boxes and columns in your form.

1.	Click the Forms button.

2.	Click [image].

3.	Select a box label or column heading.

4.	(Optional) Shift-click additional box labels and/or column headings that you want to change.

5.	Choose Object > Font. Select the font properties that you want to apply.

6.	Click OK.

Alternative method


Alternative method

This method allows you to make multiple changes to the label from one dialog box. For example, you can change the font, color, and position of the label.

(1) Select one or more boxes or tables (you cannot select both boxes and columns using this method). (2) Choose Object > Box Properties or Object > Table Properties. (3) Click the Data/Label tab, and then click Font (for label). (4) Choose the font properties that you want to apply. (5) Click OK. (6) Explore the other options on the dialog box (click the Help button for a description of each option). (7) Click OK.


To change the color of box labels and column headings

1.	Click the Forms button.

2.	Click [image].

3.	Select a box label or column heading.

4.	(Optional) Shift-click additional box labels and/or column headings that you want to change.

5.	Choose Object > Pen Color, and then choose a color.

Alternative method


Alternative method

This method allows you to make multiple changes to the label from one dialog box. For example, you can change the color, font, and position of the label.

(1) Select one or more boxes or tables (you cannot select both boxes and columns using this method). (2) Choose Object > Box Properties or Object > Table Properties. (3) Click the Data/Label tab. (4) Click the Label Color box, and then choose a color. (5) Explore the other options on the dialog box (click the Help button to see a description of each option). (6) Click OK.


To change the position of a box label or column heading

1.	Click [image].

2.	Do one of the following:

*	Select a box, and then choose Object > Box Properties.

*	Select one or more columns (in Forms mode), and then choose Object > Column Properties.

*	Select the perimeter of a table, and then choose Object > Table Properties.

3.	Click in the Label Alignment box, and then choose a position.

4.	Click OK.


Editing the Display of Informational Data

Click here for step-by-step instructions

Use this option to change how text and numeric data displays in a box or column. Text and numeric data include text, formulas, real numbers, integers, ranges, and dates.


Editing the Display of Text or Numeric Data

You can edit the following display options for text/numeric data:

*	Change the font, font size, or style of data

*	Change the color of data

*	Change the position of data

*	Change the data format within a box or column

*	Display numeric data in scientific notation

*	Set the number of decimal places for numeric data


To change the font of data in boxes and columns

Use this procedure to change the font, font size, and font style of data in boxes and columns in your form.

1.	Click the Forms button.

2.	Click [image].

3.	Select a field name inside of a box or column.

4.	(Optional) Shift-click additional field names in boxes and/or columns that you want to change.

5.	Choose Object > Font. Select the font properties that you want to apply.

6.	Click OK.

Alternative method


Alternative method

This method allows you to make multiple changes to the display of data from one dialog box. For example, you can change the font, color, and position of the data.

(1) Select one or more boxes or tables (you cannot select both boxes and columns using this method). (2) Choose Object > Box Properties or Object > Table Properties. (3) Click the Data/Label tab, and then click Font (for Data). (4) Choose the font properties that you want to apply. (5) Click OK. (6) Explore the other options on the dialog box (click the Help button to see a description of each option). (7) Click OK.


To change the color of data in boxes and columns

1.	Click the Forms button.

2.	Click [image].

3.	Select a field name inside of a box or column.

4.	(Optional) Shift-click additional field names in boxes and/or columns that you want to change.

5.	Choose Object > Pen Color and select a color of your choice.

Alternative method


Alternative method

This method allows you to make multiple changes to the display of data from one dialog box. For example, you can change the color, font, and position of the data.

(1) Select one or more boxes or tables (you cannot select both boxes and columns using this method). (2) Choose Object > Box Properties or Object > Table Properties. (3) Click the Data/Label tab. (4) Click the Data Color box, and then choose a color. (5) Explore the other options on the dialog box (click the Help button to see a description of each option). (6) Click OK.


To change the position of data in a box or column

1.	Click [image].

2.	Do one of the following:

*	Select a box, and then choose Object > Box Properties.

*	Select one or more columns (in Forms mode only), and then choose Object > Column Properties.

*	Select the perimeter of a table, and then choose Object > Table Properties.

3.	Click the Data/Label tab.

4.	Click in the Data Alignment box, and choose a position.

5.	Click OK.


Changing the Data Format Within a Box or Column

Click here for step-by-step instructions

You have three options for setting how data is formatted in a box or column:

*	Display data as one continuous line

*	Wrap data to another line

*	Truncate data at the end of the line


To change the data format within a box or column

1.	Click [image].

2.	Do one of the following:

*	Select a box, and then choose Object > Box Properties.

*	Select one or more columns (in Forms mode only), and then choose Object > Column Properties.

*	Select the perimeter of a table, and then choose Object > Table Properties.

3.	Click the Data/Label tab.

4.	Click the Data Text Format box, and choose one of these options:

*	To display data as it is stored in the database, choose As Is

*	To wrap data onto a new line when it is longer than the width of a box or column, choose Wrapped

*	To truncate data that is longer than the width of a box or column, choose Truncated

5.	Click OK.


To display numeric data in scientific notation

Use the following procedure to change the display of numeric data to scientific notation.

1.	Click [image].

2.	Do one of the following:

*	Select a box, and then choose Object > Box Properties.

*	Select one or more columns (in Forms mode only), and then choose Object > Column Properties.

*	Select the perimeter of a table, and then choose Object > Table Properties.

3.	Click the Data/Label tab.

4.	Do one of the following:

*	To display numeric data in scientific notation you require this setting: Scientific notation.

*	To display numeric data as numbers with decimals, you require this setting: Scientific notation.

5. Click OK.


To set the number of decimal places for numeric data

Use the following procedure to set the number of decimal places for numeric data display.

1.	Click [image].

2.	Do one of the following:

*	Select a box, and then choose Object > Box Properties.

*	Select one or more columns (in Forms mode only), and then choose Object > Column Properties.

*	Select the perimeter of a table, and then choose Object > Table Properties.

3.	Click the Data/Label tab.

4.	Do one of the following:

*	Click the up or down arrow on the Decimal places box to increase or decrease the number of digits following the decimal place. If you choose Auto, ISIS/Base uses the number of decimal places as registered in the database.

*	Enter the number of decimals directly into the Decimal places box.

5.	Click OK.


Editing the Chemical Display of Structures

Click here for step-by-step instructions

Use this option to change how structural data displays in a box or column. Structural data includes molecules, reactions, 3D models, residues, and sequences.


To edit the chemical display of structures

You can edit the following chemical display options:

All Structures:  Standard bond length,   Atom font,   Color,   Structure display,   Query color,   Show/hide hydrogens,   Show/hide atom numbers

Abbreviated Structures:  Expand underlying structure,   Show/hide brackets

Reactions:  Reaction conditions,   Show/hide atom-atom maps,   Show/hide reacting centers,   Show/hide inversion/retention marks

3D Models:  Orient hits to query-structure

Residues:  Expand underlying structure,   Show/hide residue brackets,   Show/hide leaving groups

Sequences:  Show/hide sequence or crosslink bonds


Changing the Standard Bond Length

Click here for step-by-step instructions

Use this option to change the standard length of the bonds in a structure that you see in a box or column on the form in ISIS/Base.


To change the standard bond length of structures in an ISIS/Base form

1.	Do one of the following:

*	Select a box connected to any structure field, and then choose Object > Box Properties.

*	Select a column connected to any structure field (in Forms mode only), and then choose Object > Column Properties.

*	Select the perimeter of a table that has a column connected to a structure field, and then choose Object > Table Properties.

2.	Click the Chem Display tab.

3.	Click the Structure Display box and choose Defaults.

4.	Click in the bond length box and enter a new value in inches or centimeters.

5.	(Optional) Click Atom Font, and choose a font size that is suitable for the new bond length.

6.	Click OK.


Changing the Color of a Structure

Click here for step-by-step instructions

Use this option to change the color of a structure that you see in a box or column in an ISIS/Base form.


To change the color of a structure in ISIS/Base forms

1.	Do one of the following:

*	Select a box connected to any structure field, and then choose Object > Box Properties.

*	Select a column connected to any structure field (in Forms mode only), and then choose Object > Column Properties.

*	Select the perimeter of a table that has a column connected to a structure field, and then choose Object > Table Properties.

2.	Click the Data/Label tab.

3.	Click the Data Color box, and choose a color.

4.	Click OK.


Changing the Atom Font Attributes

Click here for step-by-step instructions

Use this option to change the font attributes (font, font size, and style) of atoms on structures in an ISIS/Base form.


To change the atom font in ISIS/Base forms

1.	Do one of the following:

*	Select a box connected to any structure field, and then choose Object > Box Properties.

*	Select a column connected to any structure field (in Forms mode only), and then choose Object > Column Properties.

*	Select the perimeter of a table that has a column connected to a structure field, and then choose Object > Table Properties.

2.	Click the Chem Display tab.

3.	Click Atom Font and choose a font, font size, and/or font style for the atom display.

4.	Do one of the following:

*	To display the atom font that you set in Step 3, click the Structure Display box and choose Defaults.

*	To scale a structure to fit inside of a box or column using the atom font size and bond length set for the box or column, click the Structure Display box and choose Defaults (scaled).

Note: If Structure Display is set to As Drawn or As Drawn (scaled) you cannot change the atom font because ISIS/Base displays the atom font in which the structure was drawn (local databases only).

5.	Click OK twice.


Changing the Structure Display Options

Click here for step-by-step instructions

Use these options to specify how a structure displays in a box or column in an ISIS/Base form:

*	As Drawn displays a structure using the bond length and font size in which it was drawn (local databases only).

*	As Drawn (scaled) displays a structure using the bond length and font size in which it was drawn, but scaled to fit the size of the box or column. (local databases only).

*	Defaults displays a structure using the bond length and atom font specified in the form.

*	Defaults (scaled) displays a structure with the bond length and atom font size set for the box or column, but scaled to fit the size of the box or column.


To change the display of a structure in a form

1.	Do one of the following:

*	Select a box connected to any structure field, and then choose Object > Box Properties.

*	Select a column connected to any structure field (in Forms mode only), and then choose Object > Column Properties.

*	Select the perimeter of a table that has a column connected to a structure field, and then choose Object > Table Properties.

2.	Click the Chem Display tab.

3.	Click the Structure Display box, and choose an option:

*	As Drawn displays a structure as it was drawn (including font, font size, bond length, and color). (local databases only)

*	As Drawn (scaled) displays a structure as it was drawn, but scaled to fit the size of the box or column. (local databases only)

*	Defaults displays a structure using the box or column properties (including font, font size, bond length, and data color).

*	Defaults (scaled) displays a structure using the box or column properties, but scaled to fit the size of the box or column.

4.	(Optional) If you chose Defaults or Defaults (scaled) in the previous step, you can:

*	Change the standard bond length of the structure. Click in the bond length box and enter a new value in inches or centimeters.

*	Change the atom font of the structure. Click Atom Font, and choose a new font or font size. Click OK.

5.	Click OK.


Showing or Hiding Atom Numbers

Click here for step-by-step instructions

An atom number is assigned to each atom as a structure is drawn ,and you can either show or hide the numbers. Use this option to display atom numbers on a structure that you see in a box or column on the form in ISIS/Base.


To show atom numbers on structures in an ISIS/Base form

1.	Do one of the following:

*	Select a box connected to any structure field, and then choose Object > Box Properties.

*	Select a column connected to any structure field (in Forms mode only), and then choose Object > Column Properties.

*	Select the perimeter of a table that has a column connected to a structure field, and then choose Object > Table Properties.

2.	Click the Chem Display tab.

3.	Click the Atom numbers box, and choose On.

4	Click OK.


Showing or Hiding Hydrogens

Click here for step-by-step instructions

Use this option to show hydrogens in a structure. These hydrogens are implicit.

ISIS does not recognize implicit hydrogens in a search query, even if you show them. Thus, to retrieve the correct search results, always use explicit hydrogens in your search query. To create an explicit hydrogen, click here.


To show or hide hydrogens on structures in an ISIS/Base form

1.	Do one of the following:

*	Select a box connected to any structure field, and then choose Object > Box Properties.

*	Select a column connected to any structure field (in Forms mode only), and then choose Object > Column Properties.

*	Select the perimeter of a table that has a column connected to a structure field, and then choose Object > Table Properties.

2.	Click the Chem Display tab.

3.	Click the Hydrogen labels box, and choose a new option.

4.	Click OK.


Highlighting the Query-Structure in Color

Click here for step-by-step instructions

For remote databases only: Use this option to highlight the original query within 2D structures, 3D structures, or reactions that are retrieved in a search. Use this option with the following search types:

*	Substructure (SSS)

*	Reaction Substructure (RSS)

*	3D Substructure (SSS3D, SSS3D/Biopoly, CFS, and CFS/Biopoly)


To highlight the query-structure in color in an ISIS/Base form

1.	Do one of the following:

*	Select a box connected to any structure field, and then choose Object > Box Properties.

*	Select a column connected to any structure field (in Forms mode only), and then choose Object > Column Properties.

*	Select the perimeter of a table that has a column connected to a structure field, and then choose Object > Table Properties.

2.	Click the Chem Display tab.

3.	Click the Query highlight box, and choose a color. To customize a color or to create a color, click the box and choose Other.... You see the Windows color scheme or Macintosh color wheel, where you can specify a new color. Consult your system documentation for information on using this feature.

Note on highlighting queries on biopolymers

4.	Click OK.

5.	(Optional) To remove query highlighting, make the query-highlight color the same color as the Data/Color on the Data/Label tab.


Orienting Structures to Match the Query-Structure

Click here for step-by-step instructions

For remote databases only: Use this option to orient 2D or 3D structures that are retrieved in a search to the three atoms that best fit the query. To use this option, you must also set Query Highlighting.


To orient structures to match the query-structure

1.	Do one of the following:

*	Select a box connected to a structure or modelstructure field, and then choose Object > Box Properties.

*	Select a column connected to a structure or modelstructure field (in Forms mode only), and then choose Object > Column Properties.

*	Select the perimeter of a table that has a column that is connected to a structure or modelstructure field, and then choose Object > Table Properties.

2.	Click the Chem Display tab.

3.	To orient structures to match the query structure, you require this setting: Orient hits to match query.

4.	Click OK.


Displaying Reaction Conditions Within a Reaction

Click here for step-by-step instructions

Use this option to create floating boxes to display reaction-condition data within a reaction. You can choose to display the data above or below the arrow, reactants, or products. For local databases only, you must first establish the reactant and product hierarchies with an external field name. Click here for more information.

Note: You cannot type reaction-condition data into floating boxes to register in a database. You use regular boxes and/or tables to register reaction-condition data. Then, you can display the reaction-condition data within the reaction using floating boxes.


To display reaction conditions within a reaction

1.	Select a box or column that is connected to a reaction field.

2.	Choose Object > Box Properties or Object > Column Properties, and then click the Floating Boxes tab.

3.	Click a No Field radio button at the position where you want to display reaction conditions. The positions include, above or below the reactant, above or below the arrow, or above or below the product.

4.	Now choose which data to display at that position. To do so, select a field from the Database field list box. You cannot use a parent field to display data.

5.	(Optional) You have the following options:

*	To display a label that is associated with the data, enter it in the Data label box. For example, Yield.

*	To display the number in scientific notation, you require this setting: Scientific notation.

*	To change the number of decimal places (real number fields only), click the Decimal places box and enter or choose a number.

*	To change the font, font size, or style of the data, click Font, and then choose a new font. Click OK.

6.	Repeat Steps 3 through 5 to set the display of other reaction conditions.

7. Click OK. You will not see reaction conditions within the reaction until you retrieve records in a search. (You cannot use floating boxes to register data. Use form boxes and/or tables instead.)


Showing or Hiding Atom-Atom Maps

Click here for step-by-step instructions

If atom-atom mapping is present on a reaction, it specifies exactly which atom in the reactant corresponds to an atom in the product. You can set individual defaults for Query, Browse, and Update modes to determine whether you show or hide atom-atom maps in those modes. For example, you might want to display atom-atom maps on a reaction query in Query mode:

However, you might not want to see the atom-atom maps when you view reactions in Browse mode.


To show or hide atom-atom maps on reactions in ISIS/Base forms

This procedure assumes that you have already atom-atom mapped a reaction and now you want to show or hide the atom maps.

1.	In any mode, choose Options > Settings > Session.

2.	Click the Atom Maps tab.

3. The Atom-Atom Maps setting allows you to individually choose to show or hide atom-atom maps in Query, Browse, and Update modes. For each mode, choose On to show atom-atom maps, or choose Off to hide atom-atom maps.

4.	(Optional) To save this change for future ISIS/Base sessions, click Save.

5.	Click OK.

See also:

To manually atom-atom map a reaction

To automatically atom-atom map a reaction


Showing or Hiding Reacting Centers

Click here for step-by-step instructions

Reacting centers indicate where specific transformations occur on a reaction. You can set individual defaults for Query, Browse, and Update modes to determine whether you show or hide reacting centers.


To show or hide reacting centers on reactions in ISIS/Base forms

1.	In any mode, choose Options > Settings > Session.

2.	Click the Atom Maps tab.

3. The Reacting Centers setting allows you to individually choose to show or hide reacting centers in Query, Browse, and Update modes. To show reacting centers, choose to display them as follows: Hash, Color, or Thickened. To hide reacting centers, choose Off.

4.	(Optional) To save this change for future ISIS/Base sessions, click Save.

5.	Click OK.


Showing or Hiding Inversion/Retention Marks

Click here for step-by-step instructions

Inversion marks specify that a stereo center must be inverted by the reaction. Retention marks specify that a stereo center must retain its configuration. You can set individual defaults for Query, Browse, and Update modes to determine whether you show or hide the stereochemical changes that are apparent in reactions. If you show the stereochemical changes, they are indicated by inversion or retention marks. The following example shows both:


To show or hide inversion/retention marks on reactions in ISIS/Base forms

1.	In any mode, choose Options > Settings > Session.

2.	Click the Atom Maps tab.

3. The Inversion/Retention setting allows you to individually choose to show or hide inversion and retention marks in Query, Browse, and Update modes. To show inversion and retention marks, choose On. To hide inversion and retention marks, choose Off.

4.	(Optional) To save this change for future ISIS/Base sessions, click Save.

5.	Click OK.


Expanding Abbreviated Structures in an ISIS/Base Form

Click here for step-by-step instructions

An abbreviated structure is all or part of a structure (molecule or reaction component) that has been abbreviated to a text label. Structures that you abbreviate keep their chemical significance, but their underlying structure is hidden. Example

You can create an abbreviated structure from any structure; however you must include the one (and only) bond that connects the part of the structure that you want to abbreviate to the rest of the structure. You can then expand an abbreviated structure to see its underlying chemical structure.

You can use queries (including reaction queries) that contain abbreviated structures to search a database using ISIS/Base. ISIS/Base uses the underlying chemistry and ignores the name.

Note: In earlier versions of ISIS/Draw, abbreviated structures were called superatoms.


To expand abbreviated structures in an ISIS/Base form

1.	Do one of the following:

*	Select a box connected to a structure or reaction field, and then choose Object > Box Properties.

*	Select a column connected to a structure or reaction field (in Forms mode only), and then choose Object > Column Properties.

*	Select the perimeter of a table that has a column connected to a structure or reaction field, and then choose Object > Table Properties.

2.	Click the Chem Display tab.

3.	To expand the name of abbreviated structures to show their underlying structures, you require this setting: Expand residues.

4.	Click OK.


Removing Brackets on an Abbreviated Structure

Click here for step-by-step instructions

Use this option to remove the brackets on either side of an expanded abbreviated structure.


To remove the brackets on an abbreviated structure in an ISIS/Base form

1.	Do one of the following:

*	Select a box connected to a structure or reaction field, and then choose Object > Box Properties.

*	Select a column connected to a structure or reaction field (in Forms mode only), and then choose Object > Column Properties.

*	Select the perimeter of a table that has a column connected to a structure or reaction field, and then choose Object > Table Properties.

2.	Click the Chem Display tab.

3.	You now have a choice:

*	To show the brackets on an expanded abbreviated structure, you require this setting: Show residue brackets.

*	To hide the brackets on an expanded abbreviated structure, you require this setting: Show residue brackets.

4.	Click OK.


Expanding Residues to Show the Underlying Structure

Click here for step-by-step instructions

Use this option to expand the abbreviated names of residues to show the underlying chemical structures.


To expand residues in ISIS/Base forms

1.	Do one of the following:

*	Select a box connected to any structure field, and then choose Object > Box Properties.

*	Select a column connected to any structure field (in Forms mode only), and then choose Object > Column Properties.

*	Select the perimeter of a table that has a column connected to a structure field, and then choose Object > Table Properties.

2.	Click the Chem Display tab.

3.	To expand residues to show their underlying structures, you require this setting: Expand residues.

4.	Click OK.


Showing or Hiding Residue Brackets or Leaving Groups

Click here for step-by-step instructions

Use this option to show or hide residue brackets or leaving groups.


To show or hide residue brackets or leaving groups in ISIS/Base forms

1.	Do one of the following:

*	Select a box connected to any structure field, and then choose Object > Box Properties.

*	Select a column connected to any structure field (in Forms mode only), and then choose Object > Column Properties.

*	Select the perimeter of a table that has a column connected to a structure field, and then choose Object > Table Properties.

2.	Click the Chem Display tab.

3.	You now have a choice:

*	To show residue brackets, you require this setting: Show residue brackets.

*	To show residue leaving groups, you require this setting: Show leaving groups.

4.	Click OK.


Showing or Hiding Sequence Bonds or Crosslink Bonds

Click here for step-by-step instructions

Use this option to show or hide the bonds between each residue in a sequence or to show or hide bonds that cross from a residue on one line of a sequence to a residue on another line of a sequence.


To show or hide sequence bonds or crosslink bonds in ISIS/Base forms

1.	Do one of the following:

*	Select a box connected to any structure field, and then choose Object > Box Properties.

*	Select a column connected to any structure field (in Forms mode only), and then choose Object > Column Properties.

*	Select the perimeter of a table that has a column connected to a structure field, and then choose Object > Table Properties.

2.	Click the Chem Display tab.

3.	You now have a choice:

*	To show residue brackets, you require this setting: Show sequence bonds.

*	To show residue leaving groups, you require this setting: Show crosslink bonds.

4.	Click OK.


Adding or Editing Lines

Use this option to add or edit unattached lines in a form. Lines are not attached to other form objects and should not be confused with box or table borders or the dividers inside of a table. Lines are typically added to a form for emphasis or division.

You have the following options:

*	Add a line

*	Resize a line

*	Delete a line

*	Move a line

*	Align one or more lines

*	Change the width, color, or line style


To change the width, color, or line style of a line

Use the following procedure to change the characteristics of a line.

1.	Click the Forms button.

2.	Click [image].

3.	Select a line.

Do one of the following:

* 	To change the line width, choose Object > Pen Width, and then select a width. You can only use the dashed, dotted, or dashed-dotted line style with the two smallest pen widths.

*	To change the line style, choose Object > Line, and then select a style.

*	To change the line color, choose Object > Pen Color, and then select a color.


Adding or Editing Unattached Text

Use this option to add or edit unattached text in a form. This type of text is not attached to boxes and columns and should not be confused with labels and data which are attached. Text is typically added to a form to provide information about the form, for example, to give the form a title.

You have the following options:

*	Add or edit text

*	Change the font, font size, or style

*	Change the color

*	Delete

*	Move

*	Align text


To add or edit unattached text

1.	Click the Forms button.

2.	Click [image].

3.	Do one of the following:

*	Click in the drawing area and enter the text.

*	Click and drag over the text that you want to change. The text is selected, and then replaced by the new text that you enter.

4.	Click outside of the text to complete the entry.


To change the font, size, or style of text

There are two methods that allow you to change the font, size, or style of text in a form.

1.	Click the Forms button.

2.	Do one of the following:

*	Click [image]. Select the text that you want to change. Choose Object > Font.

*	Click [image]. Double-click the text that you want to change.

3.	Select a font, font size, and/or font style.

4.	Click OK.


To change the color of text

Use this procedure to change the color of text in a form.

1.	Click the Forms button.

2.	Click [image].

3.	Select the text that you want to change.

4.	Choose Object > Pen Color and select a color of your choice.


Editing an Entire Form

You have the following options:

*	Resize an entire form

*	Move an entire form

*	Delete an entire form

*	Change the color of the entire form

*	Change the width of all lines and borders

*	Change the style of all lines and borders

*	Add a sketch or logo to the form

*	Create a form calculation

*	Attach a Procedural Language function to a form

*	Change the sequence ID of boxes or tables in a form


To resize an entire form

1.	Click the Forms button.

2.	Click [image].

3.	Choose Edit > Select All.

4.	Choose Object > Group.

5.	Do one of the following:

*	To resize both the height and width of the form, drag a corner selection handle.

*	To resize only the width of the form, drag a middle selection handle on the left or right side.

*	To resize only the length of the form, drag a middle selection handle on the top or bottom.

6.	Release the mouse to fix the size and shape of the object.

7.	Choose Object > Ungroup.


To move an entire form

1.	Click the Forms button.

2.	Click [image].

3.	Choose Edit > Select All.

4.	Click on the form and drag it to a new location.


To delete an entire form

1.	Click the Forms button.

2.	Choose Edit > Select All.

3.	Choose Edit > Cut (or press the Delete key).


To change the color of the entire form

1.	Click the Forms button.

2.	Choose Edit > Select All.

3.	Choose Object > Pen Color, and then select a new pen color.


To change the width of all the lines and borders in a form

1.	Click the Forms button.

2.	Choose Edit > Select All.

3.	Choose Object > Pen Width, and then select a new pen width point size.


To change the style of all the lines and borders in a form

1.	Click the Forms button.

2. 	Choose Edit > Select All.

3.	Choose Object > Line, and then select a new line style.


Aligning boxes, tables, lines, or text

Click here for step-by-step instructions

You can align boxes, tables, lines, and text in a form by their tops, bottoms, left sides, right sides, or centers.


To align boxes, tables, lines, or text

1.	Click the Forms button.

2.	Click [image].

3.	Select the objects to align.

4.	Choose Object > Align.

5.	Do one of the following:

*	To align objects horizontally, click an option in the Horizontal box. Then, click None in the Vertical box.

*	To align objects vertically, click an option in the Vertical box. Then, click None in the Horizontal box.

6.	Click OK.


To resize boxes, tables, lines, or text

1.	Click the Forms button.

2.	Click [image].

3.	Select the object that you want to resize. You can resize multiple form objects at the same time if you group the objects together.

4.	Do one of the following:

*	To resize both the height and width, drag a corner selection handle.

*	To resize only the width, drag a left or right middle-selection handle.

*	To resize only the length, drag a top or bottom middle-selection handle.

Note: When the cursor moves over a selection handle, its appearance changes to look like a plus (+). Then, you can resize the object.

5.	Release the mouse to fix the size and shape of the object.

6.	If you grouped objects to resize them, ungroup the objects now. You cannot enter queries or data into a form that is grouped.


To group multiple objects

Use the following procedure to group multiple form objects into one object.

1.	Click the Forms button.

2.	Select the objects to group, and then choose Object > Group. The form objects are grouped into one object.


To ungroup multiple objects

Use the following procedure to ungroup one or more objects in a form.

1.	Select the object to ungroup, and then choose Object > Ungroup. The form objects return to separate objects.


To move boxes, tables, lines, or text

Use this procedure to move the following objects in a form: boxes, tables, lines, and free text.

1.	Click the Forms button.

2.	Click [image].

3.	Select the object to move.

4.	(Optional) If you want to move multiple objects at the same time, you can group the objects first.

5.	Click on a selected object (not on a selection handle), and drag one or more objects to a new location.

Note: You can move an object if the cursor over the object has the appearance of an arrow. If the cursor changes to look like a plus, then it is over a selection handle and you will resize the object instead of moving it.

6. If you grouped the objects to move them, ungroup the objects now. You cannot enter queries or data into a form that is grouped.


To delete boxes, tables, line, or text

Use this procedure to delete boxes, tables, lines, and text in a form.

1.	Click the Forms button.

2.	Click [image].

3.	Select one or more objects to delete.

4.	Choose Edit > Cut.


Creating Form Calculations

Click here for step-by-step instructions

To combine data from different fields, you need to create a form calculation. A form calculation takes data values from boxes or columns in the form that contain real numbers or integers and performs mathematical operations on the data to get a result. The mathematical operations include adding, subtracting multiplying, and dividing data. You see the calculation result when you conduct a search and view the data in the Browse mode. Calculations are not real database fields so you cannot use them for registering data or sorting.

Do not confuse form calculations with calculated fields. A calculated field calculates a value from a set of data. For example, if your molecule database contains several activity measurements of each compound, you can create a calculated field that contains the average of those measurements. You can display data from a calculated field in a form and/or use it to sort search results, just like the data in any other database field.


To create a form calculation

Use the following procedure to combine data from different fields to create a form calculation.

1.	Click the Forms button.

2.	Select a box or column that is connected to a real number or integer field.

3.	Choose Object > Box Properties or Column Properties, and then click the Function tab.

4.	Click in the Box Name box, and enter a unique name to identify the box or column in the calculation. For example, you might enter MW for a box that displays molecular weight or MPL for a box that display moles/liter.

5.	Click OK.

6.	Repeat Steps 2 through 4 to enter a unique name for every box or column that has a data value that you want to use in the calculation.

7.	Select the box or column (that is not already connected to a field) for which you will enter the calculation formula. This will be the box or column that will display the results of the calculation when you view the results of a search.

8. Click here for instructions on how to enter the formula.


To enter the calculation formula

1.	With the box or column selected, choose Object > Box Properties or Column Properties, and then click the Function tab.

2.	Click the Default data box, and choose Calculation.

3.	Enter the formula in the text box below the Default data box. Enclose the box names in both quotation marks and parentheses. For example, to multiply the contents of the Mol. Wt box by the contents of the Moles/Liter box, you enter:

box(“MW”) * box(“MPL”)

Use the + (add), - (subtract), * (multiply), and / (divide) operators. The expected value might not display if the calculation involves integer fields, and the result is a fraction. The box will display a zero instead of the decimal equivalent of the fraction. To obtain the decimal, add a real number to the calculation (for example multiply by 1.0). Operators of equivalent priority (+, -) are evaluated from right to left. Use parentheses to stipulate the order, for example:

(1.0 * 1.0) / 2.0.

4.	Click OK. You see the calculation data when you view search results in Browse mode.


Setting a Box or Column to Use Default Data

Click here for step-by-step instructions

You set a box or column to display default data as an alternative to displaying data from a field in the database. When you conduct a search and view the results in Browse mode, you see the default data.

You can register some types of default data if the box or column that is set to default data is also connected to a corresponding database field. When you create a new record in Update mode, the program automatically retrieves the default data into the box or column.

Default data types are:

*	Calculation (use solely for display)

*	Today's date (use for display and registration)

*	Text string (use for display and registration)

*	ISIS/Draw sketch (use solely for display)


To set a box or column to use default data

Use the following procedure to set a box or column to use default data. (One type of default data, form calculations, is covered in a separate procedure. Click here if you want to create a form calculation.)

1.	Click the Forms button.

2.	You now have a choice:

*	Select a box or column that is not connected to a field if you intend to use the default data for display. Click here for instructions on how to remove a field connection.

*	Select a box or column that is connected to a field that corresponds with the default data type to register the default data.

3.	Choose Object > Box Properties or Column Properties, and then click the Function tab.

4.	Click the Default data box, and choose one of the following types:

*	Today's Date

*	String

*	Sketch


Attaching a Procedural Language Function to a Box or Column

Click here for step-by-step instructions

You can attach a Procedural Language function to a box or column in a form that triggers ISIS/Base to do something when the box or column becomes active. For example, you activate a box if you click it or tab into it. This in turn might activate a custom dialog box that you do not see when you click in other boxes or columns.


To attach a PL function to a box or column

Use the following procedure to attach a Procedural Language function to a box or column to trigger an event in the form.

1.	Click the Forms button.

2.	Select a box or column.

3.	Choose Object > Box Properties or Column Properties, and then click the Function tab.

4.	Click the PL Function box, and then enter the name of the Procedural Language function.

5.	(Optional) If the PL function is connected to a box you can also make the box invisible. To make a box invisible, you require this setting: Invisible box.

6.	Click OK. The PL function will work after it is loaded into memory.


Changing the Sequence ID Number of a Box or Table

Click here for step-by-step instructions

When you enter data into a form for registration or query purposes, press the Tab key to move between boxes and tables, instead of using the mouse. The sequence of the tabbing order is determined by a number that ISIS/Base assigns to a box or table when it is created. Use this procedure to change the tabbing order to better suit your task.


To change the sequence ID number of a box or column

1.	Click the Forms button.

2.	Select the first box or column in the form that is out of the desired order.

3.	Choose Object > Box Properties or Column Properties.

4.	Click the Function tab.

5.	Click the Sequence ID box.

6.	Edit the sequence ID number.

7.	Click OK.

8.	Click the Query or Browse mode, and then press Tab to view the order in which boxes and tables are selected in the form.

9.	(Optional) Return to Forms mode, and repeat this procedure for every box or table that you want to reorder.


Differences Between ISIS and Other MDL Products: Forms

Architectural and Organizational Differences

Read all information carefully and DO NOT make assumptions!

*	ISIS/Base has a graphical user-interface for creating forms.

*	ISIS/Base form commands and box properties differ functionally from features of the same name in MACCS-II, REACCS, or CPSS.

*	ISIS/Base uses different terminology than MACCS-II, REACCS, and CPSS. For example, instead of setting an input device as a box property as in MACCS-II, you open the database or remote-access file.

*	ISIS/Base allows you to use both boxes and tables in a form.

*	ISIS/Base allows you to use multiple structure boxes in a form. However, the corresponding database must contain multiple structure fields.

*	ISIS/Base stores forms inside of a local database or remote-access file. You will not see form files in your directory, unless you save the form to a separate disk file. Form files on disk can be accessed by multiple users for use in other ISIS databases.

*	ISIS/Base form files are transferable across PC and Mac platforms for use in other ISIS databases.

*	ISIS/Base will not accept forms that were created in MACCS-II, REACCS, or CPSS.

*	ISIS/Base does not link multiple databases to a form using a box property. ISIS/Base links multiple databases, including Ingres or Oracle, with an Hview file that provides the list of database fields that you can use in a form. See your Administrator for details.

ISIS Help Information

The ISIS Help System can show you:

1.	How to open, create, or edit a form. Click Back to return to the Creating and Editing Forms screen. The Creating and Editing Forms screen provides you with all of the alternatives you need to create or edit a form. Each alternative provides you with step-by-step instructions. Always perform the tasks in the order shown.

2.	Specific exercises that show you how to create boxes and tables. Choose Create a New Form, and then choose Create a Box or Create a Table. Depending on your selection, you can choose the Box Creation Exercise or Table Creation Exercise at the top of the screen. The information is presented in a Request-A-Document format, that you can print.

3.	Specific reference information. Choose Index (Draw & Base only)... from the ISIS/Base or ISIS/Draw help menu, or click the Search button in the help system. Enter a word that describes the information you want to find. The search engine locates specific reference information.

Be careful! This information is disconnected from step-by-step instructions.


Determine the Type of Form That You Need

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Creating a form to view search results	83.1

*	Additional considerations for printing search results	83.2

*	Additional considerations for viewing and printing hierarchical data	83.3

*	Additional form considerations for registering data	83.4

We recommend that you print this 7-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

83.1 Creating a Form to View Search Results

83.1.1 What are the best form dimensions to view data?

Typically, you create a form that fits inside of the ISIS/Base window. This enables you to view all of the data in the form without having to scroll the window.

If you are going to print your search results, there are some additional factors to consider when determining the form size. See “83.2 Additional considerations for printing search results.”

An additional consideration for form distribution: If you intend to distribute a form for use on various computers, the form size might vary from one monitor to another due to differences in the screen resolution. For example, a form that fits in an ISIS/Base window on an EGA monitor might be too large on a VGA monitor. As a result, you might have to scroll the ISIS/Base window to view all of the data.

83.1.2 Should I use boxes, tables or both in my form?

After you determine the overall dimensions of your form, decide whether to use boxes, tables, or both in your form.

Create a form with boxes to view data for one record at a time:

Create a form with tables to view and compare data for multiple records at the same time:

Create a form with a combination of boxes and tables to vary your data display. For example, you can create a table to view all of the variations that are associated with a particular reaction. In the following example, the square marker highlights the current variation number in the table:

As you scroll through the variation numbers in the table, the associated data changes.

83.1.3 Which fields do I include in my form to view search results?

To search for the data that you want to view, you must have at least one box or column connected to the field that you want to search. For example, to retrieve structures within a specific formula range, you must have a box connected to the formula field.

Then, to view the search results, you can have multiple boxes or columns connected to fields that are associated with the data that interests you:

You can use the same form to search and view data, or you can search with one form, and then change forms to view the results.

83.2 Additional Considerations for Printing Search Results

83.2.1 What are the best form dimensions for printing search results?

To determine the best overall form size for printing search results, consider the following printing options:

You can print one form to a page and instruct ISIS/Base to scale the form and data, if needed, to fit the form on the page:

Note: If you do not want ISIS/Base to scale the form and data, create a form that fits within the page size.

You can print multiple forms to a page and ISIS/Base automatically scales the form and data, if needed to fit the page:

You can include both a header and a footer on a printed page.

You can set the left, right, top, and bottom margins and the distance between forms if you print more than one to a page.

83.3 Additional Considerations for Viewing and Printing Hierarchical Data

The previous examples in this document, explain how to create forms for flat databases. A flat database contains one-level of data. The database fields are all grouped under a single parent-field:

It is easy to create a form to view data in a flat database, because all of the data is organized at one level.

The rest of this section explains how to create forms to view or print data in hierarchical databases. A hierarchical database contains multiple levels of data. At each level there are parent fields that branch to specific sets of data. Parent fields do not store data, but point to one or more child fields that contain the actual data. Hierarchical databases can have multiple branches of data (for example, <VARIATION> <LITTEXT> and <CONDITIONS>):

It is more complex to create forms to view data in hierarchical databases. You have to decide how to best organize your form to view the data that interests you. You can view data at one level, multiple levels, or in multiple branches.

83.3.1 Create tables to view or print hierarchical data

There are three types of tables that you can create in ISIS/Base: simple, layered, and uncoupled. You create all three tables using the same method. What makes the tables different, is the way that they display data (explained below). Another difference is that you can only use simple tables for registration.

A simple table displays data from fields that are grouped under one parent field at the same level of the database hierarchy. (You always create a simple table in a flat database.) You can create a form that has several simple tables, each of which displays data from a different level of the hierarchy:

A layered table displays data from consecutive levels of the database in the same table so that you can compare data side-by-side:

An uncoupled table displays data from at least two different branches of the database:

Caution: Uncoupled tables are useful for tabulating data, but not for making direct comparisons because there are gaps in the data. For example, in this table you see all of the literature references and temperatures associated with a reaction. However, you are missing the data that tells you to which reaction-variation the data applies.

83.3.2 Combine boxes and tables to view or print hierarchical data

You can combine one or more simple tables with boxes to create a complex form for viewing or printing hierarchical data:

Layered or uncoupled tables can also be combined with boxes or simple tables in a form.

83.4 Additional Considerations for Registering Data

83.4.1 What are the best form dimensions to register data?

Create a form that fits inside of the ISIS/Base window. This enables you to enter data into the form without having to move your hands from the keyboard to scroll the window.

83.4.2 Can I use any type of form to register data?

You can use boxes or simple tables to register data. You cannot use layered or uncoupled tables to register data.

83.4.3 Can I draw boxes and tables in any order?

To avoid making mistakes when you enter data into a form for registration, you do not want to move your hands from the keyboard. ISIS/Base allows you to tab between boxes and tables so that you do not have to move between the keyboard and the mouse.

The order in which you draw boxes and tables determines the order in which the cursor moves through the form when you press the Tab key. ISIS/Base assigns each box or table a unique sequence ID number in sequential order. When you create a form for registration, you can either draw boxes and tables in a suitable order for data entry. Or, you can draw boxes and tables in any order, and then change their sequence ID number to create a new tabbing order.

83.4.4 Which fields do I include in my form for registration?

To enter data into an ISIS/Base form for registration, you must have boxes or columns connected to the fields for which you have data to register:

Alternatively, you can transfer data between databases, in a batch, for registration. This method imports data from SDfiles and RDfiles and does not require an ISIS/Base form.


Box Creation Tutorial
Box Creation Exercise

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Before You Begin	84.1

*	Creating Boxes in a Form	84.2

*	Labeling and Connecting Boxes to Database Fields	84.3

*	Editing the Color, Font, and Position of Labels/Data in a Box	84.4

We recommend that you print this 7-page Request-A-Document before you begin the exercise. To print this document, click the Printer icon at the top of the screen.

84.1 Before You Begin

Before you begin, open the example database.

1.	Choose File > Open Database.

2.	Navigate to the ISIS21 directory or folder, if necessary.

3.	Double-click the Sample directory or folder.

4.	Double-click the Base directory or folder.

5.	Select (Mac=localmx), and then click OK (Mac=Open).

6.	Click the Forms button.

7.	Choose File > New Form to clear the existing form.

84.2 Creating Boxes in a Form

Typically a form will have boxes of varying sizes and shapes. For example:

This section shows you how to draw the boxes in this example.

1.	Click the [image] and draw a box that is the size of the overall form in the example. Click in the upper-left corner of the drawing area and drag down diagonally:

2.	Click [image], and then select the box. Choose Object > Partition Box. Enter a 2 in the Vertical Partitions box and a 1 in the Horizontal Partitions box. Click OK. The box divides into two smaller boxes of equal size:

3.	Resize the bottom box until it is the appropriate size for the Activity data. Move the cursor over the top-middle selection handle of the bottom box. When you see the cursor change from an arrow to a crosshair (+), click the handle and then drag it down to resize the box:

4. 	Make the top box large enough to divide into boxes for the Corporate ID, Formula, Date, Structure and Molname data. Click the bottom-middle selection handle of the top box and drag down:

5.	Select the top box, and then divide it into two horizontal partitions (one vertical partition):

6.	Make the left box smaller for the display of the Corporate ID, Formula and Date data. To do so, click the right-middle selection handle of the left box and drag left:

7.	Select the left box, and then divide it into three vertical partitions for the Corporate ID, Formula, and Date data:

8.	To make the right box larger to fit the display of structures, click the left-middle selection handle and drag left:

9.	Select the right box, and then divide it into two vertical partitions:

10.	Make the middle box smaller to fit the Molname data:

11.	Make the top box larger to fit the Structure data:

After you create the boxes in your form, see "84.3 Labeling and Connecting Boxes to Database Fields."

84.2.1 Alternative Methods to Create Boxes in a Form

*	Use [image] to draw boxes of varying sizes and shapes. If you want the box borders to align, start each new box in the corner of an existing box.

*	Select a box, and then choose Object > Multiply Box to create additional boxes of equal size and shape. This option automatically aligns boxes horizontally and/or vertically in the form. In addition, you can specify whether you want space in between boxes or if you want to align the borders.

*	Select a box, and then choose Edit > Duplicate to make an exact copy of a box.

84.2.2 Manipulating Boxes

Use the [image] to manipulate boxes in the following ways:

*	To move a box, point to the center of the box and drag.

*	To resize a box, click a selection handle and drag.

*	To move or resize multiple boxes, group them together (Object > Group), and then move or resize them. Ungroup the boxes when you are done (Object > Ungroup).

*	To align multiple boxes, select the boxes you want to align and choose Object > Align. You can align the boxes either horizontally or vertically.

84.3 Labeling and Connecting Boxes to Database Fields

After you create the box outlines in your form, you must connect them to fields in the database to register, search, or view data. You can also provide each box with a descriptive label to clearly identify the type of data that it holds.

1.	Select the top-left box, and then choose Object > Box Properties. Click the Field Name tab.

2.	Scroll the Database fields list, and highlight the corp_id field.

3.	Enter Corporate ID in the Label box.

4.	Click OK. The box label, Corporate ID, appears in the top-left corner, and the field name appears in the center of the box:

Note: In Browse and Update modes, the actual data that is connected to a box replaces the field name.

5. 	Double-click the box below the Corporate ID. (Double-clicking inside of a box is a shortcut to the Box Properties dialog box.)

6.	Click the Field Name tab.

7. 	Scroll the Database fields list, and highlight the *fmla_molstructure field.

8.	Enter Formula in the Label box.

9.	Click OK.

10.	Repeat Steps 5 through 9 to label and connect fields to the remaining boxes, as follows:

84.3.1 Editing a Box Label

There are two ways to edit a box label:

*	Double-click the box with the [image]. Click the Data/Label tab. Edit the existing label in the Label text box.

*	Click [image]. Select the label and edit the text.

84.3.2 Changing a Box Field-Connection

1.	Double click the field name inside of the box with the [image]. Click the Field Name tab.

2.	Choose a different field from the Database fields list.

3.	Click OK.

84.4 Editing the Color, Font, and Position of Labels and Data in a Box

You can edit the appearance of labels and data in one or more boxes to provide more contrast and make the overall form look better.

For both labels and data you can:

*	Change their position inside of a box. There are nine positions to choose from: top left, top middle, top right, center left, center middle, center right, bottom left, bottom middle, bottom center.

*	Change their fonts. You can display labels and data in different fonts, font sizes, and styles to provide contrast.

*	Change their color. You can display labels and data in different colors to provide contrast.

84.4.1 Changing the Color, Font, and Position of Labels and Data

1.	To select all of the boxes in the form, click a box, and then Shift-click the remaining boxes in the form.

2.	Choose Object > Box Properties, and then click the Data/Label tab.

3.	(Optional) To edit labels, choose from the following alternatives:

*	To change the position of labels, click the Label Alignment box, and choose a new position.

*	To change the color of labels, click the Label Color box, and choose a new color.

*	To change the label font, click the Label Font button. Select a new font, font size, and/or font style. Click OK.

4.	(Optional) To edit data, choose from the following alternatives:

*	To change the position of data, click the Data Alignment box, and choose a new position.

*	To change the color of data, click the Data Color box, and choose a new color.

*	To change the data font, click the Data Font button. Select a new font, font size, and/or font style. Click OK.

5.	Click OK.

Note: To also change the color of box borders, select the boxes. Choose Object > Box Properties, and then click the Border/Pattern tab. Click Color and choose a border style color.


Table Creation Tutorial
Table Creation Exercise

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Before You Begin	85.1

*	Creating Tables in a Form	85.2

*	Changing the Appearance of the Table Header	85.3

We recommend that you print this 5-page Request-A-Document before you begin the exercise. To print this document, click the Printer icon at the top of the screen.

85.1 Before You Begin

Before you begin, open the example database.

1.	Choose File > Open Database.

2.	Navigate to the ISIS21 directory or folder, if necessary.

3.	Double-click the Sample directory or folder.

4.	Double-click the Base directory or folder.

5.	Select localmx.db (Mac=localmx), and then click OK (Mac=Open).

6.	Click the Forms button.

7.	Choose File > New Form to clear the existing form.

85.2 Creating Tables in a Form

Tables can vary in size depending on the number of columns and the width of each column:

This section shows you how to draw the table in this example. First, you learn how to draw the table outline, and then connect the table to database fields to create columns. You will also learn how to adjust the width of columns as well as reorder, replace, and delete columns.

85.2.1 Drawing a Table Outline

1.	Click [image]. Click in the left-side of the screen and drag horizontally to the right to draw the outline of a table:

85.2.2 Adding and Connecting Columns to Database Fields

1.	Click [image]. Select the table outline, if it is not selected.

2.	Choose Object > Table Properties, and then click the Field Name tab.

3.	To create a column to display corporate ID numbers, scroll the Database fields list box until you see the corp_id field. Highlight the corp_id field. Click Add.

4. 	To provide a heading to identify the column, enter ID Number in the Column label box.

5.	To create a column to display molecule names, double-click the molname field in the Database fields list box. (Double-clicking on a field name is a shortcut to add the field as a column.)

6.	Enter Name as the column heading in the Column label box.

7. 	To create a column to display structures, double-click the molstructure field in the Database fields list box.

8.	Enter Structure as the column heading in the Column label box.

9.	To create a column to display molecular weights, double-click the *mol.weight_molstructure field, and then enter Mol. Weight as the column heading.

10.	Click OK. You see a table with four columns of equal size:

85.2.3 Selecting Individual Columns or the Entire Table

You select an entire table to resize or move the table. You can also select an entire table to edit the properties of all the columns in the table, such as changing the data font. Do one of the following:

*	To select an entire table to move or resize, click anywhere on the table except for on a field name.

*	To edit the properties of all the columns in the table, double-click on the table. You see the properties that you can edit.

You select an individual column to replace the field to which the column is connected or to style the column properties separately from other columns. To select and edit the properties of an individual column in the table, double-click on the field name in the column. You see the properties that you can edit.

85.2.4 Adjusting the Width of Columns in a Table

This section explains how to adjust the width of each column in the table to fit the size of the data display:

1.	To adjust the ID Number column to make it narrower, click on the column divider to the right of the ID Number column. Drag the column divider to the left.

2.	To adjust the Name column to make it wider, click on the column divider to the right of the Name column. Drag the column divider to the right.

3.	Adjust the Structure column to the right to make it wider.

4.	Adjust the Mol. Weight column to the left make it narrower.

Tip:	To resize a single column without changing the size of any other columns in the table, press and hold the Ctrl (Mac: Command) key as you drag the column divider. The overall size of the table is adjusted to accommodate the new size of the column.

When you create your own table, conduct a small search and view the data in the table to help you determine how far to adjust the width of each column.

85.2.5 Changing the Order of Columns in a Table

This section shows you how to change the order of columns so that the Structure column comes before the Name column:

1.	Select the table, and then choose Object > Table Properties.

2.	Select the MOL>MOLSTRUCTURE field in the Columns list box (not the Database fields list box).

3.	Click [image] under Reorder columns one time.

4.	Click OK.

85.2.6 Replacing a Column in an Existing Table

This section shows you how to replace the molname field with a formula field:

1.	Select the table, and then choose Object > Table Properties.

2.	Select the MOL>MOLNAME field in the Columns list box.

3.	Select the *fmla_molstructure field in the Database fields list box, and then click Replace.

4.	Enter Formula in the Column label box.

5.	Click OK.

85.2.7 Deleting a Column From a Table

This section shows you how to delete the *fmla_molstructure column:

1.	Select the table, and then choose Object > Table Properties.

2.	Select the MOL>*fmla_MOLSTRUCTURE field in the Columns list box.

3.	Click Delete.

4.	Click OK. The table size is adjusted to fit the remaining columns.

Alternative method: To select a column, select the column field name (in the form-drawing area). Choose Edit > Cut, or press the Delete key.

85.3 Changing the Appearance of the Table Header

The table header displays the column headings at the top of the table. It is followed by a table header bar that separates the headings from the data. You can change the appearance of the table header to provide contrast between the headings and the data.

In this section you learn how to change the font size and style of the column headings, and then center them over the columns. You also learn how to increase the width of the table header bar:

85.3.1 Changing the font size and style of column headings

1.	Select a column heading inside of a column.

2.	Shift-click the remaining column headings in the table.

3.	Choose Object > Font.

4.	Choose Times New Roman (Macintosh: Helvetica) from the Font list box.

5. Choose 10 pt from the Size list box.

6.	To make the font style boldface, you require this setting: Bold.

7.	Click OK.

Note: You can also change the font, font size, font style, and color of data. Select the field names in each column, and then choose Object > Font.

85.3.2 Centering all of the column headings in a table

1.	Select the table.

2.	Choose Object > Table Properties, and then click the Data/Label tab.

3.	Click in the Label Alignment box, and choose Top Center.

4.	Click OK.

Note: You can also change the alignment of data from this dialog box. We recommend the Middle Center alignment option to display data.

85.3.3 Increasing the width of the table header bar

1.	Select the table. You see selection handles at both ends of the table header bar.

2.	Choose Object > Table Properties, and then click the Border/Pattern tab.

3.	Click the Header Bar Width box and choose 2 pt.

4. 	Click OK.

Note: You can also change the width of the table border and row dividers from this dialog box.


Determining the Type of Table That You Need

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Overview on Tables	86.1

*	Creating a Simple Table	86.2

*	Creating a Layered Table	86.3

*	Creating an Uncoupled Table	86.4

We recommend that you print this 3-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

86.1 Table Overview

Use this document to determine the type of table to create. There are three types of tables in ISIS/Base: simple, layered, and uncoupled.

You use the same method to create all three types of tables. The difference between the three types of tables is the way in which they display data. The way each type of table displays data is determined by the fields that are connected to the columns in the table. The remainder of this document explains the differences between the three types of tables.

Note: For registration purposes, you must use simple tables.

86.2 What is a Simple Table?

To create a simple table, you draw the table, and then connect all of the columns to fields that are grouped under the same parent field in the database. For example, if you have this set of fields under the parent field <MOL>:

Then the following table is a simple table:

Note: If you have a flat (single-level) database, you can only create a simple table.

86.3 What is a Layered Table?

To create a layered table, you must have a hierarchical (multi-level) database. After you draw the table, you connect the columns to fields that are from different, but sequential levels of the same branch in the database hierarchy.

For example, you might want to view structure data, such as the Corp_ID and Structure. You also want to view the test results that are associated with the structure data, such as the Test No. and Result. The structure data comes from the level 1 of the database, and the test data comes from level 2:

To view the data, you could create two simple tables, one for the structure data and the other for the test data:

Or, you can combine both sets of data into one layered table:

86.4 What is an Uncoupled Table?

To create an uncoupled table, you must have a hierarchical (multi-level) database. After you draw the table, you connect the columns to fields that are located in different branches of the database hierarchy.

For example, you might have an uncoupled table that displays the reaction ID number, literature text, and temperature:

If you look at the database hierarchy, you see that the first column is connected to the Rxnregno field in the top-level of the database hierarchy. The second column is connected to the Lit_ref field in the left branch of the database hierarchy. The third column is connected to the Temperature field in the right branch of the database hierarchy:


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Database Field

A database field is an area in a database that contains information in a specific format. A database typically contains many database fields. For example, the database field:

PRODUCT_STRUCTURE contains all the products in the database in the format of a 2D graphical structure (molecule).

LITREF_JOURNAL contains all the names of the journals in the database in a text format.


Boxes, Tables, and Forms

A form is the set of boxes and/or tables that you use to hold your query and to view the records that you retrieve after a search. At least one box or table in the form must be linked to the database field that you want to search. This box or table holds your query. The other boxes or tables must be linked to the database fields that you want to view for each record after you conduct a search.

For example, in the following form you can enter a graphical query into the Structure box, or you can enter a text/numeric query into the Grade column of the MW versus Grade table:


Boxes, Tables, and Forms

A form is the set of boxes and/or tables that you use to view the records that you retrieve after a search. The boxes or tables must be linked to the database fields that you want to view for each record after you conduct a search. For example:


Boxes, Tables, and Forms

A form is the set of boxes and/or tables that you use to view the records that you retrieve after a search. The boxes or tables must be linked to the database fields that you want to view for each record after you conduct a search. For example:


Boxes, Tables, and Forms

A form is the set of boxes and/or tables that you use to hold your query and to view the records that you retrieve after a search. At least one box or table in the form must be linked to the database field that you want to search. This box or table holds your query. The other boxes or tables must be linked to the database fields that you want to view for each record after you conduct a search.

For example, in the following form you can enter a graphical query into the Structure box, or you can enter a text/numeric query into the Grade column of the MW versus Grade table:


Boxes, Tables, and Forms

A form is the set of boxes and/or tables that you use to view the records that you retrieve after a search. The boxes or tables must be linked to the database fields that you want to view for each record after you conduct a search. For example:


Boxes, Tables, and Forms

A form is the set of boxes and/or tables that you use to hold your query and to view the records that you retrieve after a search. At least one box or table in the form must be linked to the database field that you want to search. This box or table holds your query. The other boxes or tables must be linked to the database fields that you want to view for each record after you conduct a search.

For example, in the following form you can enter a graphical query into the Structure box, or you can enter a text/numeric query into the Grade column of the MW versus Grade table:


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your MEXACT query. For example, in an MDL database this field is MOL>MOLSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your MEXACT query. For example, in an MDL database this field is MOL>MOLSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your REXACT/Comp query. For example, in an MDL database this field is RXN>RXNSTRUCTURE.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your REXACT/Comp query. For example, in an MDL database this field is RXN>RXNSTRUCTURE.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your 3DEXACT query. For example, in an MDL database this field is MODEL>MODELSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your 3DEXACT query. For example, in an MDL database this field is MODEL>MODELSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your MEXACT query. For example, in an MDL database the field for a reactant is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your MEXACT query. For example, in an MDL database the field for a reactant is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your REXACT/Rxn query. For example, in an MDL database this field is RXN>RXNSTRUCTURE.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your REXACT/Rxn query. For example, in an MDL database this field is RXN>RXNSTRUCTURE.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your SSS query. For example, in an MDL database this field is MOL>MOLSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your SSS query. For example, in an MDL database this field is MOL>MOLSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your RGROUP query. For example, in an MDL database this field is MOL>MOLSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your SSS/Rigid query. For example, in an MDL database this field is MODEL>MODELSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your SSS/Any query. For example, in an MDL database this field is MODEL>MODELSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your SSS3D/Biopoly query. For example, in an MDL database this field is MODEL>MODELSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search. You also need to check that the box or column that displays the 3D structures highlights the query on the structures that you retrieve.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your CFS query. For example, in an MDL database this field is MODEL>MODELSTRUCTURE.

3.	Double-click the box or table column that is connected to the MODELSTRUCTURE field. A dialog box appears.

4.	Click the Chem Display tab (if not selected).

5.	If the Query highlight box contains None, choose an other color.

6.	Click OK.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database fields to hold your SBF query.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your SSS query. For example, in an MDL database the field for a reactant is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your SSS query. For example, in an MDL database the field for a reactant is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your RSS/Rxn query. For example, in an MDL database this field is RXN>RXNSTRUCTURE.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your RSS/Rxn query. For example, in an MDL database this field is RXN>RXNSTRUCTURE.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your RSS/Comp query. For example, in an MDL database this field is RXN>RXNSTRUCTURE.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your RSS/Comp query. For example, in an MDL database this field is RXN>RXNSTRUCTURE.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database fields to hold your SBF query.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database fields to hold your SBF query.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database fields to hold your SBF query.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database fields to hold your SBF query.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your RSim query. For example, in an MDL database this field is RXN>RXNSTRUCTURE.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your MSim query. For example, in an MDL database this field is MOL>MOLSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your FLEX query. For example, in an MDL database this field is MOL>MOLSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your TAUT query. For example, in an MDL database this field is MOL>MOLSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your ISOMER query. For example, in an MDL database this field is MOL>MOLSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your PARENT query. For example, in an MDL database this field is MOL>MOLSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your MSim query. For example, in an MDL database the field for a reactant is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your FLEX query. For example, in an MDL database the field for a reactant is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your TAUT query. For example, in an MDL database the field for a reactant is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your ISOMER query. For example, in an MDL database the field for a reactant is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your PARENT query. For example, in an MDL database the field for a reactant is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your RGROUP query. For example, in an MDL database the field for a reactant is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check the contents of the current form to be certain that it contains the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check the contents of the current form to be certain that it contains the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check the contents of the current form to be certain that it contains the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check the contents of the current form to be certain that it contains the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check the contents of the current form to be certain that it contains the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check the contents of the current form to be certain that it contains the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check the contents of the current form to be certain that it contains the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check the contents of the current form to be certain that it contains the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	If you are searching an MDL database, check that you have a database field to hold your ID query. This field is connected to the corporate identification number of each record in your database. (If you are not searching an MDL database, see your ISIS Administrator.)

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check the contents of the current form to be certain that it contains the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field for the molecule whose formula you want to find. For example, in an MDL database the molecule field is MOL>MOLSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check the contents of the current form to be certain that it contains the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field for the molecule whose formula you want to find. For example, in an MDL database the molecule field is MOL>MOLSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check the contents of the current form to be certain that it contains the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field for the reaction component whose formula you want to find. For example, in an MDL database the reactant field is RXN>reactant_link>MOL>MOLFORMULA.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check the contents of the current form to be certain that it contains the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field for the reaction component whose formula you want to find. For example, in an MDL database the reactant field is RXN>reactant_link>MOL>MOLFORMULA.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	If you are searching an MDL database, check that you have a database field to hold your ID query. This field is connected to the corporate identification number of each record in your database. (If you are not searching an MDL database, see your ISIS Administrator.)

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	If you are searching an MDL database, check that you have a database field to hold your ID query. This field is connected to the corporate identification number of each record in your database. (If you are not searching an MDL database, see your ISIS Administrator.)

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check the contents of the current form to be certain that it contains the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	If you are searching an MDL database, check that you have a database field to hold your ID query. This field is connected to the corporate identification number of each record in your database. (If you are not searching an MDL database, see your ISIS Administrator.)

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	If you are searching an MDL database, check that you have a database field to hold your ID query. This field is connected to the corporate identification number of each record in your database. (If you are not searching an MDL database, see your ISIS Administrator.)

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	If you are searching an MDL database, check that you have a database field to hold your ID query. This field is connected to the corporate identification number of each record in your database. (If you are not searching an MDL database, see your ISIS Administrator.)

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your SSS/Biopoly query. For example, in an MDL database this field is MOL>MOLSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your SSS/Biopoly query. For example, in an MDL database this field is MOL>MOLSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your CFS/Biopoly query. For example, in an MDL database this field is MODEL>MODELSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


To restore a form

1.	Choose File > Open Form.

2.	Click the name of the form that you want to restore.

3.	(Optional) To see this form each time you open the database, you require this setting: Set Default.

4.	Click OK.


Importing a Form

Click here for step-by-step instructions

You can import a form from another remote-access file or another program.

Note: If you import a form from a database that contains different database fields, you need to edit the existing form to connect the boxes and table columns new database fields.


Editing an Existing Form

Click here for step-by-step instructions

To edit a form, you make changes to a form that already exists. There are many options that allow you to edit a form. For example, you can change a field that is connected to a box or column, change the font and color of labels and data, or change the display of structures.


Creating a New Form

Click here for step-by-step instructions

To create a new form, you draw boxes and/or tables. Then, you connect the boxes and/or tables to the database fields that are associated with the data that you want to view or register.


Restoring a Form

Click here for step-by-step instructions

You can restore a form that you previously saved as an object in the remote-access file of your database.


Calculations

You can perform any of the following calculations on the data:


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your SSS/Poly query. For example, in an MDL database this field is MOL>MOLSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your Polymer query. For example, in an MDL database this field is MOL>MOLSTRUCTURE.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your polymer query. For example, in an MDL database this field is MOL>MOLSTRUCTURE.

3.	Check that you have the database fields to hold optional text/numeric strings.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your polymer query.. For example, in an MDL database this field is MOL>MOLSTRUCTURE.

3.	Check that you have the database fields to hold optional text/numeric strings.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your polymer query.. For example, in an MDL database this field is MOL>MOLSTRUCTURE.

3.	Check that you have the database fields to hold optional text/numeric strings.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your polymer query.. For example, in an MDL database this field is MOL>MOLSTRUCTURE.

3.	Check that you have the database fields to hold optional text/numeric strings.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


 Defining a Search Domain

A search domain is the set of records that are being searched. You can choose the search domain that you want to search. To see the current search domain, check the status bar. For example:

In this example from a reaction database, the message Search Domain: All shows that you search over all records in the database. When the search domain is a list of search results, you see Search Domain: Subset or Search Domain: <listname>, where <listname> is the name of a list of search results.

Click one of the following:

*	To choose one or more databases as the search domain

*	To choose a list of search results as the search domain


Defining a Search Domain

Click here for step-by-step instructions

A search domain is the set of records that are being searched. In an ALL search, you set the search domain to all the records in one or more remote databases that you access through a remote-access file.

To see the current search domain, check the status bar. For example:

In this example from a reaction database, the message Search Domain: All shows that you search over all records in the database. When the search domain is a list of search results, you see Search Domain: Subset or Search Domain: <listname>, where <listname> is the name of a list of search results.


Defining a Search Domain

Click here for step-by-step instructions

A search domain is the set of records that are being searched. In an ALL search, you set the search domain to all the records in a databases. To see the current search domain, check the status bar. For example:

In this example from a reaction database, the message Search Domain: All shows that you search over all records in the database. When the search domain is a list of search results, you see Search Domain: Subset or Search Domain: <listname>, where <listname> is the name of a list of search results.


To close a database

Use the following procedure to close the database in the active window.

1.	Choose File > Close Database.

2.	If ISIS prompts you to save database objects such as the current form or sorting instructions, follow the instructions on the screen to save or discard these objects.


To open a remote database

Use the following procedure to open one or more remote databases.

1.	Choose File > Open Database. You see a dialog box.

2.	Change to the appropriate directory (Mac=folder) if necessary.

3.	Click the name of the remote-access file that you want to open. It highlights.

Note: Your ISIS Administrator will supply you with a remote-access file, the name of which will appear here.

4.	Click OK (Mac=Open). If a password is required, you see a prompt to enter it.

5.	If ISIS prompts you for network connectivity information, enter the information that you received from your ISIS Administrator.

6.	Enter the host password and click OK. You see Search Domain: All in the status bar.


To open a local database

Use the following procedure to open a local database.

1.	Choose File > Open Database. You see a dialog box.

2.	Change to the appropriate directory (Mac=folder) if necessary.

3.	Click the name of the database that you want to open. It highlights.

4.	Click OK (Mac=Open). If a password is required, you see a prompt to enter it. You see Search Domain: All in the status bar.


To reset the search domain to the entire database

Use the following procedure if you previously restricted the search domain to a subset of the database and now want to search the entire database.

1.	Click the Query mode (if not selected).

2.	Choose Search > Set Search Domain To > Entire Database.


To choose one or more databases as the search domain

Use this procedure to open one or more databases and set the search domain to all records in the chosen database or databases.

1.	Choose File > Open Database. You see a dialog box.

2.	Change to the appropriate directory (Mac=folder) if necessary.

3.	Click the name of the remote-access file (RAF) that you want to open. It highlights. Note on concatenated databases

4.	Click OK (Mac=Open). If a password is required, you see a prompt to enter it.

5.	If ISIS prompts you for network connectivity information, enter the information that you received from your ISIS Administrator.

6.	Enter the host password and click OK. You see Search Domain: All in the status bar.


Note
Note on concatenated databases

Your ISIS Administrator will supply you with a RAF that you will see here.

Your RAF might specify Hviews for multiple databases (a maximum of 32). The databases that you open through this RAF are concatenated. (A search over the full set of databases of a specific type, such as the full set of reaction databases, is called a global search.)


To choose one or more databases as the search domain

Use this procedure to set the search domain to all records in the chosen database or databases.

1.	Choose File > Open Database. You see a dialog box.

2.	Change to the appropriate directory (Mac=folder) if necessary.

3.	Click the name of the remote-access file (RAF) that you want to open. It highlights. Note

Note: Your ISIS Administrator will supply you with a remote-access file, the name of which will appear here.

4.	Click OK (Mac=Open). If a password is required, you see a prompt to enter it.

5.	If ISIS prompts you for network connectivity information, enter the information that you received from your ISIS Administrator.

6.	Enter the host password and click OK.


To choose a single database as the search domain

Use this procedure to set the search domain to all records in the chosen database.

1.	Choose File > Open Database. You see a dialog box.

2.	Change to the appropriate directory (Mac=folder) if necessary.

3.	Click the name of the database that you want to open. It highlights.

4.	Click OK (Mac=Open). If a password is required, you see a prompt to enter it.


To choose a portion of a database as the search domain

Use this procedure to set the search domain to a list of search results from the chosen database or databases.

1.	Open the remote database.

2.	Do one of the following:

*	Open a list of search results that you previously stored as an object in the database.

*	Import a list of search results from a file on your host computer.


To use the current list of search results as the search domain

Use the following procedure to set the search domain to the current list of search results. In REACCS, this list is called the Reference.

1.	Click the Query mode (if not highlighted).

2.	Choose Search > Set Search Domain To > Current List. The text in the status bar changes to Search Domain: Subset.


To open a list of search results

Use the following procedure to set the search domain to a list of search results that is stored as an object in the database.

1.	Click the Query mode (if not highlighted).

2.	Choose Search > Set Search Domain To > Other List. You see a dialog box.

3.	Click the name of the list that you want to open.

4.	To set the search domain to the list, click [image] Set search domain to opened list.

5.	Click OK. The text in the status bar changes to show the name of the list that you opened.


To import a list of search results

Use the following procedure to set the search domain to a list of search results that you import from your host computer.

1.	Click the Browse mode (if not selected).

2.	Choose File > Import > List. You see the Host File Name dialog box.

3.	Enter the name of the file on your host computer that you want to import.

4.	Click OK (Mac=Open). The text in the status bar changes to Search Domain: Subset.


To choose a list of search results as the search domain

Use this procedure to open one or more databases and to set the search domain to a list of search results that is stored in the remote-access file.

1.	Open the remote database.

2.	Do one of the following:

*	Open a list of search results that you previously stored as an object in the database.

*	Import a list of search results from a file on your host computer.


To choose a combination of lists as the search domain

Use this procedure to set the search domain to a combination of lists of search results from the chosen database or databases.

1.	Open the remote database. You see Search Domain: All in the status bar.

2.	Do one of the following:

*	Merge two or more lists of search results.

*	Intersect two or more lists of search results.

*	Subtract two or more lists of search results from another list.

3.	Click the Query mode.

4.	Choose Search > Set Search Domain To > Current List.


To intersect two or more lists of search results

You can intersect two or more lists of search results to create a new list that contains only the records that appear on all lists (logical AND).

1.	Click the Browse mode (if not selected).

2.	Choose List > Logic.

3.	Click [image] AND.

4.	Click the name of the list from which you want to subtract records in the List 1 box.

5.	Click the name of the list that contains the records that you want to subtract in the List 2 box.

6.	Click Apply. The subtracted list is now current.

7.	(Optional) To subtract additional lists from the first list, repeat Steps 4 through 6.

8.	Click Close.

9.	Click Back (at top of help screen) to return to the previous screen and continue with Step 7 on that screen.


To merge two or more lists of search results

You can merge two or more lists of search results to create a new list that contains all the records on all the lists (logical OR).

1.	Click the Browse mode (if not selected).

2.	Choose List > Logic.

3.	Click [image] OR.

4.	Click the name of one of the lists that you want to merge in the List 1 box.

5.	Click the name of the other list that you want to merge in the List 2 box.

6.	Click Apply. The merged list is now current.

7.	(Optional) To merge additional lists, repeat Steps 4 through 6.

8.	Click Close.

9.	Click Back (at top of help screen) to return to the previous screen and continue with Step 7 on that screen.


To subtract one or more lists of search results from another list

You can subtract the records on one list of search results from the records on another list. When you do this, ISIS creates a new list that contains only the records from the first list that are not also on the second list (logical NOT).

1.	Click the Browse mode (if not selected).

2.	Choose List > Logic.

3.	Click [image] NOT.

4.	Click the name of the list from which you want to subtract records in the List 1 box.

5.	Click the name of the list that contains the records that you want to subtract in the List 2 box.

6.	Click Apply. The subtracted list is now current.

7.	(Optional) To subtract additional lists from the first list, repeat Steps 4 through 6.

8.	Click Close.

9.	Click Back (at top of help screen) to return to the previous screen and continue with Step 7 on that screen.


Defining a Search Domain

A search domain is the set of records that are being searched. You can choose the search domain that you want to search. To see the current search domain, check the status bar. For example:

In this example from a reaction database, the message Search Domain: All shows that you search over all records in the database. When the search domain is a list of search results, you see Search Domain: Subset or Search Domain: <listname>, where <listname> is the name of a list of search results.

Click one of the following:

*	To choose one or more databases as the search domain

*	To choose a list of search results as the search domain


Defining a Search Domain

A search domain is the set of records that are being searched. You can choose the search domain that you want to search. To see the current search domain, check the status bar. For example:

In this example from a reaction database, the message Search Domain: All shows that you search over all records in the database. When the search domain is a list of search results, you see Search Domain: Subset or Search Domain: <listname>, where <listname> is the name of a list of search results.

Click one of the following:

*	To choose one or more databases as the search domain

*	To choose a list of search results as the search domain


Defining a Search Domain

A search domain is the set of records that are being searched. You can choose the search domain that you want to search. To see the current search domain, check the status bar. For example:

In this example from a reaction database, the message Search Domain: All shows that you search over all records in the database. When the search domain is a list of search results, you see Search Domain: Subset or Search Domain: <listname>, where <listname> is the name of a list of search results.

Click one of the following:

*	To choose a single database as the search domain

*	To choose a list of search results as the search domain


To choose a single database as the search domain

Use this procedure to open a local database and set the search domain to all records in the chosen database.

1.	Choose File > Open Database. You see a dialog box.

2.	Change to the appropriate directory (Mac=folder) if necessary.

3.	Click the name of the database that you want to open. It highlights.

4.	Click OK (Mac=Open). If a password is required, you see a prompt to enter it. You see Search Domain: All in the status bar.


To choose a portion of a database as the search domain

Use this procedure to set the search domain to a list of search results from the chosen database or databases.

1.	Open the local database.

2.	Do one of the following:

*	Open a list of search results that you previously stored as an object in the database.

*	Import a list of search results from a file on your host computer.


To choose a list of search results as the search domain

Use this procedure to open one or more databases and to set the search domain to a list of search results from the chosen database.

1.	Open the local database.

2.	Do one of the following:

*	Open a list of search results that you previously stored as an object in the database.

*	Import a list of search results from a file on your workstation.


To open a list of search results

Use the following procedure to set the search domain to a list of search results that is stored as an object in the database. This procedure assumes that a database is open in the active window.

1.	Click the Query mode (if not highlighted).

2.	Choose Search > Set Search Domain To > Other List. You see a dialog box.

3.	Click the name of the list that you want to open.

4.	To set the search domain to the list, click [image] Set search domain to opened list.

5.	Click OK. The text in the status bar changes to display the name of the opened list.


To open a list of search results

Use the following procedure to obtain a list that is stored as an object in the database. This procedure assumes that a database is open in the active window.

1.	Click the Query mode (if not highlighted).

2.	Choose Search > Set Search Domain To > Other List.

3.	Click the name of the list that you want to open.

4.	Do one of the following:

*	To reset the search domain to the opened list, click [image] Set search domain to opened list

*	To use the entire database as the search domain, click [image] Set search domain to entire database

5.	Click OK.


To import a list of search results

Use the following procedure to set the search domain to a list of search results that you import from a file on your workstation. This procedure assumes that a database is open in the active window.

1.	Click the Browse mode (if not selected).

2.	Choose File > Import > List. (To retrieve a PC-list file on the Macintosh, press and hold the Option key while you complete this step.)

3.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

4.	Click OK (Mac=Open). The text in the status bar changes to Search Domain: Subset.


To choose a combination of lists as the search domain

Use this procedure to set the search domain to a combination of lists of search results from the chosen database.

1.	Open the local database.

2.	Do one of the following:

*	Merge two or more lists of search results.

*	Intersect two or more lists of search results.

*	Subtract two or more lists of search results from another list.

3.	Click the Query mode.

4.	Choose Search > Set Search Domain To > Current List.


To intersect two or more lists of search results

You can intersect two or more lists of search results to create a new list that contains only the records that appear on all lists (logical AND).

1.	Click the Browse mode (if not selected).

2.	Choose List > Logic.

3.	Click [image] AND.

4.	Click the name of the first list that you want to intersect in the List 1 box.

5.	Click the name of the other list that you want to intersect in the List 2 box.

6.	Click Apply. The intersected list is now current.

7.	(Optional) To intersect additional lists, repeat Steps 4 through 6.

8.	Click Close.

9.	Click Back (at top of help screen) to return to the previous screen and continue with Step 6 on that screen.


To merge two or more lists of search results

You can merge two or more lists of search results to create a new list that contains all the records on all the lists (logical OR).

1.	Click the Browse mode (if not selected).

2.	Choose List > Logic.

3.	Click [image] OR.

4.	Click the name of one of the lists that you want to merge in the List 1 box.

5.	Click the name of the other list that you want to merge in the List 2 box.

6.	Click Apply. The merged list is now current.

7.	(Optional) To merge additional lists, repeat Steps 4 through 6.

8.	Click Close.

9.	Click Back (at top of help screen) to return to the previous screen and continue with Step 6 on that screen.


To subtract one or more lists of search results from another list

You can subtract the records on one list of search results from the records on another list. When you do this, ISIS creates a new list that contains only the records from the first list that are not also on the second list (logical NOT). You can subtract additional lists of records from the new list.

1.	Click the Browse mode (if not selected).

2.	Choose List > Logic.

3.	Click [image] NOT.

4.	Click the name of the list from which you want to subtract records in the List 1 box.

5.	Click the name of the list that contains the records that you want to subtract in the List 2 box.

6.	Click Apply. The subtracted list is now current.

7.	(Optional) To subtract additional lists from List 1, repeat Steps 4 through 6.

8.	Click Close.

9.	Click Back (at top of help screen) to return to the previous screen and continue with Step 6 on that screen.


Defining a Search Domain

A search domain is the set of records that are being searched. You can choose the search domain that you want to search. To see the current search domain, check the status bar. For example:

In this example from a reaction database, the message Search Domain: All shows that you search over all records in the database. When the search domain is a list of search results, you see Search Domain: Subset or Search Domain: <listname>, where <listname> is the name of a list of search results.

Click one of the following:

*	To choose a single database as the search domain

*	To choose a list of search results as the search domain


Defining a Search Domain

A search domain is the set of records that are being searched. You can choose the search domain that you want to search. To see the current search domain, check the status bar. For example:

In this example from a reaction database, the message Search Domain: All shows that you search over all records in the database. When the search domain is a list of search results, you see Search Domain: Subset or Search Domain: <listname>, where <listname> is the name of a list of search results.

Click one of the following:

*	To choose a single database as the search domain

*	To choose a list of search results as the search domain


To abandon a search

Use this procedure to abandon a search before ISIS completes the search.

Note: For some searches, you might obtain a partial list of search results after you abandon the search.

1.	To abandon a search:

*	On the PC, press and hold the Esc key.

*	On the Macintosh, press and hold the Command key and the period key.


Switching to Another Application

You can switch to another application during an ISIS/Base search, or when you are printing from ISIS/Base.

Click one of the following:

To switch to another application on the PC

To switch to another application on the Macintosh


To switch to another application (PC only)

You cannot use Alt-TAB to switch to another application during an ISIS/Base search, or when you are printing from ISIS/Base. Use Control-ESC instead:

1.	Press Control-ESC. You see the Task List.

2.	Double-click the name of the application that you want to use.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results only if the boxes or tables on your form are connected to the database fields that you want to view.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results only if the boxes or tables on your form are connected to the database fields that you want to view.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results only if the boxes or tables on your form are connected to the database fields that you want to view.

For example, if you want to view the similarity values that ISIS derives from the similarity search, your form must contain boxes or table columns that can display this data.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results only if the boxes or tables on your form are connected to the database fields that you want to view.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results only if the boxes or tables on your form are connected to the database fields that you want to view.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results only if the boxes or tables on your form are connected to the database fields that you want to view.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results only if the boxes or tables on your form are connected to the database fields that you want to view.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results only if the boxes or tables on your form are connected to the database fields that you want to view.

For example, if you want to view the similarity values that ISIS derives from the similarity search, your form must contain boxes or table columns that can display this data.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results only if the boxes or tables on your form are connected to the database fields that you want to view.

For example, if you want to view the similarity values that ISIS derives from the similarity search, your form must contain boxes or table columns that can display this data.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results only if the boxes or tables on your form are connected to the database fields that you want to view.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results only if the boxes or tables on your form are connected to the database fields that you want to view.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results only if the boxes or tables on your form are connected to the database fields that you want to view.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results solely if the boxes or tables on your form are connected to the database fields that you want to view.

For example, if ISIS calculated values for torsional degrees of freedom (TDF), RMS deviation, or van der Waals energy difference during the search, your form must contain boxes or table columns that can display this data.

Note: If did not perform a bump-checking CFS search, you must perform bump checking on individual 3D structures as you view them (view-time bump checking). If a fitted 3D structure contains atoms that bump into one another, ISIS displays the 3D structure without overlaying the query.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results solely if the boxes or tables on your form are connected to the database fields that you want to view.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results only if the boxes or tables on your form are linked to the database fields that you want to view.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results only if the boxes or tables on your form are linked to the database fields that you want to view.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results only if the boxes or tables on your form are connected to the database fields that you want to view.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results only if the boxes or tables on your form are linked to the database fields that you want to view.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results solely if the boxes or tables on your form are connected to the database fields that you want to view.

For example, if ISIS calculated values for torsional degrees of freedom (TDF), RMS deviation, or van der Waals energy difference during the search, your form must contain boxes or table columns that can display this data.

Note: If did not perform a bump-checking CFS/Biopoly search, you must perform bump checking on individual 3D structures as you view them (view-time bump checking). If a fitted 3D structure contains atoms that bump into one another, ISIS displays the 3D structure without overlaying the query.


Viewing Search Results

Click here for step-by-step instructions

You can view the search results only if the boxes or tables on your form are connected to the database fields that you want to view.


To view search results

1.	Click the Browse mode (if not highlighted). You see the first record displayed on the boxes and tables in your form.

2.	To see how many records you retrieved, check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

See also:

To view stored search results

Viewing truncated data


To view search results

1.	Click the Browse mode (if not highlighted). You see the first record displayed on the boxes and tables in your form.

2.	To see how many records you retrieved, click the MOLSTRUCTURE box (if not selected) and check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

See also:

To view stored search results

Viewing truncated data


To view search results

1.	Click the Browse mode (if not highlighted). You see the first record displayed on the boxes and tables in your form.

2.	To see how many records you retrieved, click the MOLSTRUCTURE box (if not selected) and check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

See also:

To view stored search results

Viewing truncated data


To view search results

1.	Click the Browse mode (if not highlighted). You see the first record displayed on the boxes and tables in your form.

2.	To see how many records you retrieved, click the MOLSTRUCTURE box and check the status bar.

Note: For 3D databases, click the MODELSTRUCTURE box.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

See also:

To view stored search results

Viewing truncated data


To view search results

1.	Click the Browse mode (if not highlighted). You see the first record displayed on the boxes and tables in your form.

2.	To see how many records you retrieved, click the RXNSTRUCTURE box (if not selected) and check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

5.	(Optional) To view the variation subrecords, select the box or column row that contains the first variation subrecord. To view another variation subrecord, click one of the browsing tools shown in Step 4.

See also:

To view stored search results

Viewing truncated data


To view search results

1.	Click the Browse mode (if not highlighted). You see the first record displayed on the boxes and tables in your form.

2.	To see how many records you retrieved, click the RXNSTRUCTURE box (if not selected) and check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

5.	(Optional) To view the variation subrecords, select the box or column row that contains the first variation subrecord. To view another variation subrecord, click one of the browsing tools shown in Step 4.

See also:

To view stored search results

Viewing truncated data


To view search results

1.	Click the Browse mode (if not highlighted). You see the first record displayed on the boxes and tables in your form.

2.	To see how many records you retrieved, click the RXNSTRUCTURE box and check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

5.	(Optional) To view the variation subrecords, select the box or column row that contains the first variation subrecord. To view another variation subrecord, click one of the browsing tools shown in Step 4.

See also:

To view stored search results

Viewing truncated data


To view search results

1.	Click the Browse mode (if not highlighted). You see the first record displayed on the boxes and tables in your form.

2.	To see how many records you retrieved, click the RXNSTRUCTURE box and check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

5.	(Optional) To view the variation subrecords, select the box or column row that contains the first variation subrecord. To view another variation subrecord, click one of the browsing tools shown in Step 4.

See also:

To view stored search results

Viewing truncated data


To view search results

1.	Click the Browse mode (if not highlighted). You see the first record displayed on the boxes and tables in your form.

2.	To see how many records you retrieved, click the RXNSTRUCTURE box (if not selected) and check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

5.	(Optional) To view the variation subrecords, select the box or column row that contains the first variation subrecord. To view another variation subrecord, click one of the browsing tools shown in Step 4.

See also:

To view stored search results

Viewing truncated data


To view search results

1.	Click the Browse mode (if not highlighted). You see the first record displayed on the boxes and tables in your form.

2.	To see how many records you retrieved, click the RXNSTRUCTURE box (if not selected) and check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

5.	(Optional) To view the variation subrecords, select the box or column row that contains the first variation subrecord. To view another variation subrecord, click one of the browsing tools shown in Step 4.

See also:

To view stored search results

Viewing truncated data


To view search results

1.	Click the Browse mode (if not highlighted). You see the first record displayed on the boxes and tables in your form.

2.	To see how many records you retrieved, click the MODELSTRUCTURE box (if not selected) and check the status bar.

3.	(Optional) Sprout hydrogens on 3D structures.

4.	(Optional) Edit the chemical display of structures.

5.	Do one of the following:

*	View 3D structures in ISIS/Draw and ISIS/Base simultaneously.

*	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

See also:

To view stored search results

Viewing truncated data


To view search results

1.	Click the Browse mode (if not highlighted). You see the first record displayed on the boxes and tables in your form.

2.	To see how many records you retrieved, click the MODELSTRUCTURE box (if not selected) and check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Do one of the following:

*	View 3D structures in ISIS/Draw and ISIS/Base simultaneously.

*	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

See also:

To view stored search results

Viewing truncated data


To view search results

1.	Click the Browse mode (if not highlighted). You see the first record displayed on the boxes and tables in your form.

2.	To see how many records you retrieved, click the MOLSTRUCTURE box (if not selected) and check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

See also:

To view stored search results

Viewing truncated data


To view search results

1.	(Optional) Specify options for bump checking.

2.	Click the Query mode (if not already highlighted).

3.	You require [image] CFS View on the Options menu. (If you see [image] CFS View, do nothing at this step; otherwise, select this command.)

4.	Choose Options > CFS Options.

5.	Click OK.

6.	Click the Browse mode (if not highlighted). You see the first record displayed on the boxes and tables in your form.

7.	To see how many records you retrieved, click the MODELSTRUCTURE box and check the status bar.

8.	(Optional) Edit the chemical display of structures.

9.	Do one of the following:

*	View 3D structures in ISIS/Draw and ISIS/Base simultaneously.

*	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

See also:

To view stored search results

Viewing truncated data


To view search results

1.	Click the Query mode (if not already highlighted).

2.	You require CFS View on the Options menu. (If you see [image] CFS View, select this command; otherwise, do nothing at this step.)

3.	Click the Browse mode (if not highlighted). You see the first record displayed on the boxes and tables in your form.

4.	To see how many records you retrieved, click the MODELSTRUCTURE box and check the status bar.

5.	(Optional) Edit the chemical display of structures.

6.	Do one of the following:

*	View 3D structures in ISIS/Draw and ISIS/Base simultaneously.

*	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

See also:

To view stored search results

Viewing truncated data


To view search results

1.	Click the Browse mode (if it is not highlighted). You see the first record displayed on the boxes and tables in your form.

2.	To see how many records you retrieved, click the RXNSTRUCTURE box (if not selected) and check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

5.	(Optional) To view the variation subrecords, select the box or column row that contains the first variation subrecord. To view another variation subrecord, click one of the browsing tools shown in Step 4.

See also:

To view stored search results

To view reactions that precede or follow the current reaction in the path

Viewing truncated data


To view search results

1.	Click the Browse mode (if it is not highlighted). You see the first record displayed on the boxes and tables in your form.

2.	To see how many records you retrieved, click the RXNSTRUCTURE box (if not selected) and check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

5.	(Optional) To view the variation subrecords, select the box or column row that contains the first variation subrecord. To view another variation subrecord, click one of the browsing tools shown in Step 4.

See also:

To view stored search results

To view reactions that precede or follow the current reaction in the path

Viewing truncated data


To view search results

1.	Click the Browse mode (if not highlighted). You see the first record displayed on the boxes and tables in your form.

2.	To see how many records you retrieved, click the MOLSTRUCTURE box (if not selected) and check the status bar.

3.	(Optional) Edit the chemical display of structures.

Note on highlighting queries on biopolymers

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

See also:

To view stored search results

Viewing truncated data


Caution for Highlighting Biopolymer Queries
Note on highlighting queries on biopolymers

If you highlight the query within a biopolymer, the entire residue code is highlighted if any portion of its underlying structure matches the query. Thus, we recommend that you use the query-highlighting feature solely to view biopolymers in which you can see the underlying chemical structures of the residues.


To view search results

1.	Click the Browse mode (if it is not highlighted). You see the first record displayed on the boxes and tables in your form.

2.	To see how many records you retrieved, click the MOLSTRUCTURE box (if not selected) and check the status bar.

3.	(Optional) Edit the chemical display of structures.

Note on highlighting queries on biopolymers

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

See also:

To view stored search results

Viewing truncated data


To view search results

1.	Click the Browse mode (if not highlighted). You see the first record displayed on the boxes and tables in your form.

2.	To see how many records you retrieved, click the MOLSTRUCTURE box (if not selected) and check the status bar.

3.	(Optional) Edit the chemical display of structures.

Note on highlighting queries on biopolymers

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

See also:

To view stored search results

Viewing truncated data


To view stored search results

You can view search results that you have previously saved in the database or exported to a file.

1.	Do one of the following:

*	Open a list of search results.

*	Import a list of search results.

2.	To see how many records you retrieved, check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents


To view stored search results

You can view search results that you have previously saved in the database or exported to a file.

1.	Do one of the following:

*	Open a list of search results.

*	Import a list of search results.

2.	To see how many records you retrieved, click the MOLSTRUCTURE box (if not selected) and check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents


To view stored search results

You can view search results that you have previously saved in the database or exported to a file.

1.	Do one of the following:

*	Open a list of search results.

*	Import a list of search results.

2.	To see how many records you retrieved, click the MOLSTRUCTURE box (if not selected) and check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents


To view stored search results

You can view search results that you have previously saved in the database or exported to a file.

Note: You cannot view similarity data for a list that you have previously saved or exported. If you want to view similarity data, you must repeat the search.

1.	Do one of the following:

*	Open a list of search results.

*	Import a list of search results.

2.	To see how many records you retrieved, click the MOLSTRUCTURE box (if not selected) and check the status bar.

Note: For 3D databases, click the MODELSTRUCTURE box.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents


To view stored search results

You can view search results that you have previously saved in the database or exported to a file.

1.	Do one of the following:

*	Open a list of search results.

*	Import a list of search results.

2.	To see how many records you retrieved, click the RXNSTRUCTURE box (if not selected) check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

5.	(Optional) To view the variation subrecords, select the box or column row that contains the first variation subrecord. To view another variation subrecord, click one of the browsing tools shown in Step 4.


To view stored search results

You can view search results that you have previously saved in the database or exported to a file.

1.	Do one of the following:

*	Open a list of search results.

*	Import a list of search results.

2.	To see how many records you retrieved, click the RXNSTRUCTURE box (if not selected) check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

5.	(Optional) To view the variation subrecords, select the box or column row that contains the first variation subrecord. To view another variation subrecord, click one of the browsing tools shown in Step 4.


To view stored search results

You can view search results that you have previously saved in the database or exported to a file.

Note: You cannot view similarity data for a list that you have previously saved or exported. If you want to view similarity data, you must repeat the search.

1.	Do one of the following:

*	Open a list of search results.

*	Import a list of search results.

2.	To see how many records you retrieved, click the RXNSTRUCTURE box (if not selected) check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

5.	(Optional) To view the variation subrecords, select the box or column row that contains the first variation subrecord. To view another variation subrecord, click one of the browsing tools shown in Step 4.


To view stored search results

You can view search results that you have previously saved in the database or exported to a file.

1.	Do one of the following:

*	Open a list of search results.

*	Import a list of search results.

2.	To see how many records you retrieved, click the RXNSTRUCTURE box (if not selected) check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

5.	(Optional) To view the variation subrecords, select the box or column row that contains the first variation subrecord. To view another variation subrecord, click one of the browsing tools shown in Step 4.


To view stored search results

You can view search results that you have previously saved in the database or exported to a file.

1.	Do one of the following:

*	Open a list of search results.

*	Import a list of search results.

2.	To see how many records you retrieved, click the RXNSTRUCTURE box (if not selected) check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

5.	(Optional) To view the variation subrecords, select the box or column row that contains the first variation subrecord. To view another variation subrecord, click one of the browsing tools shown in Step 4.


To view stored search results

You can view search results that you have previously saved in the database or exported to a file.

Note: You cannot view similarity data for a list that you have previously saved or exported. If you want to view similarity data, you must repeat the search.

1.	Do one of the following:

*	Open a list of search results.

*	Import a list of search results.

2.	To see how many records you retrieved, click the RXNSTRUCTURE box (if not selected) check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

5.	(Optional) To view the variation subrecords, select the box or column row that contains the first variation subrecord. To view another variation subrecord, click one of the browsing tools shown in Step 4.


To view stored search results

You can view CFS search results that you have previously saved in the database or exported to a file.

1.	Specify the CFS options that you used for the original CFS search.

2.	You require [image] CFS View on the Options menu. If you see [image], do nothing at this step; otherwise, choose this command.

3.	Do one of the following:

*	Open a list of search results with the query that you used in the original CFS search.

*	Import a list of search results with the query that you used in the original CFS search.

4.	(Optional) Sprout hydrogens and lone pairs for bump checking.

5.	To see how many records you retrieved, click the MODELSTRUCTURE box (if not selected) and check the status bar.

6.	(Optional) Edit the chemical display of structures.

7.	Do one of the following:

*	View 3D structures in ISIS/Draw and ISIS/Base simultaneously.

*	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents


To view stored search results

You can view search results that you have previously saved in the database or exported to a file.

1.	Do one of the following:

*	Open a list of search results.

*	Import a list of search results.

2.	To see how many records you retrieved, click the MODELSTRUCTURE box (if not selected) and check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Do one of the following:

*	View 3D structures in ISIS/Draw and ISIS/Base simultaneously.

*	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents


To view stored search results

You can view search results that you have previously saved in the database or exported to a file.

1.	Do one of the following:

*	Open a list of search results.

*	Import a list of search results.

2.	To see how many records you retrieved, click the MODELSTRUCTURE box (if not selected) and check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Do one of the following:

*	View 3D structures in ISIS/Draw and ISIS/Base simultaneously.

*	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents


To sprout hydrogens and lone pairs on 3D structures

Use this procedure to specify how you want to sprout hydrogens and lone-pairs on the 3D structures that you retrieve from a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search.

1.	Choose Options > Settings > Session.

2.	Click the Search tab (if not selected).

3.	Do one of the following:

*	To prevent sprouting hydrogens and lone pairs, click the Sprout hydrogens and lone pairs box and choose Off.

*	To sprout hydrogens and lone pairs solely at sites where hydrogens and lone pairs appear on the query, click the Sprout hydrogens and lone pairs box and choose Query Atoms Only.

*	To sprout hydrogens at all sites, and lone pairs at sites where lone pairs appear on the query, click the Sprout hydrogens and lone pairs box and choose All.

4.	Click OK.


Sprouting Hydrogens on 3D Structures

Click here for step-by-step instructions

3D structures in a molecule database generally do not contain explicit hydrogen atoms. Consequently, if you want to export the 3D structure to a molfile or SDfile for use in a modeling software program that cannot sprout hydrogens, you must sprout hydrogens on the structures.

You also might want to sprout hydrogens to provide a more realistic representation of the 3D structures when you view them.


To sprout hydrogens on 3D structures

1.	Click Options > Settings > Session.

2.	Click the Search tab (if not selected).

3.	Click the Sprout hydrogens and lone pairs box and choose All.

4.	Click OK.


Why Specify Options For Bump Checking?

Click here for step-by-step instructions

If you did not perform a bump-checking CFS search, you can perform bump-checking on each 3D structure as you view it (view-time bump checking). Bump checking eliminates fitted 3D structures that have energetically unfavorable nonbonded (van der Waals) interactions. You must perform bump checking if you want to export fitted structures to a molfile or CFS SDfile to use in modeling software programs.

If any structures on your list have unfavorable nonbonded interactions, ISIS displays these structures without overlaying the query.


To specify options for bump checking

To perform bump checking as you view the fitted 3D structures from a CFS search, you need to activate the CFS option for bump checking and to sprout hydrogen atoms at all sites.

1.	Click the Query mode (if not already highlighted).

2.	Choose Options > CFS Options. You see the CFS Options dialog box.

3.	To perform bump checking as you view fitted structures, you require this setting:

Bump Checking at: View Time

4.	Click OK.

5.	Click Options > Settings > Session.

6.	Click the Search tab (if not selected).

7.	Click the Sprout hydrogens and lone pairs box and choose All.

8.	Click OK.


Why View a 3D Structure in ISIS/Draw?

Click here for step-by-step instructions

You can view each 3D structure that you retrieve in your ISIS/Base form and in an ISIS/Draw transfer window simultaneously. Viewing the structure to ISIS/Draw allows you to perform operations that are not available in ISIS/Base.


To view structures in both ISIS/Draw and ISIS/Base
To view structures in ISIS/Draw and ISIS/Base simultaneously

1.	(Optional) Specify automatic transfer to ISIS/Draw.

2.	Click Browse (if not selected).

3.	Use [image], [image], [image], [image], and [image] to display another 3D structure.

Keyboard Equivalents

4.	Transfer to ISIS/Draw.

5.	Click the Transfer Options box and choose Browse (if not already selected).

6.	Click one of the following:

*	Rotate the structure for a better view

*	Measure distances, angles, or other geometric features on the 3D structure

7.	Return to ISIS/Base.

8.	(Optional) Repeat Steps 3 through 7 for other 3D structures on your list.


To rotate a 3D structure for a better view

To rotate a 3D structure, use the 3D rotate tool. This procedure assumes that you are viewing a 3D structure that you retrieved in ISIS/Base.

1.	Click

2.	Select the 3D structure.

3.	Rotate the 3D structure to the desired orientation.

See also:

To restore the original orientation of a 3D structure or query


Transfer Options Box

The Transfer Options Box shows the ISIS/Base mode that you see when you transfer the structure in the ISIS/Draw window back to ISIS/Base. When you transfer a structure from ISIS/Draw to ISIS/Base, you can specify the ISIS/Base mode (Query, Browse, or Update) in which you want the structure to appear. For example:


To measure 3D spatial relationships on a structure

This procedure assumes that you are viewing a 3D structure that you retrieved in ISIS/Base.

1.	You require [image] Measure on the 3D Chemistry menu. (If you see [image] Measure, do nothing at this step; otherwise, select this command.)

2.	Specify the 3D geometric constraints that you want to measure. You see the measured values of the constraints that you create. If you need help, click:

Specifying 3D geometric constraints

See also:

To remove 3D query features from a structure


Specifying Automatic Transfer of Structures to ISIS/Draw

Click here for step-by-step instructions

If you view many 3D structures in ISIS/Draw, you might want ISIS/Base to automatically transfer structures to ISIS/Draw as you view them. If you specify manual transfer (the default), you must click [image] each time you view a new structure in ISIS/Base.

To transfer structures automatically, you require [image] Automatic transfer to ISIS/Draw in the General tab of ISIS/Base Session Settings.


To specify automatic transfer of structures to ISIS/Draw

1.	Choose Options > Settings > Session.

2.	Choose the General tab (if not already selected).

3.	You require the following setting:

Automatic transfer to ISIS/Draw

4.	Click OK.

5.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


Transfer to ISIS/Draw


To measure 3D spatial relationships on 3D structures

This procedure assumes that you have a 3D structure in the ISIS/Draw window.

1.	You require [image] Measure on the 3D Chemistry menu. (If you see [image] Measure, do nothing at this step; otherwise, select this command.)

2.	Specify the  3D geometric constraints that you want to measure. You see the measured values of the constraints that you create. If you need help, click one of the following:

Specifying 3D geometric constraints or

Specifying 3D objects or

Tips for selecting 3D objects and constraints or

To remove 3D query features from a structure


Return to ISIS/Base

You see your 3D structure in the box or table on the form, exactly as it appeared before you transferred it to ISIS/Draw. To view the changes that you made in ISIS/Draw, click [image] to return to ISIS/Draw.


Viewing Truncated Data

You can view data that is too lengthy to fit into a box or table.

Click one of the following:

To view truncated reactions in a box

To view truncated structures in a box

To view truncated data in a box

To view truncated data in a table cell


Viewing Truncated Data

You can view data that is too lengthy to fit into a box or table.

Click one of the following:

To view truncated structures in a box

To view truncated data in a box

To view truncated data in a table cell


To view truncated data in a box

If a box is too small to display all lines of data that it retrieves, you see an X in the lower right corner of the box. To view all of the information:

1.	Select the box.

2.	Click the X in the lower right corner of the box. You see a window that shows all the data.

3.	(Optional) To scroll the data in the data window, point to an arrow in a horizontal or vertical scroll bar, and then press and hold the mouse button.

4.	To close a data window, click anywhere outside the window.


To view truncated data in a table cell

If data in a table cell is truncated, you must change the data format for that column to see all the data:

1.	Click the Forms mode.

2.	Click the table cell that contains the truncated data.

3.	Choose Object > Box/Column Properties.

4.	Click the Data/Label tab (if not selected).

5.	Choose Text Format > Wrapped.

6.	Click OK.

7.	Click the Browse mode. The data wraps within the column.


To view truncated structures in a box

If a box is too small to display an entire 2D or 3D structure, you see an X in the lower right corner of the box. To view the entire structure:

1.	Select the box.

2.	Click the X in the lower right corner of the box. You see a window that shows the complete structure, scaled to fit the window.

3.	To close a data window, click anywhere outside the window.


To view truncated reactions in a box

If a box is too small to display an entire reaction, you see an X in the lower right corner of the box. To view the entire reaction:

1.	Select the box.

2.	Click the X in the lower right corner of the box. You see a window that shows the entire reaction.

3.	To close a data window, click anywhere outside the window.


To show or hide atom-atom maps

You can show or hide atom-atom maps on the reactions that you view. If you hide atom-atom maps, ISIS can display reactions more quickly.

1.	Choose Options > Settings > Session.

2.	Click the Atom Maps tab (if not selected).

3.	In the box that corresponds to atom-atom maps for Browse mode, do one of the following:

*	To hide atom-atom maps, choose Off.

*	To display atom-atom maps, choose On.

4.	Click OK.


To show or hide inversion/retention marks

You can show or hide inversion and retention marks on the reactions that you view. If you hide inversion and retention marks, ISIS can display reactions more quickly.

1.	Choose Options > Settings > Session.

2.	Click the Atom Maps tab (if not selected).

3.	In the box that corresponds to inversion/retention marks for Browse mode, do one of the following:

*	To hide inversion/retention marks, choose Off.

*	To display inversion/retention marks, choose On.

4.	Click OK.


To show or hide reacting centers

You can show or hide reacting center marks on the reactions that you view. If you hide reacting center marks, ISIS can display reactions more quickly.

1.	Choose Options > Settings > Session.

2.	Click the Atom Maps tab (if not selected).

3.	In the box that corresponds to reacting centers for Browse mode, do one of the following:

*	To hide reacting centers, choose Off.

*	To use color to show reacting centers, choose Color.

*	To use thickened lines to show reacting centers, choose Thickened.

*	To use hash marks to show reacting centers, choose Hash.

4.	Click OK.


To view reactions that precede or follow the current reaction in the path

This procedure assumes that you have conducted a search in IRDAS and that you have a reaction record on display.

1.	Click Browse in IRDAS (if not highlighted).

2.	Do one of the following:

*	To view the preceding reaction in the path, click Previous Step.

*	To view the next reaction in the path, click Next Step.

3.	(Optional) To view your original list of search results in IRDAS, choose List > Resume Browsing.


Finding Other Records that are Related to the Record on Display

You can find other records that are related to your record on display that:

*	Are part of the same reaction scheme.

*	Are part of the same path within a reaction scheme.


Finding Records that are Part of the Same Reaction Scheme

You can find records in ISIS/Base only or in ISIS/Base with IRDAS. Each procedure is unique.

Instructions for finding records in ISIS/Base

This procedure assumes that you have conducted a search and that you have a reaction record on display.

1.	Click Browse (if not highlighted).

2.	Click the EXTREG box.

3.	Choose Edit > Copy.

4.	Click Query.

5.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

6.	Click the EXTREG box.

7.	Choose Edit > Paste.

8.	Do one of the following:

*	If your extreg is a numerical value only (no text), go to Step 9.

*	If your extreg contains text, you need to add the search operator LIKE and place the extreg in double quotes. For example, enter: LIKE "TG092545"

9.	Click Search > By Form.

10. View your results.


Using IRDAS to Find Records that Share the Same Scheme

This procedure assumes that you have conducted a search in IRDAS and that you have a reaction record on display.

1.	Click Browse in IRDAS (if not highlighted).

2.	Click Get Scheme. You see the first reaction in the reaction scheme.

3.	View your results.

4.	(Optional) To view your original list of search results in IRDAS, choose List > Resume Browsing.


Finding Records that are Part of the Same Path Within a Reaction Scheme

You can find records in ISIS/Base only or in ISIS/Base with IRDAS. Each procedure is unique.

Instructions for finding records in ISIS/Base

This procedure assumes that you have conducted a search and that you have a reaction record on display.

1.	Click Browse (if not highlighted).

2.	Click the EXTREG box.

3.	Choose Edit > Copy.

4.	Click Query.

5.	Choose Edit > Clear Data > Form.

6.	Double-click the EXTREG box.

7.	Choose Edit > Paste.

8.	Do one of the following:

*	If your extreg is a numerical value only (no text), go to Step 9.

*	If your extreg contains text, you need to add the search operator LIKE and place the extreg in double quotes. For example, enter: LIKE "TG092545"

9.  Double-click the Path box.

10. Enter the path of your choice (such as A or B).

11. Choose Search > By Form.

12. View your results.


Using IRDAS to Find Records that Share the Same Path

This procedure assumes that you have conducted a search in IRDAS and that you have a reaction record on display.

1.	Click Browse in IRDAS (if not highlighted).

2.	Click Get Path. You see the first reaction in the reaction scheme.

3.	View your results.

4.	(Optional) To view your original list of search results in IRDAS, choose List > Resume Browsing.


Finding Other Records that are Related to the Record on Display

You can find other records that are related to your record on display that:

*	Are part of the same reaction scheme.

*	Are part of the same path within a reaction scheme.


Finding Records that are Part of the Same Reaction Scheme

You can find records in ISIS/Base only or in ISIS/Base with IRDAS. Each procedure is unique.

Instructions for finding records in ISIS/Base

This procedure assumes that you have conducted a search and that you have a reaction record on display.

1.	Click Browse (if not highlighted).

2.	Click the EXTREG box.

3.	Choose Edit > Copy.

4.	Click Query.

5.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

6.	Click the EXTREG box.

7.	Choose Edit > Paste.

8.	Do one of the following:

*	If your extreg is a numerical value only (no text), go to Step 9.

*	If your extreg contains text, you need to add the search operator LIKE and place the extreg in double quotes. For example, enter: LIKE "TG092545"

9.	Click Search > By Form.

10. View your results.


Using IRDAS to Find Records that Share the Same Scheme

This procedure assumes that you have conducted a search in IRDAS and that you have a reaction record on display.

1.	Click Browse in IRDAS (if not highlighted).

2.	Click Get Scheme. You see the first reaction in the reaction scheme.

3.	View your results.

4.	(Optional) To view your original list of search results in IRDAS, choose List > Resume Browsing.


Finding Records that are Part of the Same Path Within a Reaction Scheme

You can find records in ISIS/Base only or in ISIS/Base with IRDAS. Each procedure is unique.

Instructions for finding records in ISIS/Base

This procedure assumes that you have conducted a search and that you have a reaction record on display.

1.	Click Browse (if not highlighted).

2.	Click the EXTREG box.

3.	Choose Edit > Copy.

4.	Click Query.

5.	Choose Edit > Clear Data > Form.

6.	Double-click the EXTREG box.

7.	Choose Edit > Paste.

8.	Do one of the following:

*	If your extreg is a numerical value only (no text), go to Step 9.

*	If your extreg contains text, you need to add the search operator LIKE and place the extreg in double quotes. For example, enter: LIKE "TG092545"

9.  Double-click the Path box.

10. Enter the path of your choice (such as A or B).

11. Choose Search > By Form.

12. View your results.


Using IRDAS to Find Records that Share the Same Path

This procedure assumes that you have conducted a search in IRDAS and that you have a reaction record on display.

1.	Click Browse in IRDAS (if not highlighted).

2.	Click Get Path. You see the first reaction in the reaction scheme.

3.	View your results.

4.	(Optional) To view your original list of search results in IRDAS, choose List > Resume Browsing.


To save a form

Use this procedure to save the current form inside the database.

1.	Click the Forms mode.

2.	Do one of the following:

*	To save the new form or an existing form under the same name, choose File > Save Form. For new forms only, enter a name and an optional description for the form.

*	To save the existing form under a new name, choose File > Save Form As. Enter a name and an optional description for the form.

3.	Click OK. The form is saved inside the database and you will not see it as a separate form file on disk.

4.	Click the Browse mode.

5.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


Restoring Search Results
Opening Search Results

Click here for step-by-step instructions

You can open a list of search results that you previously saved in the remote-access file of your database.

Note: When you open a list that is stored within the database, you can either set the search domain to the list that you opened, or to the entire database. When you import a list, however, ISIS/Base always resets the search domain to the list that you import.


Restoring CFS Search Results
Opening CFS Search Results

Click here for step-by-step instructions

You can open a list of search results that you previously saved in the remote-access file of your database.

Notes: (1) To use a list from a CFS search, you must also restore the query that you used in the CFS search that produced the list. ISIS uses this information to fit 3D structures in the database to the constraints of the query. If you do not restore the query, ISIS displays the 3D structures that are stored in the database, not the fitted conformations that result from conformational fitting. (2) When you open a list that is stored as an object within the database, you can either set the search domain to the list that you opened, or to the entire database. When you import a list, however, ISIS/Base always resets the search domain to the list that you import.


Restoring Search Results
Opening Search Results

Click here for step-by-step instructions

You can open a list of search results that you previously saved in your database.

Note: When you open a list that is stored within the database, you can either set the search domain to the list that you opened, or to the entire database. When you import a list, however, ISIS/Base always resets the search domain to the list that you import.


To open a list of search results

1.	Click the Browse mode (if not highlighted).

2.	Choose List > Open List. You see a dialog box.

3.	Click the name of the list of search results that you want to open.

4.	Do one of the following:

*	To reset the search domain to the opened list, click [image] Set search domain to opened list.

*	To reset the search domain to the entire database, click [image] Set search domain to entire database.

5.	Click OK.

6.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To open a list of search results

1.	Click the Browse mode (if not already highlighted).

2.	Choose List > Open List. You see a dialog box.

3.	Click the name of the list of search results that you want to open.

4.	Do one of the following:

*	To reset the search domain to the opened list, click [image] Set search domain to opened list.

*	To reset the search domain to the entire database, click [image] Set search domain to entire database

5.	Click OK.


To open a list of CFS search results with the query

1.	Click the Query mode (if not highlighted).

2.	Choose Search > Restore Query. You see a dialog box.

3.	Click the name of the query that you want to restore.

4.	Click OK.

5.	Click the Browse mode.

6.	Choose List > Open List.

7.	Click the name of the list of search results that you want to open.

8.	Do one of the following:

*	To reset the search domain to the opened list, click [image] Set search domain to opened list.

*	To reset the search domain to the entire database, click [image] Set search domain to entire database.

9.	Click OK.

10.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To open a list of CFS search results with the query

1.	Click the Query mode (if not highlighted).

2.	Choose Search > Restore Query. You see a dialog box.

3.	Click the name of the query that you used in the CFS search.

4.	Click OK.

5.	Click the Browse mode.

6.	Choose List > Open List.

7.	Click the name of the list of search results that you want to open.

8.	(Optional) To reset the search domain to the opened list, click [image] Set search domain to opened list.

9.	Click OK.


To specify the original CFS options

If you want to view CFS search results that you have previously stored, you need to specify the CFS options that you used when you performed the original CFS search that created those results. ISIS needs this information to correctly fit 3D structures in the database to the constraints of the query.

1.	Click the Query mode (if not already highlighted).

2.	Choose Options > CFS Options.

3.	Enter the options that you used when you performed the original CFS search.

Note: If you are not sure  which CFS options you used, click Default to use the default CFS options.

4.	(Optional) To perform bump checking as you view the fitted structures, you require this setting:

Bump Checking at: View Time [image] Search Time

5.	Click OK.

6.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To specify the original CFS options

If you want to view CFS search results that you have previously stored, you need to specify the CFS options that you used when you performed the original CFS search that created those results. ISIS needs this information to correctly fit 3D structures in the database to the constraints of the query.

1.	Click the Query mode (if not already highlighted).

2.	Choose Options > CFS Options.

3.	Enter the options that you used when you performed the original CFS search.

Note: If you are not sure  which CFS options you used, click Default to use the default CFS options.

4.	(Optional) To perform bump checking as you view the fitted structures, you require this setting:

Bump Checking at: View Time [image] Search Time

5.	Click OK.


Importing Search Results

Click here for step-by-step instructions

You can import a list of search results that you previously exported to a file on your host computer.

Note: When you import a list, ISIS/Base automatically resets the search domain to the list that you import. When you open a list that is stored within the database, you can either set the search domain to the list that you opened, or to the entire database.


Importing CFS Search Results

Click here for step-by-step instructions

You can import a list of CFS search results that you previously exported to a file on your host computer.

Notes: (1) To import a list of search results from a CFS search, you also must import the query that you used in the CFS search that produced the list. If you do not import the query with the search results, ISIS displays the 3D structures that are stored in the database, not the fitted structures from the CFS search. (2) When you import a list, ISIS/Base automatically resets the search domain to the list that you import. When you open a list that is stored within the database, you can either set the search domain to the list that you opened, or to the entire database.


Importing Search Results

Click here for step-by-step instructions

You can import a list of search results that you previously exported to a file on your workstation.

Note: When you import a list, ISIS/Base automatically resets the search domain to the list that you import. When you open a list that is stored within the database, you can either set the search domain to the list that you opened, or to the entire database.


To import a list of search results

1.	Click the Browse mode (if not selected).

2.	Choose File > Import > List. You see the Host File Name dialog box.

3.	Enter the name of the file on your host computer that you want to import. Use the file-naming conventions of the operating system on your host computer.

4.	Click OK (Mac=Open). ISIS resets the search domain to the imported list (You see Search Domain: Subset in the status bar).

5.	(Optional) To reset the search domain to a different list or to the entire database, click the Query mode, choose Search > Set Search Domain To, and choose the search domain that you want.

6.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To import a list of search results

1.	Click the Browse mode (if not selected).

2.	Choose File > Import > List. You see the Host File Name dialog box.

3.	Enter the name of the file on your host computer that you want to import. Use the file-naming conventions of the operating system on your host computer.

4.	Click OK (Mac=Open). ISIS resets the search domain to the imported list (You see Search Domain: Subset in the status bar).

5.	(Optional) To reset the search domain to a different list or to the entire database, click the Query mode, choose Search > Set Search Domain To, and choose the search domain that you want.


To import a list of search results

1.	Click the Browse mode (if not selected).

2.	Choose File > Import > List. (To retrieve a PC-list file on the Macintosh, press and hold the Option key while you complete this step.)

3.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

4.	Click OK (Mac=Open). ISIS resets the search domain to the imported list (You see Search Domain: Subset in the status bar).

5.	(Optional) To reset the search domain to a different list or to the entire database, click the Query mode, choose Search > Set Search Domain To, and choose the search domain that you want.

6.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To import a list of search results

1.	Click the Browse mode (if not selected).

2.	Choose File > Import > List. (To retrieve a PC-list file on the Macintosh, press and hold the Option key while you complete this step.)

3.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

4.	Click OK (Mac=Open). ISIS resets the search domain to the imported list (You see Search Domain: Subset in the status bar).

5.	(Optional) To reset the search domain to a different list or to the entire database, click the Query mode, choose Search > Set Search Domain To, and choose the search domain that you want.


To import a list of CFS search results with the query

1.	Click the Query mode (if not selected).

2.	Click the MODELSTRUCTURE box. It highlights.

3.	Choose File > Import > MolFile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of the molfile that contains the search query.

5.	Click OK (Mac=Open).

6.	Click the Browse mode.

7.	Choose File > Import > List.

8.	Enter the name of the list file on your host computer that you want to import.

9.	Click OK (Mac=Open). ISIS resets the search domain to the imported list (You see Search Domain: Subset in the status bar).

10.	(Optional) To reset the search domain to a different list or to the entire database, click the Query mode, choose Search > Set Search Domain To, and choose the search domain that you want.

11.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To import a list of CFS search results with the query

1.	Click the Query mode (if not selected).

2.	Click the MODELSTRUCTURE box. It highlights.

3.	Choose File > Import > MolFile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of the molfile that contains the search query.

5.	Click OK (Mac=Open).

6.	Click the Browse mode.

7.	Choose File > Import > List.

8.	Enter the name of the list file on your host computer that you want to import.

9.	Click OK (Mac=Open). ISIS resets the search domain to the imported list (You see Search Domain: Subset in the status bar).

10.	(Optional) To reset the search domain to a different list or to the entire database, click the Query mode, choose Search > Set Search Domain To, and choose the search domain that you want.


Saving the Search Results

Click here for step-by-step instructions

You can save your search results in the remote-access file of your database. This allows you to retrieve the same list of records without executing the search again. Anyone who accesses the same remote database from the same remote-access file can open the search results and use them.

You can also export your search results to a text file on your host computer. Export your search results when you want to exchange search results with users who access the database through a different remote-access file or when you want to exchange search results with MACCS-II and REACCS users.

Note: You can save a list of records only if your Hview contains a TINFO KEY line. The TINFO KEY line specifies field whose values are used in the list. For more information, see your ISIS Administrator.


 Saving the Search Results

You can save your search results as an object in the remote-access file of your database. This allows you to retrieve the same list of records without executing the search again. Anyone who accesses the same remote-access file can open the search results and use them.

You can also export your search results to a list file or to a CFS SDfile. Export your search results to a list file when you want to exchange search results with users who access the database through a different remote-access file or to exchange search results with MACCS-II users. Export to a CFS SDfile when you want to use the fitted conformations from the CFS search in a modeling software program.

Click one of the following:

*	Save the list alone

*	Save the query with the list

Note: You can save a list of records solely if the Hview for the database contains a TINFO KEY line. The TINFO KEY line specifies either the internal registry number (regno) or the external registry number (extreg). When you save a list, however, ISIS saves the internal registry numbers of the records, even if the TINFO KEY line specifies the external registry number. If the Hview for your database specifies the extreg in the TINFO KEY line, and you want to save the list as extregs, use File > Export List. For more information on Hviews, see your ISIS Administrator.


Saving the List Alone

Click here for step-by-step instructions

Save the list alone when you want to use your search results solely as a search domain for a future search, or when you are not interested in viewing the fitted 3D conformations from the CFS search.

Note: If you view a saved list without the query, ISIS displays the 3D conformations that are stored in the database, not the fitted conformations from the CFS search. If you want to view the fitted conformations from a saved list of CFS search results, you must save the query with the list.


Saving the Query With the List

Click here for step-by-step instructions

Save the query with the list when you want to view the fitted conformations from a CFS search at a later time. You can also use the saved list as a search domain for a future search.

Note: If you view a saved list without the query, ISIS displays the 3D conformations that are stored in the database, not the fitted conformations from the CFS search. If you want to view the fitted conformations from a saved list of CFS search results, you must save the query with the list.


Saving the Search Results

Click here for step-by-step instructions

You can save your search results in your database. This allows you to retrieve the same list of records without executing the search again. Anyone who accesses the same local database can open the search results and use them.

You cannot save your search results permanently in a local database that is read-only. If the database is read-only, you can export your list of search results to a text file on your workstation.

For more information on read-only databases, see your ISIS Administrator.


Caution

When you save a list of search results in the remote-access file of your database, ISIS creates a file on your host computer that contains important information. Do not delete this file! If you delete this file, you will lose your search results.


Caution

When you save a list of search results in the remote-access file of your database, ISIS creates a file on your host computer that contains important information. Do not delete this file! If you delete this file, you will lose your search results.

ISIS does not save fitted 3D conformations with the saved search results. If you want to save fitted 3D conformations, you must export your search results to a CFS SDfile.


To save the search results

Caution

1.	Click the Browse mode (if not highlighted).

2.	Choose List > Save.

3.	Click the List Name box and enter a name for the list (without a file-name extension).

4.	(Optional) To save the query with the same name as the list name, you require this setting: Save query under the same name.

5.	Do one of the following:

*	To store the list as a permanent database object, you require this setting: Permanent.

*	To delete the list when you close the database, you require this setting: Permanent.

6.	Click OK.


To save the search results

Caution

1.	Click the Browse mode (if not highlighted).

2.	Choose List > Save.

3.	Click the List Name box and enter a name for the list (without a file-name extension).

4.	(Optional) To save the query with the same name as the list name, you require this setting: Save query under the same name.

5.	Do one of the following:

*	To store the list as a permanent database object, you require this setting: Permanent.

*	To delete the list when you close the database, you require this setting: Permanent.

6.	Click OK.


To save the search results

1.	Click the Browse mode (if not highlighted).

2.	Choose List > Save.

3.	Click the List Name box and enter a name for the list (without a file-name extension).

4.	(Optional) To save the query with the same name as the list name, you require this setting: Save query under the same name.

5.	Do one of the following:

*	To store the list as a permanent database object, you require this setting: Permanent.

*	To delete the list when you close the database, you require this setting: Permanent.

6.	Click OK.


To save the list alone

Caution

1.	Click the Browse mode (if not highlighted).

2.	Choose List > Save.

3.	Click the List Name box and enter a name for the list (without a file-name extension).

4.	To save the list alone, you require this setting: Save query under the same name.

5.	Do one of the following:

*	To store the list as a permanent database object, you require this setting: Permanent.

*	To delete the list when you close the database, you require this setting: Permanent.

6.	Click OK.


To save the query with the list

Caution

1.	Write down the CFS Options that you used to conduct the search. You will need these when you view the search results later.

2.	Click the Browse mode (if not highlighted).

3.	Choose List > Save.

4.	Click the List Name box and enter a name for the list (without a file-name extension).

5.	To save the query with the same name as the list name, you require this setting: Save query under the same name.

6.	Do one of the following:

*	To store the list as a permanent database object, you require this setting: Permanent.

*	To delete the list when you close the database, you require this setting: Permanent.

7.	Click OK.


Manipulating Search Results

Click one of the following:

*	Delete records from the list of search results

*	Copy records from the list of search results to another list of search results

*	Move records from the list of search results to another list of search results

*	Intersect two or more lists of search results

*	Merge two or more lists of search results

*	Subtract two or more lists of search results


Manipulating Search Results

Click one of the following:

*	Delete records from the list of search results

*	Copy records from the list of search results to another list of search results

*	Move records from the list of search results to another list of search results

*	Intersect two or more lists of search results

*	Merge two or more lists of search results

*	Subtract two or more lists of search results


Manipulating Search Results

Click one of the following:

*	Delete records from the list of search results

*	Copy records from the list of search results to another list of search results

*	Move records from the list of search results to another list of search results

*	Intersect two or more lists of search results

*	Merge two or more lists of search results

*	Subtract two or more lists of search results


Manipulating Search Results

Click one of the following:

*	Delete records from the list of search results

*	Copy records from the list of search results to another list of search results

*	Move records from the list of search results to another list of search results

*	Intersect two or more lists of search results

*	Merge two or more lists of search results

*	Subtract two or more lists of search results


Manipulating Search Results

Click one of the following:

*	Delete records from the list of search results

*	Copy records from the list of search results to another list of search results

*	Move records from the list of search results to another list of search results

*	Intersect two or more lists of search results

*	Merge two or more lists of search results

*	Subtract two or more lists of search results


Manipulating Search Results

Click one of the following:

*	Delete records from the list of search results

*	Copy records from the list of search results to another list of search results

*	Move records from the list of search results to another list of search results

*	Intersect two or more lists of search results

*	Merge two or more lists of search results

*	Subtract two or more lists of search results


Manipulating Search Results

Click one of the following:

*	Delete records from the list of search results

*	Copy records from the list of search results to another list of search results

*	Move records from the list of search results to another list of search results

*	Intersect two or more lists of search results

*	Merge two or more lists of search results

*	Subtract two or more lists of search results


Manipulating Search Results

Click one of the following:

*	Delete records from the list of search results

*	Copy records from the list of search results to another list of search results

*	Move records from the list of search results to another list of search results

*	Intersect two or more lists of search results

*	Merge two or more lists of search results

*	Subtract two or more lists of search results


Manipulating Search Results

Click one of the following:

*	Delete records from the list of search results

*	Copy records from the list of search results to another list of search results

*	Move records from the list of search results to another list of search results

*	Intersect two or more lists of search results

*	Merge two or more lists of search results

*	Subtract two or more lists of search results


Manipulating Search Results

Click one of the following:

*	Delete records from the list of search results

*	Copy records from the list of search results to another list of search results

*	Move records from the list of search results to another list of search results

*	Intersect two or more lists of search results

*	Merge two or more lists of search results

*	Subtract two or more lists of search results


Manipulating Search Results

Click one of the following:

*	Delete records from the list of search results

*	Copy records from the list of search results to another list of search results

*	Move records from the list of search results to another list of search results

*	Intersect two or more lists of search results

*	Merge two or more lists of search results

*	Subtract two or more lists of search results


Manipulating Search Results

Click one of the following:

*	Delete records from the list of search results

*	Copy records from the list of search results to another list of search results

*	Move records from the list of search results to another list of search results

*	Intersect two or more lists of search results

*	Merge two or more lists of search results

*	Subtract two or more lists of search results


Manipulating Search Results

Click one of the following:

*	Delete records from the list of search results

*	Copy records from the list of search results to another list of search results

*	Move records from the list of search results to another list of search results

*	Intersect two or more lists of search results

*	Merge two or more lists of search results

*	Subtract two or more lists of search results


Manipulating Search Results

Click one of the following:

*	Delete records from the list of search results

*	Copy records from the list of search results to another list of search results

*	Move records from the list of search results to another list of search results

*	Intersect two or more lists of search results

*	Merge two or more lists of search results

*	Subtract two or more lists of search results


Manipulating Search Results

Click one of the following:

*	Delete records from the list of search results

*	Copy records from the list of search results to another list of search results

*	Move records from the list of search results to another list of search results

*	Intersect two or more lists of search results

*	Merge two or more lists of search results

*	Subtract two or more lists of search results


Manipulating Search Results

Click one of the following:

*	Delete records from the list of search results

*	Copy records from the list of search results to another list of search results

*	Move records from the list of search results to another list of search results

*	Intersect two or more lists of search results

*	Merge two or more lists of search results

*	Subtract two or more lists of search results


To delete records from a list of search results

Use this procedure to delete records from a list of search results.

1.	Click the Browse mode (if not selected).

2.	Use [image], [image], [image], [image], and [image] to display the record that you want to delete.

Keyboard Equivalents

3.	Choose List > Discard Item.

4.	(Optional) To delete additional records, repeat Steps 2 and 3.

See also:

To restore deleted records


To delete records from a list of search results

Use this procedure to delete records from a list of search results.

1.	Click the Browse mode (if not selected).

2.	Use [image], [image], [image], [image], and [image] to display the record that you want to move.

Keyboard Equivalents

3.	Choose List > Discard Item.

4.	(Optional) To delete additional records, repeat Steps 2 and 3.

See also:

To restore deleted records


To move records to another list of search results

You can move records from the current list of search results to another list of search results called the target list. When you move a record to the target list, ISIS deletes that record from the current list.

1.	Click the Browse mode (if not selected).

2.	Use [image], [image], [image], [image], and [image] to display the record that you want to move.

Keyboard Equivalents

3.	Do one of the following:

*	To move the record to an existing target list, choose List > Move Item To > List. When you see the dialog box, choose the target list from the Target List box and click Move.

*	To create a new target list and move the record to that list, choose List > Move Item To > New List. Enter the required information into the dialog box. Click OK, then click Move.

4.	(Optional) To move additional records to the target list, choose List > Repeat Move To.

See also:

To restore moved records to the original list


To copy records to another list of search results

You can copy records from the current list of search results to another list of search results called the target list.

1.	Click the Browse mode (if not selected).

2.	Use [image], [image], [image], [image], and [image] to display the record that you want to move.

Keyboard Equivalents

3.	Do one of the following:

*	To copy the record to an existing target list, choose List > Move Item To > List. When you see the dialog box, choose the target list from the Target List box and click Copy.

*	To create a new target list and copy the record to that list, choose List > Move Item To > New List. Enter the required information into the dialog box. Click OK, then click Copy.

4.	(Optional) To copy additional records to the target list, choose List > Repeat Copy To.


To intersect two or more lists of search results

You can intersect two or more lists of search results to create a new list that contains only the records that appear on all lists (logical AND).

1.	Click the Browse mode (if not selected).

2.	Choose List > Logic.

3.	Click [image] AND.

4.	Click the name of the first list that you want to intersect in the List 1 box.

5.	Click the name of the other list that you want to intersect in the List 2 box.

6.	Click Apply. The intersected list is now the current list.

7.	(Optional) To intersect additional lists, repeat Steps 4 through 6.

8.	Click Close.


To merge two or more lists of search results

You can merge two or more lists of search results to create a new list that contains all the records on all the lists (logical OR).

1.	Click the Browse mode (if not selected).

2.	Choose List > Logic.

3.	Click [image] OR.

4.	Click the name of one of the lists that you want to merge in the List 1 box.

5.	Click the name of the other list that you want to merge in the List 2 box.

6.	Click Apply. The merged list is now current.

7.	(Optional) To merge additional lists, repeat Steps 4 through 6.

8.	Click Close.


To subtract one or more lists of search results from another list

You can subtract the records on one list of search results from the records on another list. When you do this, ISIS creates a new list that contains only the records from the first list that are not also on the second list (logical NOT).

1.	Click the Browse mode (if not selected).

2.	Choose List > Logic.

3.	Click [image] NOT.

4.	Click the name of the list from which you want to subtract records in the List 1 box.

5.	Click the name of the list that contains the records that you want to subtract in the List 2 box.

6.	Click Apply. The subtracted list is now current.

7.	(Optional) To subtract additional lists from the first list, repeat Steps 4 through 6.

8.	Click Close.


Exporting Search Results From a Remote Database

Click here for step-by-step instructions

You can export your list of search results to an ASCII text file on your host computer. This allows you to share search results with users who access the database through a different remote-access file, and to share search results with users of MACCS-II or REACCS. Any ISIS user who can access the text file on your host computer can import the search results and use them.

Note: You can export a list of records only if your Hview contains a TINFO KEY line. For ASCII lists, the TINFO KEY line specifies the field whose values are used in the list. For binary lists, REGNO values are always used, regardless of what appears in the TINFO KEY line. For more information, see your ISIS Administrator.

You can also save your search results in the remote-access file of your database. However, anyone who wants to use the saved search results must access the database through the same remote-access file.


Exporting Search Results

Dead topic?

Click here for step-by-step instructions

You can export your list of search results to a text file on your host computer. This allows you to share search results with users who access the database through a different remote-access file, and to share search results with users of MACCS-II or REACCS. Any ISIS user who can access the text file on your host computer can import the search results and use them.

Note: You can export a list of records only if your Hview contains a TINFO line. For more information, see your ISIS Administrator.

You can also save your search results in the remote-access file of your database. However, anyone who wants to use the saved search results must access the database through the same remote-access file.


Exporting Search Results From a Local Database

Click here for step-by-step instructions

You can export your search results to a text file on your workstation. Export search results when your local database is read-only, or when you want to exchange search results with users who have a copy of your local database. Anyone who can access the text file on your workstation can import the search results and use them.

If your database is not read-only, you can also save your search results in the database. However, anyone who wants to use the saved search results must access the same local database.


To export the search results

1.	Click the Browse mode (if not selected).

2.	Choose File > Export > List. You see the Host File Name text box.

3.	Enter a name in the Host File Name text box. Use the file-naming conventions of the operating system of your host computer.

4.	Click OK (Mac=Save).


To export the search results

1.	Click the Browse mode (if not selected).

2.	Choose File > Export > List. You see a dialog box.

3.	Do one of the following:

*	To create a new file that contains the list of search results, enter a name in the Save As File Name text box (PC: Use the default .LST file extension that is displayed in the text box. Mac: To save a list that can be opened on the PC, press and hold the Option key while you complete this step.)

*	To overwrite an existing file with the list of search results, click the name of an existing file in the Files list box, then click Yes when you see the prompt on overwriting the file.

4.	Click OK (Mac=Save).


Exporting Search Results

You can export your CFS search results to a list file or to a CFS SDfile. Exporting your search results to a list file allows you to share search results with users who access the database through a different remote-access file and to share search results with users of MACCS-II. Exporting your search results to a CFS SDfile allows you to use the fitted 3D conformations from the CFS search in a modeling software program.

You can also save your search results as a object in the remote-access file of your database. However, anyone who wants to use the saved search results must access the database through the same remote-access file.

Click one of the following:

*	Export the list alone

*	Export the query with the list

*	Export the fitted 3D structures to a CFS SDfile

Note: You can export a list of records only if your Hview contains a TINFO line. For more information, see your ISIS Administrator.


Exporting the List Alone

Click here for step-by-step instructions

Export the list alone when you want to use your search results solely as a search domain for a future search, or when you are not interested in viewing the fitted 3D conformations. If you view a list of CFS search results without the query, ISIS displays solely the 3D conformations that are stored in the database. Consequently, if you want to view the fitted conformations in ISIS/Base, you must save both the query and the list.

If you want to save the fitted 3D conformations so that you can import them into a modeling software program, you must export them to a CFS SDfile.

Note: You can export a list of records only if your Hview contains a TINFO line. For more information, see your ISIS Administrator.


Exporting the Query With the List

Click here for step-by-step instructions

Export the query with the list when you want to view the fitted conformations in ISIS/Base at a later time. If you view a list of CFS search results without the query, ISIS displays the 3D conformations that are stored in the database, not the fitted conformations from the CFS search. To view the fitted conformations in ISIS/Base, you must save both the query and the list.

If you want to save the fitted 3D conformations so that you can use them in a modeling software program, you must export them to a CFS SDfile.

Note: You can export a list of records only if your Hview contains a TINFO line. For more information, see your ISIS Administrator.


Exporting Fitted 3D Structures to a CFS SDfile

Click here for step-by-step instructions

Export the results of a CFS search to a CFS SDfile when you want to use the fitted conformations that result from the CFS search in a modeling software program.

If you want to export your search results so that you can view them later in ISIS/Base, you must export the list and the query. If you want to export your search results so that you can use the list as a search domain, you can export the list alone.

Note: You can export fitted structures to a CFS SDfile solely if your Hview contains a TINFO line. For more information, see your ISIS Administrator.


To export the list of search results alone

1.	Click the Browse mode (if not highlighted).

2.	Choose File > Export > List. You see the Host File Name text box.

3.	Enter a name in the Host File Name text box. Use the file-naming conventions of the operating system of your host computer.

4.	Click OK (Mac=Save).


To export the query with the list of search results

To export a CFS query with the list of search results, you export the 3D graphical query to a molfile and export the list to a list file.

1.	Write down the CFS Options that you used to conduct the search. You will need these when you view the search results later.

2.	Click the Query mode (if not selected).

3.	Click the box or column that contains the CFS query.

4.	Choose File > Export > MolFile. (Mac: To save a molfile that can be opened on the PC, press and hold the Option key while you complete this step.)

5.	Enter a name for the molfile.

6.	Click OK (Mac=Save).

7.	Click the Browse mode.

8.	Choose File > Export > List. You see the Host File Name text box.

9.	Enter a name in the Host File Name text box. Use the file-naming conventions of the operating system of your host computer.

10.	Click OK (Mac=Save).


To export search results to a CFS SDfile

Note: To export search results to a CFS SDfile, the PL Startup directory on your workstation must contain enough disk space to duplicate the CFS SDfile in your directory on the host computer.

1,	Click the Query mode.

2.	Choose File > Export > CFS SDfile. You see the Output SDfile Name text box. (Mac: To save a CFS SDfile that can be opened on the PC, press and hold the Option key while you complete this step.)

3.	Do one of the following:

*	To export the CFS SDfile solely to the PL Startup directory on your workstation, enter a filename.

*	To export the CFS SDfile to both the PL Startup directory and to your host computer, enter the text HOST:: followed by a filename. Use the file-naming conventions of the operating system of your host computer.

4.	Click OK (Mac=Save).

See also:

To abandon exporting the CFS SDfile


To abandon exporting the CFS SDfile

Use this procedure to abandon exporting a CFS SDfile before ISIS completes the exporting process.

1.	To abandon exporting the CFS SDfile:

*	On the PC, press and hold the Esc key.

*	On the Macintosh, press and hold the Command key and the period key.


To save the query

You can save the current molecule query as an object in the remote-access file of your database. You can later restore the query and change it, or use it as part of a new query.

Note

1.	Click the Query mode (if not selected).

2.	Click the box or column that contains the structure that you want to save.

3.	Choose Database > Save Molecule. You see a dialog box.

4.	Enter a name for the structure.

5.	(Optional) To enter a description of the structure, click the Description box and enter the description.

6.	Click OK.


To save the query

You can save the current query as an object in the remote-access file of your database. You can later restore the query and change it, or use it as part of a new query.

Note

1.	Click the Query mode (if not selected).

2.	Choose Search > Save Query. You see a dialog box.

3.	Enter a name for the query.

4.	Do one of the following:

*	To save the current query, click [image] Current Query.

*	To save the query from the most recent search, click [image] Last Executed Query.

5.	Click OK.


Note

You can also export your molecule query to a molfile on disk. Export your query when you want to exchange queries with users who access the database through a different remote-access file, or to exchange queries with MACCS-II, REACCS, or CPSS users.


Note

You can also export the graphical portion of your MSim query to a molfile on disk. Export your query when you want to exchange queries with users who access the database through a different remote-access file, or to exchange queries with MACCS-II, REACCS, or CPSS users.


To save the query

You can save the current reaction query as an object in the remote-access file of your database. You can later restore the query and change it, or use it as part of a new query.

Note

1.	Click the Query mode (if not selected).

2.	Click the box or column that contains the reaction that you want to save.

3.	Choose Database > Save Reaction. You see a dialog box.

4.	Enter a name for the reaction.

5.	(Optional) To enter a description of the reaction, click the Description box and enter the description.

6.	Click OK.


To save the query

You can save the current query as an object in the remote-access file of your database. You can later restore the query and change it, or use it as part of a new query.

Note

1.	Click the Query mode (if not selected).

2.	Choose Search > Save Query. You see a dialog box.

3.	Enter a name for the query.

4.	Do one of the following:

*	To save the current query, click [image] Current Query.

*	To save the query from the most recent search, click [image] Last Executed Query.

5.	Click OK.


Note

You can also export your reaction query to a file on disk. Export your query when you want to exchange queries with users who access the database through a different remote-access file, or when you want to exchange queries with REACCS or CPSS users.


Note

You can also export the graphical portion of your reaction query to a file on disk. Export your query when you want to exchange queries with users who access the database through a different remote-access file, or when you want to exchange queries with REACCS or CPSS users.


To save the query

You can save the current 3D query as an object in the remote-access file of your database. You can later restore the query and change it, or use it as part of a new query.

Note

1.	Click the Query mode (if not selected).

2.	Click the box or column that contains the 3D query that you want to save.

3.	Choose Database > Save Molecule. You see a dialog box.

4.	Enter a name for the query.

5.	(Optional) To enter a description of the query, click the Description box and enter the description.

6.	Click OK.


To save the query

You can save your CFS query as an object in the remote-access file of your database. You can later restore the query and change it, or use it as part of a new query.

Note

1.	Click the Query mode (if not selected).

2.	Choose Search > Save Query. You see a dialog box.

3.	Enter a name for the query.

4.	Do one of the following:

*	To save the current query, click [image] Current Query.

*	To save the query from the most recent search, click [image] Last Executed Query.

5.	Click OK.


Note

You can also export your 3D query to a molfile on disk. Export your query when you want to exchange queries with users who access the database through a different remote-access file, or to exchange queries with MACCS-II users.


Note

You can also export the graphical portion of your CFS query to a molfile on disk. Export your query when you want to exchange queries with users who access the database through a different remote-access file, or to exchange queries with MACCS-II users.


To save the query

You can save your molecule query as an object in your database. You can later restore the structure and change it, or use it as part of a new query.

Note

1.	Click the Query mode (if not selected).

2.	Click the box or column that contains the structure that you want to save.

3.	Choose Database > Save Molecule. You see a dialog box.

4.	Enter a name for the structure.

5.	(Optional) To enter a description of the structure, click the Description box and enter the description.

6.	Click OK.


Note

You cannot save your molecule query permanently in a local database that is read-only. If the database is read-only, you can export the structure to a molfile on your workstation. For more information on read-only databases, see your ISIS Administrator.


To save the query

You can save your reaction query as an object in your database. You can later restore the reaction and change it, or use it as part of a new query.

Note

1.	Click the Query mode (if not selected).

2.	Click the box or column that contains the reaction that you want to save.

3.	Choose Database > Save Reaction. You see a dialog box.

4.	Enter a name for the reaction.

5.	(Optional) To enter a description of the reaction, click the Description box and enter the description.

6.	Click OK.


Note

You cannot save your reaction query permanently in a local database that is read-only. If the database is read-only, you can export the structure to a molfile on your workstation. For more information on read-only databases, see your ISIS Administrator.


To save the query

You can save your 3D query as an object in your database. You can later restore the query and change it, or use it as part of a new query.

Note

1.	Click the Query mode (if not selected).

2.	Click the box or column that contains the 3D query that you want to save.

3.	Choose Database > Save Molecule. You see a dialog box.

4.	Enter a name for the 3D query.

5.	(Optional) To enter a description of the 3D query, click the Description box and enter the description.

6.	Click OK.


Note

You cannot save your 3D query permanently in a local database that is read-only. If the database is read-only, you can export the 3D query to a molfile on your workstation. For more information on read-only databases, see your ISIS Administrator.


To save the query

You can save your query as an object in the remote-access file of your database. You can later restore the query and change it, or use it as part of a new query.

1.	Click the Query mode (if not selected).

2.	Choose Search > Save Query. You see a dialog box.

3.	Enter a name for the query.

4.	Do one of the following:

*	To save the current query, click [image] Current Query.

*	To save the query from the most recent search, click [image] Last Executed Query.

5.	Click OK.


To save the query

You can save your query as an object in the remote-access file of your database. You can later restore the query and change it, or use it as part of a new query.

1.	Click the Query mode (if not selected).

2.	Choose Search > Save Query. You see a dialog box.

3.	Enter a name for the query.

4.	Do one of the following:

*	To save the current query, click [image] Current Query.

*	To save the query from the most recent search, click [image] Last Executed Query.

5.	Click OK.


To save the query

You can save your query as an object in the remote-access file of your database. You can later restore the query and change it, or use it as part of a new query.

1.	Click the Query mode (if not selected).

2.	Choose Search > Save Query. You see a dialog box.

3.	Enter a name for the query.

4.	Do one of the following:

*	To save the current query, click [image] Current Query.

*	To save the query from the most recent search, click [image] Last Executed Query.

5.	Click OK.


To save the query

You can save your formula query as an object in the remote-access file of your database. You can later restore the query and change it, or use it as part of a new query.

1.	Click the Query mode (if not selected).

2.	Choose Search > Save Query. You see a dialog box.

3.	Enter a name for the query.

4.	Do one of the following:

*	To save the current query, click [image] Current Query.

*	To save the query from the most recent search, click [image] Last Executed Query.

5.	Click OK.


To save the query

You can save your query as an object in your database. You can later restore the query and change it, or use it as part of a new query.

Note

1.	Click the Query mode (if not selected).

2.	Choose Search > Save Query. You see a dialog box.

3.	Enter a name for the query.

4.	Do one of the following:

*	To save the current query, click [image] Current Query.

*	To save the query from the most recent search, click [image] Last Executed Query.

5.	Click OK.


Note

You cannot save your query permanently in a database that is read-only. For more information on read-only databases, see your ISIS Administrator.


To save the query

You can save your query as an object in your database. You can later restore the query and change it, or use it as part of a new query.

Note

1.	Click the Query mode (if not selected).

2.	Choose Search > Save Query. You see a dialog box.

3.	Enter a name for the query.

4.	Do one of the following:

*	To save the current query, click [image] Current Query.

*	To save the query from the most recent search, click [image] Last Executed Query.

5.	Click OK.


To save the query

You can save your query as an object in your database. You can later restore the query and change it, or use it as part of a new query.

Note

1.	Click the Query mode (if not selected).

2.	Choose Search > Save Query. You see a dialog box.

3.	Enter a name for the query.

4.	Do one of the following:

*	To save the current query, click [image] Current Query.

*	To save the query from the most recent search, click [image] Last Executed Query.

5.	Click OK.


To save the query

You can save your formula query as an object in your database. You can later restore the query and change it, or use it as part of a new query.

Note

1.	Click the Query mode (if not selected).

2.	Choose Search > Save Query. You see a dialog box.

3.	Enter a name for the query.

4.	Do one of the following:

*	To save the current query, click [image] Current Query.

*	To save the query from the most recent search, click [image] Last Executed Query.

5.	Click OK.


To save the query

You can save your query as an object in the remote-access file of your database. You can later restore the query and change it, or use it as part of a new query.

1.	Click the Query mode (if not selected).

2.	Choose Search > Save Query. You see a dialog box.

3.	Enter a name for the query.

4.	Do one of the following:

*	To save the current query, click [image] Current Query.

*	To save the query from the most recent search, click [image] Last Executed Query.

5.	Click OK.


To save the query

You can save your query as an object in your database. You can later restore the query and change it, or use it as part of a new query.

Note

1.	Click the Query mode (if not selected).

2.	Choose Search > Save Query. You see a dialog box.

3.	Enter a name for the query.

4.	Do one of the following:

*	To save the current query, click [image] Current Query.

*	To save the query from the most recent search, click [image] Last Executed Query.

5.	Click OK.


To print the query

Use this procedure to print the query with the form.

1.	Click the Query mode (if not highlighted).

2.	(Optional) To check the page size or orientation, choose File >Print Setup. Click OK when you are finished.

3.	Choose File > Print.

4.	Click OK.

5.	Click OK to begin printing. You might observe a pause before printing begins and additional pauses between pages.


Exporting the Query

Click here for step-by-step instructions

You can export your molecule query to a file on disk. This allows you to share molecule queries with users who access the database through a different remote-access file, and to share queries with users of MACCS-II, REACCS, and CPSS. Any ISIS user who can access the molfile can import the structure and use it.

You can also save your molecule query as an object in the remote-access file of your database. However, anyone who wants to use the molecule must access the database through the same remote-access file.


To export a molecule query

1.	Click the Query mode (if not selected).

2.	Click the box or column that contains the structure that you want to export.

3.	Choose File > Export > MolFile. You see a dialog box. (Mac: To save a molfile that can be opened on the PC, press and hold the Option key while you complete this step.)

4.	Enter a name for the molfile.

5.	Click OK (Mac=Save).


To export a molecule query

You can export your molecule query to a molfile on disk. This allows you to share molecule queries with users of MACCS-II, REACCS, and CPSS. Any ISIS user who can access the molfile can import the structure and use it.

1.	Click the Query mode (if not selected).

2.	Click the box or column that contains the structure that you want to export.

3.	Choose File > Export > MolFile. You see a dialog box. (Mac: To save a molfile that can be opened on the PC, press and hold the Option key while you complete this step.)

4.	Enter a name for the molfile.

5.	Click OK (Mac=Save).


Exporting the Query

Click here for step-by-step instructions

You can export your reaction query to a file on disk. This allows you to share reaction queries with users who access the database through a different remote-access file, and to share queries with users of REACCS or CPSS. Any ISIS user who can access the rxnfile can import the reaction and use it.

You can also save your reaction query as an object in the remote-access file of your database. However, anyone who wants to use the reaction must access the database through the same remote-access file.


To export a reaction query

1.	Click the Query mode (if not selected).

2.	Click the box or column that contains the reaction that you want to export.

3.	Do one of the following:

*	To save the reaction as a CPSS rxnfile, choose File > Export > CPSS RxnFile. You see a dialog box.

*	To save the reaction as a REACCS rxnfile, choose File > Export > REACCS RxnFile. You see a dialog box.

Note:  (Mac: To save a rxnfile that can be opened on the PC, press and hold the Option key while you complete this step.)

4.	Enter a name for the rxnfile.

5.	Click OK (Mac=Save).


To export a reaction query

You can export your reaction query to a rxnfile on disk. This allows you to share reaction queries with users of REACCS and CPSS. Any ISIS user who can access the rxnfile can import the reaction and use it.

1.	Click the Query mode (if not selected).

2.	Click the box or column that contains the reaction that you want to export.

3.	Do one of the following:

*	To save the reaction as a CPSS rxnfile, choose File > Export > CPSS RxnFile. You see a dialog box.

*	To save the reaction as a REACCS rxnfile, choose File > Export > REACCS RxnFile. You see a dialog box.

Note:  (Mac: To save a rxnfile that can be opened on the PC, press and hold the Option key while you complete this step.)

4.	Enter a name for the rxnfile.

5.	Click OK (Mac=Save).


Exporting the Query

Click here for step-by-step instructions

You can export your 3D query to a file on disk. This allows you to share queries with users who access the database through a different remote-access file, and to share queries with users of MACCS-II. Any ISIS user who can access the query can import the query and use it.

You can also save your 3D query as an object in the remote-access file of your database. However, anyone who wants to use the query must access the database through the same remote-access file.


To export a 3D query

1.	Click the Query mode (if not selected).

2.	Click the box or column that contains the 3D query that you want to export.

3.	Choose File > Export > MolFile. You see a dialog box. (Mac: To save a molfile that can be opened on the PC, press and hold the Option key while you complete this step.)

4.	Enter a name for the molfile.

5.	Click OK (Mac=Save).


Exporting the Query

Click here for step-by-step instructions

You can export your molecule query to a file on disk. This allows you to share molecule queries with users of MACCS-II, REACCS, and CPSS. Any ISIS user who can access the molfile can import the structure and use it.

If your database is not read-only, you can also save your molecule query as an object in the database. However, anyone who wants to use the saved structure must access the same local database. For more information on read-only databases, see your ISIS Administrator.


To export a molecule query

1.	Click the Query mode (if not selected).

2.	Click the box or column that contains the structure that you want to export.

3.	Choose File > Export > MolFile. You see a dialog box. (Mac: To save a molfile that can be opened on the PC, press and hold the Option key while you complete this step.)

4.	Enter a name for the molfile.

5.	Click OK (Mac=Save).


Exporting the Query

Click here for step-by-step instructions

You can export your reaction query to a file on disk. This allows you to share reaction queries with users of REACCS or CPSS. Any ISIS user who can access the file can import the reaction and use it.

If your database is not read-only, you can also save your reaction query as an object in the database. However, anyone who wants to use the saved reaction must access the same local database.

For more information on read-only databases, see your ISIS Administrator.


To export a reaction query

1.	Click the Query mode (if not selected).

2.	Click the box or column that contains the reaction that you want to export.

3.	Do one of the following:

*	To save the reaction as a CPSS rxnfile, choose File > Export > CPSS RxnFile. You see a dialog box.

*	To save the reaction as a REACCS rxnfile, choose File > Export > REACCS RxnFile. You see a dialog box.

Note:  (Mac: To save a rxnfile that can be opened on the PC, press and hold the Option key while you complete this step.)

4.	Enter a name for the rxnfile.

5.	Click OK (Mac=Save).


Exporting the Query

Click here for step-by-step instructions

You can export your 3D query to a file on disk. This allows you to share queries with users of MACCS-II. Any ISIS user who can access the query can import the query and use it.

If your database is not read-only, you can also save your 3D query as an object in the database. However, anyone who wants to use the saved query must access the same local database. For more information on read-only databases, see your ISIS Administrator.


To export the query

1.	Click the Query mode (if not selected).

2.	Click the box or column that contains the structure that you want to export.

3.	Choose File > Export > MolFile. You see a dialog box. (Mac: To save a molfile that can be opened on the PC, press and hold the Option key while you complete this step.)

4.	Enter a name for the molfile.

5.	Click OK (Mac=Save).


To restore deleted records to the current list

If you accidentally delete a record from the current list, you can move it back to the current list before you close the database. When you delete records from the current list, ISIS places the deleted records on a temporary list called Discard. You can recover deleted records by moving them from Discard to the list from which you deleted them.

1.	Save the current list.

2.	Open the Discard list.

3.	Use [image], [image], [image], [image], and [image] to display the record that you accidentally deleted.

Keyboard Equivalents

4.	Move the deleted record to the list that you want to correct.

5.	(Optional) To move additional deleted records to the list, repeat Steps 3 and 4.

6.	Open the corrected list.


To save the current list

1.	Click the Browse mode (if not selected).

2.	Choose List > Save List.

3.	Click the List name box and enter a name for the current list (without a file-name extension).

4.	Do one of the following:

*	To store the list as a permanent database object, you require this setting: Permanent.

*	To delete the list when you close the database, you require this setting: Permanent.

5.	Click OK.


To open the Discard list

1.	Choose List > Open List.

2.	Choose Discard from the Open List box.

3.	Click OK. Discard becomes the current list.


To move a deleted record to the list that you want to correct

1.	Choose List > Move Item To > List.

2.	Click the name of the list that you want to correct. You see a dialog box.

3.	Click Move.


To open the corrected list

1.	Choose List > Open List.

2.	Choose the corrected list from the Open List box.

3.	Click OK. The corrected list becomes the current list.


To restore a moved record to the original list
To restore moved records to the original list

If you accidentally move a record from the current list to another list, you can move the record back to the list before you close the database.

1.	Save the current list.

2.	Open the original target list.

3.	Use [image], [image], [image], [image], and [image] to display the record that you accidentally moved.

Keyboard Equivalents

4.	Move the deleted record back to the original current list (the list that you saved in Step 1).

5.	Open the corrected list.


To open the original target list

Use this procedure to open the target list to which you accidentally moved records (original target list).

1.	Choose List > Open List.

2.	Click the name of the list to which you accidentally moved records.

3.	Click OK. The original target list becomes the current list.


To print the form with database fields

Use this procedure to print the current form with the names of database fields that are connected to boxes and columns in the form.

1.	Click the Forms mode (if not selected).

2.	(Optional) To check the page size or orientation, choose File >Print Setup. Click OK when you are finished.

3.	Choose File > Print.

4.	Click OK.

5.	Click OK to begin printing. You might observe a pause before printing begins and additional pauses between pages.


To save a 2D or 3D structure as a database object

You can save a 2D or 3D structure as an object in your database. You can later restore the structure and change it, or use it as part of a query.

This procedure assumes that you are in Query, Browse, or Update mode.

1.	Click the box or column that contains the structure that you want to save.

2.	Choose Database > Save Molecule. You see a dialog box.

3.	Enter a name for the structure.

4.	(Optional) To enter a description of the structure, click the Description box and enter the description.

5.	Click OK.


To save a reaction as a database object

You can save a reaction as an object in your database. You can later restore the reaction and change it, or use it as part of a query.

This procedure assumes that you are in Query, Browse, or Update mode.

1.	Click the box or column that contains the reaction that you want to save.

2.	Choose Database > Save Reaction. You see a dialog box.

3.	Enter a name for the reaction.

4.	(Optional) To enter a description of the reaction, click the Description box and enter the description.

5.	Click OK.


To restore a reaction from the database

You can restore a reaction that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a reaction from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Click a box or table cell that is connected to a reaction structure (RXNSTRUCTURE) database field.

3.	Choose Database > Restore Reaction.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). You see the selected reaction on your form.


To restore a 2D or 3D structure from the database

You can restore a 2D or 3D structure that you previously saved as an object in your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click the Query mode (if not highlighted).

2.	Click a box or table cell that is connected to a 2D structure (MOLSTRUCTURE) or 3D structure (MODELSTRUCTURE) database field.

3.	Choose Database > Restore Molecule. You see the Select Object dialog box.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). You see the structure on your form.


To import a molfile

You can import a 2D or 3D structure from a molfile that you created in CPSS, ISIS, REACCS, or MACCS-II.

This procedure assumes that you are in Query or Update mode.

1.	Click a box or table cell that is connected to a 2D structure (MOLSTRUCTURE) or 3D structure (MODELSTRUCTURE) database field.

2.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

3.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

4.	Click OK (Mac=Open). The structure is imported into your form.


To import a rxnfile

Use this procedure to import a reaction from a rxnfile that you created in CPSS, ISIS, or REACCS.

This procedure assumes that you are in Query or Update mode.

1.	Select a box or table cell that is connected to a reaction (RXNSTRUCTURE) database field.

2.	Choose File > Import > Rxnfile. (To retrieve a PC-rxnfile on the Macintosh, press and hold the Option key while you complete this step.)

3.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

4.	Click OK (Mac=Open). The selected reaction is imported into your form.


To export a 2D or 3D structure to a molfile

You can export a 2D or 3D structure on your form to a molfile on disk. This allows you to share molecule queries with users of MACCS-II, REACCS, and CPSS. Any ISIS user who can access the molfile can import the structure and use it.

This procedure assumes that you are in Query, Browse, or Update mode.

1.	Click the box or column that contains the structure that you want to export.

2.	Choose File > Export > MolFile. You see a dialog box. (Mac: To save a molfile that can be opened on the PC, press and hold the Option key while you complete this step.)

3.	Enter a name for the molfile.

4.	Click OK (Mac=Save).


To export a reaction to a rxnfile

You can export a reaction on your form to a rxnfile on disk. This allows you to share reaction queries with users of REACCS and CPSS. Any ISIS user who can access the rxnfile can import the reaction and use it.

This procedure assumes that you are in Query, Browse, or Update mode.

1.	Click the box or column that contains the reaction that you want to export.

2.	Do one of the following:

*	To save the reaction as a CPSS rxnfile, choose File > Export > CPSS RxnFile. You see a dialog box.

*	To save the reaction as a REACCS rxnfile, choose File > Export > REACCS RxnFile. You see a dialog box.

Note:  (Mac: To save a rxnfile that can be opened on the PC, press and hold the Option key while you complete this step.)

3.	Enter a name for the rxnfile.

4.	Click OK (Mac=Save).


Why Not Sort Search Results?

You need not sort your search results. If you do not sort your search results, the records appear in the order in which ISIS retrieved them from the database.

If you want to sort search results automatically after the search, you must define the sorting instructions before the search.

Note: If you sort by structural and/or transformational similarity, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.


What Is Sorting by Structural Similarity?

Click here for step-by-step instructions

Structural similarity is the degree of similarity between the molecules in your reaction query (reactants and products) and the molecules in the reactions that you retrieve during the search. For example, you can sort your search results so that reactions with the highest (or lowest) structural similarity to the query appear first on the list.

Note: If you sort by structural similarity, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.


What Is Sorting by Transformational Similarity?

Click here for step-by-step instructions

Transformational similarity is the degree of similarity between the reacting center of your query and the reacting center of the reactions that ISIS retrieves during the search. For example, you can sort your search results so that reactions with the highest (or lowest) transformational similarity to the query appear first on the list.

Note: If you want to sort your results by transformational similarity, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.


What Is Sorting by Both Structural and Transformational Similarity?

Click here for step-by-step instructions

Transformational similarity is the degree of similarity between the reacting center of your reaction query and the reacting center of the reactions that ISIS retrieves from the database. Structural similarity is the degree of similarity between the molecules that participate in your reaction query and the molecules that participate in the reactions that ISIS retrieves from the database. You can use both types of similarity to sort your search results.

Note: If you want to sort by transformational and structural similarity, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.


What Is Sorting by Data in a Single Database Field?

Click here for step-by-step instructions

You can use data in any database field to sort your search results into a specific order. For example, you might want to sort your search results so that reactions with the highest yields appear first on the list.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

Note: If you want to sort your search results automatically after the search, you must define sorting instructions before the search.


What Is Sorting by More Than One Kind of Data?

Click here for step-by-step instructions

You can use up to three different kinds of data to sort your search results into a particular order. For example, you might want to sort your search results so that reactions with the highest yields, the lowest reaction temperatures, and the shortest reaction times appear first on the list.

You can also sort your search results with any combination of data from database fields, structural similarity, and transformational similarity.

Note: If you sort by structural and/or transformational similarity, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.


Why Not Sort Search Results?

You need not sort your search results. If you do not sort your search results, the records appear in the order in which ISIS retrieved them from the database.

If you store (save or export) your search results, you can sort them later. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in a Single Database Field?

Click here for step-by-step instructions

You can use data in any database field to sort your search results into a specific order. For example, you might want to sort your search results so that reactions with the highest yields appear first on the list.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in More Than One Database Field?

Click here for step-by-step instructions

You can use data in up to three different database fields to sort your search results into a particular order. For example, you might want to sort your search results so that reactions with the highest yields, the lowest reaction temperatures, and the shortest reaction times appear first on the list.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

Note: If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in a Single Database Field?

Click here for step-by-step instructions

You can use data in any database field to sort your search results into a specific order. For example, you might want to sort your search results so that reactions with the highest yields appear first on the list.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in More Than One Database Field?

Click here for step-by-step instructions

You can use data in up to three different database fields to sort your search results into a particular order. For example, you might want to sort your search results so that reactions with the highest yields, the lowest reaction temperatures, and the shortest reaction times appear first on the list.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

Note: If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


Why Not Sort Search Results?

You need not sort your search results. If you do not sort your search results, the records appear in the order in which ISIS retrieved them from the database.

If you want to sort search results automatically after the search, you must define the sorting instructions before the search.

Note: If you sort by structural similarity, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.


What Is Sorting by Structural Similarity?

Click here for step-by-step instructions

Structural similarity is the degree of similarity between the reaction component (reactant, product, solvent, or catalyst) in your query and the  corresponding component in the reactions that ISIS retrieves during the search. You can use structural similarity data to sort your results so that reaction components with the highest (or lowest) structural similarity to the query appear first on the list.

Note: If you want to sort by structural similarity, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.


What Is Sorting by Data in a Single Database Field?

Click here for step-by-step instructions

You can use data in a database field to sort your search results into a specific order. For example, you might want to sort your search results so that reactions with the highest yields appear first on the list.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

Note: If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by More Than One Kind of Data?

Click here for step-by-step instructions

You can use up to three different kinds of data to sort your search results into a particular order. For example, you might want to sort your search results so that reactions with the highest yields, the lowest reaction temperatures, and the shortest reaction times appear first on the list.

You can also sort your search results with any combination of structural similarity and data from database fields.

If you want to sort search results automatically after the search, you must define the sorting instructions before the search.

Note: If you sort by structural similarity, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.


Why Not Sort Search Results?

You need not sort your search results. If you do not sort your search results, the records appear in the order in which ISIS retrieved them from the database.

If you store (save or export) your search results, you can sort them later. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in a Single Database Field?

Click here for step-by-step instructions

You can use data in a database field to sort your search results into a specific order. For example, you might want to sort your search results so that reactions with the highest yields appear first on the list.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

Note: If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in More Than One Database Field?

Click here for step-by-step instructions

You can use data in up to three different database fields to sort your search results into a particular order. For example, you might want to sort your search results so that reactions with the highest yields, the lowest reaction temperatures, and the shortest reaction times appear first on the list.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results by data in database fields does not affect the order of the sorted records.

Note: If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in a Single Database Field?

Click here for step-by-step instructions

You can use data in a database field to sort your search results into a specific order. For example, you might want to sort your search results so that reactions with the highest yields appear first on the list.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

Note: If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in More Than One Database Field?

Click here for step-by-step instructions

You can use data in up to three different database fields to sort your search results into a particular order. For example, you might want to sort your search results so that reactions with the highest yields, the lowest reaction temperatures, and the shortest reaction times appear first on the list.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

Note: If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


Why Not Sort Search Results?

You need not sort your search results. If you do not sort your search results, the records appear in the order in which ISIS retrieved them from the database.

If you want to sort search results automatically after the search, you must define the sorting instructions before the search.

Note: If you sort by structural similarity, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.


What Is Sorting by Structural Similarity?

Click here for step-by-step instructions

Structural similarity is the degree of similarity between the query and the molecules that ISIS retrieves during the search. You can use structural similarity data to sort your results so that molecules with the highest (or lowest) structural similarity to the query appear first on the list.

Note: If you want to sort by structural similarity, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.


What Is Sorting by Data in a Single Database Field?

Click here for step-by-step instructions

You can use data in a database field to sort your search results into a particular order. For example, you might want to sort your list of molecule records alphabetically by type of activity. This groups molecules with the same activity together on the list.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by More Than One Kind of Data?

Click here for step-by-step instructions

You can use up to three different kinds of data to sort your search results into a particular order. For example, you might want to sort your list of records so that structures with the highest activities and lowest molecular weights appear first.

You can also sort your search results with any combination of structural similarity and data from database fields.

If you want to sort search results automatically after the search, you must define the sorting instructions before the search.

Note: If you sort by structural similarity, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.


Why Not Sort Search Results?

You need not sort your search results. If you do not sort your search results, the records appear in the order in which ISIS retrieved them from the database.

If you store (save or export) your search results, you can sort them later. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in a Single Database Field?

Click here for step-by-step instructions

You can use data in any field of your database to sort your search results into a particular order. For example, if your database contains a database field with the molecular weight of each structure, you might want to sort your list of records so that structures with the lowest molecular weight appear first.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in More Than One Database Field?

Click here for step-by-step instructions

You can use data in up to three different database fields to sort your search results into a particular order. For example, if your database contains database fields that contain information on biological activity and molecular weight of each structure, you might want to sort your list of records so that structures with the highest activity and lowest molecular weight appear first.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in a Single Database Field?

Click here for step-by-step instructions

You can use data in any field of your database to sort your search results into a particular order. For example, if your database contains a database field with the molecular weight of each structure, you might want to sort your list of records so that structures with the lowest molecular weight appear first.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in More Than One Database Field?

Click here for step-by-step instructions

You can use data in up to three different database fields to sort your search results into a particular order. For example, if your database contains database fields that contain information on biological activity and molecular weight of each structure, you might want to sort your list of records so that structures with the highest activity and lowest molecular weight appear first.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


Why Not Sort Search Results?

You need not sort your search results. If you do not sort your search results, the records appear in the order in which ISIS retrieved them from the database.

If you want to sort search results automatically after the search, you must define the sorting instructions before the search.

Note: If you sort by torsional degrees of freedom and/or RMS deviation, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.


Why Not Sort Search Results?

You need not sort your search results. If you do not sort your search results, the records appear in the order in which ISIS retrieved them from the database.

If you want to sort search results automatically after the search, you must define the sorting instructions before the search.

Note: If you sort by van der Waals energy difference, torsional degrees of freedom and/or RMS deviation, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.


What Is Sorting by van der Waals Energy Difference?

Click here for step-by-step instructions

Van der Waals energy difference is the difference in nonbonded (van der Waals) interaction energy between the 3D structure that is stored in the database and the fitted 3D structure that results from the CFS search. For example, you might want to sort your search results so that fitted structures with the smallest van der Waals energy difference appear first on your list.

Note: If you sort by van der Waals energy difference, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.


What Is Sorting by Torsional Degrees of Freedom (TDF)?

Click here for step-by-step instructions

Torsional degrees of freedom (TDF) is the number of rotatable bonds in the region that matches the query. The higher the TDF, the more flexible the molecule is in the region that matches the query.

If you are interested in structures that are relatively rigid in the region that matches the query, you might want to sort your search results so that molecules with a low TDF appear first on your list of search results.

Note: If you sort by TDF, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.


What Is Sorting by RMS Deviation?

Click here for step-by-step instructions

RMS deviation measures how well a fitted 3D structure fits the constraints of the query (goodness-of-fit). The lower the RMS deviation, the better the fit to the constraints of the query. You might want to sort your search results so that fitted structures that best fit the query appear first on the list.

Notes: (1) To sort by RMS deviation, we strongly recommend that you specify the sorting instructions before the search, and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data. (2) If you sort by RMS deviation, your query can contain solely the following 3D components: atoms, ring centroids, distances defined by two atoms or ring centroids, and angles defined by three atoms or ring centroids.


What Is Sorting by Both TDF and RMS Deviation?

Click here for step-by-step instructions

You can sort your CFS search results by both torsional degrees of freedom (TDF) and RMS deviation.

Notes: (1) To sort by TDF and RMS deviation, we strongly recommend that you specify the sorting instructions before the search, and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data. (2) If you sort by RMS deviation, your query can contain solely the following 3D components: atoms, ring centroids, distances defined by two atoms or ring centroids, and angles defined by three atoms or ring centroids.


What Is Sorting by a Combination of CFS Derived Data?

Click here for step-by-step instructions

In the bump checking CFS search, ISIS can derive three different kinds of data from the 3D structures that it retrieves during a CFS search: torsional degrees of freedom (TDF), RMS deviation, and van der Waals energy difference (vdW). You can sort your search results by any combination of CFS derived data. For example, you might want structures with the lowest TDF and the lowest van der Waals energy difference to appear first.

Notes: (1) To sort by a combination of CFS data, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data. (2) If you sort by RMS deviation, your query can contain solely the following 3D components: atoms, ring centroids, distances defined by two atoms or ring centroids, and angles defined by three atoms or ring centroids.


What Is Sorting by Data in a Database Field?

Click here for step-by-step instructions

You can use data in any field of your database to sort your search results into a specific order. For example, if your database contains a database field with information on the toxicity of each structure, you might want to sort your list of records so that structures with the lowest toxicity appear first.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by More Than One Kind of Data?

Click here for step-by-step instructions

You can use data from up to three different database fields to sort your search results into a particular order. You can also sort your search results by a combination of data from database fields and data that ISIS derives from the initial CFS search, such as torsional degrees of freedom (TDF) or RMS deviation. For example, you can sort by TDF and molecular weight.

Notes: (1) To sort by TDF or RMS deviation, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data. (2) If you sort by RMS deviation, your query can contain solely the following 3D components: atoms, ring centroids, distances defined by two atoms or ring centroids, and angles defined by three atoms or ring centroids.


What Is Sorting by More Than One Kind of Data?

Click here for step-by-step instructions

You use data from up to three different database fields to sort your search results into a particular order. You can also sort your search results with a combination of data from database fields and CFS data that ISIS derives from the bump checking CFS search, such as torsional degrees of freedom (TDF), RMS deviation, or van der Waals energy difference (vdW). For example, you can sort by TDF and molecular weight.

Notes: (1) If you sort by RMS deviation, your query can contain solely the following 3D components: atoms, ring centroids, distances defined by two atoms or ring centroids, and angles defined by three atoms or ring centroids. (2) To sort by CFS data, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.


Why Not Sort Search Results?

You need not sort your search results. If you do not sort your search results, the records appear in the order in which ISIS retrieved them from the database.

If you store (save or export) your search results, you can sort them later. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in a Database Field?

Click here for step-by-step instructions

You can use data in any field of your database to sort your search results into a particular order. For example, if your database contains a database field with information on the toxicity of each structure, you might want to sort your search results so that structures with the lowest toxicity appear first.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in More Than One Database Field?

Click here for step-by-step instructions

You can use data in up to three database fields to sort your search results into a particular order. For example, if your database contains database fields that contain information on biological activity and molecular weight, you might want molecules with the highest activity and lowest molecular weight to appear first on the list.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in a Database Field?

Click here for step-by-step instructions

You can use data in any field of your database to sort your search results into a particular order. For example, if your database contains a database field with information on the toxicity of each structure, you might want to sort your search results so that structures with the lowest toxicity appear first.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in More Than One Database Field?

Click here for step-by-step instructions

You can use data in up to three database fields to sort your search results into a particular order. For example, if your database contains database fields that contain information on biological activity and molecular weight, you might want molecules with the highest activity and lowest molecular weight to appear first on the list.

You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


Why Not Sort Search Results?

You need not sort your search results. If you do not sort your search results, ISIS orders your search results by database ID number.

If you store (save or export) your search results, you can sort them later. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in a Single Database Field?

Click here for step-by-step instructions

You can use data in any database field to sort your search results into a particular order. You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in More Than One Database Field?

Click here for step-by-step instructions

You can use data in up to three database fields to sort your search results into a particular order. You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in a Single Database Field?

Click here for step-by-step instructions

You can use data in any database field to sort your search results into a particular order. You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in More Than One Database Field?

Click here for step-by-step instructions

You can use data in up to three database fields to sort your search results into a particular order. You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


Why Not Sort Search Results?

You need not sort your search results. If you do not sort your search results, ISIS orders your search results by database ID number.

If you store (save or export) your search results, you can sort them later. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in a Single Database Field?

Click here for step-by-step instructions

You can use data in any database field to sort your search results into a particular order. You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in More Than One Database Field?

Click here for step-by-step instructions

You can use data in up to three database fields to sort your search results into a particular order. You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in a Single Database Field?

Click here for step-by-step instructions

You can use data in any database field to sort your search results into a particular order. You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in More Than One Database Field?

Click here for step-by-step instructions

You can use data in up to three database fields to sort your search results into a particular order. You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


Why Not Sort Search Results?

You need not sort your search results. If you do not sort your search results, ISIS orders your search results by database ID number.

If you store (save or export) your search results, you can sort them later. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in a Single Database Field?

Click here for step-by-step instructions

You can use data in any database field to sort your search results into a particular order. You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in More Than One Database Field?

Click here for step-by-step instructions

You can use data in up to three database fields to sort your search results into a particular order. You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in a Single Database Field?

Click here for step-by-step instructions

You can use data in any database field to sort your search results into a particular order. You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in More Than One Database Field?

Click here for step-by-step instructions

You can use data in up to three database fields to sort your search results into a particular order. You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


Why Not Sort Search Results?

You need not sort your search results. If you do not sort your search results, ISIS orders your search results by database ID number.

If you store (save or export) your search results, you can sort them later. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in a Single Database Field?

Click here for step-by-step instructions

You can use data in any database field to sort your search results into a particular order. You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in More Than One Database Field?

Click here for step-by-step instructions

You can use data in up to three database fields to sort your search results into a particular order. You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in a Single Database Field?

Click here for step-by-step instructions

You can use data in any database field to sort your search results into a particular order. You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


What Is Sorting by Data in More Than One Database Field?

Click here for step-by-step instructions

You can use data in up to three database fields to sort your search results into a particular order. You can sort your search results automatically after the search. Alternatively, you can sort your search results at a later time. You can also sort a list of search results that you have previously saved. When you choose to sort your search results does not affect the order of the sorted records.

If you want to sort your search results automatically after the search, you must define the sorting instructions before the search.


To sort by structural similarity

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

2.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by transformational similarity

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

2.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by both structural and transformational similarity

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

2.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in a single database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by more than one kind of data

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in a single database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in more than one database field

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in a single database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in more than one database field

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by similarity

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

2.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in a single database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by more than one kind of data

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in a single database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.


To sort by data in more than one database field

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.


To sort by data in a single database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in more than one database field

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following;

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by similarity

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

2.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in a single database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by more than one kind of data

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in a single database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.


To sort by data in more than one database field

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.


To sort by data in a single database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in more than one database field

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by van der Waals energy difference

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

2.	Choose Options > CFS Options.

3.	To sort by van der Waals energy difference, you require these settings:

Bump Checking at: View Time [image] Search Time

4.	Click OK.

5.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by torsional degrees of freedom (TDF)

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

2.	Choose Options > CFS Options.

3.	To sort by torsional degrees of freedom, you require this setting:

4.	Click OK.

5.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by RMS deviation

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

2.	Choose Options > CFS Options.

3.	To specify the derivative fitter, click [image] Derivative

4.	To sort by RMS deviation, you require this setting:

5.	Click OK.

6.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by both TDF and RMS deviation

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

2.	Choose Options > CFS Options.

3.	To specify the derivative fitter, click [image] Derivative

4.	To sort by TDF and RMS deviation, you require these settings:

5.	Click OK.

6.	You require [image] Sort On List on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by more than one kind of CFS data

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

2.	Choose Options > CFS Options.

3.	Specify CFS options for sorting.

4.	Click OK.

5.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in a single database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by more than one kind of data

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	(Optional) Specify CFS options for sorting.

5.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


Specifying CFS Options For Sorting

Click here for step-by-step instructions

If you sort by any kind of CFS derived data (torsional degrees of freedom, van der Waals energy difference, or RMS deviation), you must specify the CFS options that instruct ISIS to calculate that data. If you do not specify the correct CFS options, ISIS cannot sort your search results correctly.

Note: CFS searching provides many options that allow you to control how ISIS fits 3D structures to your query. These options subtly interact with each other and can produce undesirable results if improperly used. We strongly recommend that you study CFS Searching Concepts/Examples before you attempt CFS searching.


To specify CFS options for sorting

1.	Click the Query mode (if not selected).

2.	Choose Options > CFS Options. You see the CFS Options dialog box.

3.	Set [image] to specify the type of CFS data that you want to use for sorting:

4.	(Optional) To sort by RMS deviation, click [image] Derivative

5.	(Optional) To sort by van der Waals energy difference, you require these settings:

Bump Checking at: View Time [image] Search Time

6.	Click OK.


To sort by data in a single database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in more than one database field

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in a single database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in more than one database field

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in a single database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

3.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in more than one database field

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

3.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in a single database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

3.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in more than one database field

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

3.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in a single database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.


To sort by data in more than one database field

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	(Optional) Create calculated fields as necessary.

3.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

4.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in a single database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

3.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in more than one database field

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

3.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in a database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

3.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in more than one database field

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

3.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in a database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

3.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in more than one database field

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

3.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in a single database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

3.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in more than one database field

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

3.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in a single database field

To sort your search results automatically after the search, you must specify a sorting instruction and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

3.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


To sort by data in more than one database field

To sort your search results automatically after the search, you must specify sorting instructions and activate automatic sorting.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.

3.	You require [image] Sort On Search on the List menu. If you see [image], do nothing at this step; otherwise, choose this command.


Deciding the Order of the Sorting Instructions

If you sort search results by more than one kind of data, the order of the sorting instructions affects how ISIS sorts the search results. You generally want to place the sorting instruction that contains the most important data first, because ISIS uses that data to sort all records on the list.

For example, if you specify structural similarity first, ISIS sorts all the records by structural similarity. If several reaction records have the same structural similarity, ISIS uses transformational similarity to order those records.

We recommend the following:

*	If you are primarily interested in the types of molecules that participate in the reaction, specify structural similarity first.

*	If you are primarily interested in transformations, specify transformational similarity first.


Deciding What You Want To Sort - And How To Sort It

You might want to sort reaction records in the following ways:

*	By product yield. For example, place reactions with the highest yields first.

*	By reaction conditions, such as pressure, time, or temperature. For example, place reactions that require the shortest reaction times or the lowest temperatures first.

*	By the year that the reaction was published. For example, place the most recently published reaction first.

You can also perform more complex sorting tasks. For example, you can sort by data in calculated fields. You can also sort the variation subrecords within reaction records. To understand how to perform these tasks, we recommend that you study Reactions: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort reaction records in the following ways:

*	By reaction conditions, such as temperature, time, and pressure.

*	By a combination of similarity data and other data such as product yield or reaction temperature.

Note: If you sort by transformational and/or structural similarity, we strongly recommend that you define your sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.

You can also perform more complex sorting tasks. For example, you can sort by data in calculated fields. You can also sort the variation subrecords within reaction records. To understand how to perform these tasks, we recommend that you study Reactions: Sorting Examples.


Deciding the Order of the Sorting Instructions

If you sort search results by more than one kind of data, the order of the sorting instructions affects how ISIS sorts the search results. You generally want to place the sorting instruction that contains the most important data first, because ISIS uses that data to sort all records on the list.

For example, you might want to sort your reaction records so that reactions with the lowest reaction temperatures and shortest reaction times appear first on the list. If you specify temperature first, ISIS sorts all the records by reaction temperature. If several reaction records have the same reaction temperature, ISIS uses reaction time to sort those records. Therefore, if you are primarily interested in reaction temperature, you want to specify the sorting instruction for reaction temperature first.


Deciding What You Want To Sort - And How To Sort It

You might want to sort reaction records in the following ways:

*	By product yield. For example, place reactions with the highest yields first.

*	By reaction conditions, such as pressure, time, or temperature. For example, place reactions that require the shortest reaction times or the lowest temperatures first.

*	By the year that the reaction was published. For example, place the most recently published reaction first.

You can also perform more complex sorting tasks. For example, you can sort by data in calculated fields. You can also sort the variation subrecords within reaction records. To understand how to perform these tasks, we recommend that you study Reactions: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort reaction records in the following ways:

*	By reaction conditions, such as pressure, time, and temperature.

*	By a combination of yield and reaction conditions. For example, sort reactions by yield and reaction temperature.

You can also perform more complex sorting tasks. For example, you can sort by data in calculated fields. You can also sort the variation subrecords within reaction records. To understand how to perform these tasks, we recommend that you study Reactions: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort the reaction records that you retrieve from an MSim search for reaction components in the following ways:

*	By product yield. For example, place reactions with the highest yields first.

*	By reaction conditions, such as pressure, time, or temperature. For example, place reactions that require the shortest reaction times or the lowest temperatures first.

You can also perform more complex sorting tasks. For example, you can sort by data in calculated fields. You can also sort the variation subrecords within reaction records. To understand how to perform these tasks, we recommend that you study Reaction Components: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort the reaction records that you retrieve from an MSim search for reaction components in the following ways:

*	By a combination of structural similarity and product yield.

*	By reaction conditions, such as pressure, time, and temperature.

Note: If you sort your search results by structural similarity, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.

You can also perform more complex sorting tasks. For example, you can sort by data in calculated fields. You can also sort the variation subrecords within reaction records. To understand how to perform these tasks, we recommend that you study Reaction Components: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort the reaction records that you retrieve from a search for reaction components in the following ways:

*	By product yield. For example, place reactions with the highest yields first.

*	By reaction conditions, such as pressure, time, or temperature. For example, place reactions that require the shortest reaction times or the lowest temperatures first.

You can also perform more complex sorting tasks. For example, you can sort by data in calculated fields. You can also sort the variation subrecords within reaction records. To understand how to perform these tasks, we recommend that you study Reaction Components: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort the reaction records that you retrieve from a search for reaction components in the following ways:

*	By reaction conditions, such as pressure, time, and temperature.

*	By a combination of yield and reaction conditions. For example, sort reactions by yield and reaction temperature.

You can also perform more complex sorting tasks. For example, you can sort by data in calculated fields. You can also sort the variation subrecords within reaction records. To understand how to perform these tasks, we recommend that you study Reaction Components: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort molecule records in the following ways:

*	By activity. For example, sort the list of compounds so that all thromboxane synthetase inhibitors appear together.

*	By molecular weight. For example, sort the list of compounds so that those with the lowest molecular weights appear first.

Note: If you want to sort your search results by structural similarity, we strongly recommend that you sort the search results immediately after the search.

You can also perform more complex sorting tasks. For example, you can sort by data in calculated fields. You can also sort the subrecords (subordinate records, such as data on individual bottles of a compound) within each molecule record. To understand how to perform these tasks, we recommend that you study Molecules: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort the molecule records that you retrieve in an MSim search in the following ways:

*	By the properties of a compound, such as activity and molecular weight.

*	By a combination of similarity data and data from database fields. For example, sort molecule records by structural similarity and activity.

Note: If you sort your search results by structural similarity, we strongly recommend that you specify the sorting instructions before the search and sort your search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.

You can also perform more complex sorting tasks. For example, you can sort by data in calculated fields. You can also sort the subrecords (subordinate records, such as data on individual bottles of a compound) within each molecule record. To understand how to perform these tasks, we recommend that you study Molecules: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort your molecule records in the following ways:

*	By activity. For example, sort the list of compounds so that all thromboxane synthetase inhibitors appear together.

*	By molecular weight. For example, sort the list of compounds so that those with the lowest molecular weights appear first.

You can also perform more complex sorting tasks. For example, you can sort by data in calculated fields. You can also sort the subrecords (subordinate records, such as data on individual bottles of a compound) within each molecule record. To understand how to perform these tasks, we recommend that you study Molecules: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort molecule records by more than one kind of data. For example, you might want to sort by type of activity and by molecular weight.

You can also perform more complex sorting tasks. For example, you can sort by data in calculated fields. You can also sort the subrecords (subordinate records, such as data on individual bottles of a compound) within each molecule record. To understand how to perform these tasks, we recommend that you study Molecules: Sorting Examples.


Deciding Whether TDF or RMS Deviation Is More Important

When you sort by more than one kind of data, the order in which you specify the sorting instructions affects how ISIS sorts the data. You generally want to place the most important data first. This is because ISIS sorts all records by the data in the first sorting instruction. ISIS uses the data in the remaining sorting instructions solely to specify the order of records that have the same value for the data in the first sorting instruction.

For example, if you specify TDF first, ISIS sorts all the records by TDF. If several records have the same TDF value, ISIS uses RMS deviation to order those records.

Therefore, when you sort by both TDF and RMS deviation, you must decide which data is more important, and specify the sorting instruction for that data first.


Deciding the Order of the Sorting Instructions

When you sort by more than one kind of data, the order in which you specify the sorting instructions affects how ISIS sorts the data. You generally want to place the most important data first. This is because ISIS sorts all records by the data in the first sorting instruction. ISIS uses the data in the remaining sorting instructions solely to specify the order of records that have the same value for the data in the first sorting instruction.

For example, if you specify TDF first, ISIS sorts all the records by TDF. If several records have the same TDF value, ISIS uses the data that you specify in the second sorting instruction to order those records.


Deciding What You Want To Sort - And How To Sort It

You might want to sort your 3D structure records in the following ways:

*	By activity. For example, sort the list of compounds so that all thromboxane synthetase inhibitors appear together.

*	By molecular weight. For example, sort the list of compounds so that those with the lowest molecular weights appear first.

You can also perform more complex sorting tasks. For example, you can sort by data in calculated fields. You can also sort the subrecords (subordinate records, such as data on individual bottles of a compound) within each molecule record. To understand how to perform these tasks, we recommend that you study 3D Structures: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort the 3D structure records that you retrieve in a CFS search in the following ways:

*	By the properties of a compound, such as molecular weight and activity.

*	By a combination of CFS derived data and data from database fields. For example, sort 3D structure records by activity and by torsional degrees of freedom (TDF).

Note: If you want to sort your search results by CFS derived data, we strongly recommend that you sort the search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.

You can also perform more complex sorting tasks. For example, you can sort by data in calculated fields. You can also sort the subrecords (subordinate records, such as data on individual bottles of a compound) within each molecule record. To understand how to perform these tasks, we recommend that you study 3D Structures: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort your 3D structure records in the following ways:

*	By activity. For example, sort the list of compounds so that all thromboxane synthetase inhibitors appear together.

*	By molecular weight. For example, sort the list of compounds so that those with the lowest molecular weights appear first.

You can also perform more complex sorting tasks. For example, you can sort by data in calculated fields. You can also sort the subrecords (subordinate records, such as data on individual bottles of a compound) within each molecule record. To understand how to perform these tasks, we recommend that you study 3D Structures: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort molecule records by more than one kind of data. For example, you might want to sort by activity and molecular weight.

You can also perform more complex types of sorting. For example, you can define calculated fields that allow you to sort search results by the result of a calculation on a set of similar data (for example, the average value of a set of measurements). You can also sort the subrecords (subordinate records, such as data on individual bottles of a compound) within each 3D structure record. To understand how to perform these tasks, we recommend that you study 3D Structures: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You can sort your list of search results in the following ways:

*	If your database is flat (one level of data), you can sort your search results by data in any field of the database.

*	If your database is hierarchical (more than one level of data), you can sort your search results by data in any field at the top level of the hierarchy. You can also sort data at each level of the hierarchy.

You can also perform more complex types of sorting. For example, you can sort subrecords (subordinate records, such as data on individual bottles of a compound) within each record. To understand how to perform these tasks, we recommend that you study Local Databases: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You can sort your list of search results in the following ways:

*	If your database is flat (one level of data), you can sort your search results by data in any field of the database.

*	If your database is hierarchical (more than one level of data), you can sort your search results by data in any field at the top level of the hierarchy. You can also sort data at each level of the hierarchy.

You can also perform more complex types of sorting. For example, you can sort subrecords (subordinate records, such as data on individual bottles of a compound) within each record. To understand how to perform these tasks, we recommend that you study Local Databases: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You can sort your list of search results in the following ways:

*	If your database is flat (one level of data), you can sort your search results by data in any field of the database.

*	If your database is hierarchical (more than one level of data), you can sort your search results by data in any field at the top level of the hierarchy. You can also sort data at each level of the hierarchy.

You can also perform more complex types of sorting. For example, you can sort subrecords (subordinate records, such as data on individual bottles of a compound) within each record. To understand how to perform these tasks, we recommend that you study Local Databases: Sorting Examples.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions. You see <RXN> in the Sort each box.

4.	In the By box, click RXNSTRUCTURESIMILARITY.

5.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

6.	Click Add. You see the sorting instruction in the Sorting Instructions box.

7.	(Optional) Save the sorting instructions.

8.	Click Close.

9.	Click Back (at top of help screen) to return to the previous screen and continue with Step 2 on that screen.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions. You see <RXN> in the Sort each box.

4.	In the By box, click RXNCENTERSIMILARITY.

5.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

6.	Click Add. You see the sorting instruction in the Sorting Instructions box.

7.	(Optional) Save the sorting instructions.

8.	Click Close.

9.	Click Back (at top of help screen) to return to the previous screen and continue with Step 2 on that screen.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions. You see <RXN> in the Sort each box.

4.	Decide the order of the sorting instructions.

5.	Do one of the following:

*	To sort by structural similarity first, click RXNSTRUCTURESIMILARITY in the By box.

*	To sort by transformational similarity first, click RXNCENTERSIMILARITY in the By box.

6.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

7.	Click Add. You see the sorting instruction in the Sorting Instructions box.

8.	Repeat Steps 5 through 7 for the other type of similarity.

9.	(Optional) Save the sorting instructions.

10.	Click Close.

11.	Click Back (at top of help screen) to return to the previous screen and continue with Step 2 on that screen.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions. You see <RXN> in the Sort each box.

4.	In the By box, click the field that contains the data that you want to use.

5.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

6.	Click Add. You see the sorting instruction in the Sorting Instructions box.

7.	(Optional) Save the sorting instructions.

8.	Click Close.

9.	Click Back (at top of help screen) to return to the previous screen and continue with Step 3 on that screen.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions. You see <RXN> in the Sort each box.

4.	Decide the order of the sorting instructions.

5.	In the By box, click the database field that contains the data for the first sorting instruction.

6.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

7.	Click Add. You see the sorting instruction in the Sorting Instructions box.

8.	Repeat Steps 5 through 7 for the second type of data.

9.	(Optional) To sort by a third type of data, repeat Steps 5 through 7.

10.	(Optional) Save the sorting instructions..	Click Close.

11.	Click Back (at top of help screen) to return to the previous screen and continue with Step 3 on that screen.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions. You see <RXN> in the Sort each box. In the By box, you see a list of database fields at lower levels of the database hierarchy.

4.	Do one of the following:

*	To sort by the similarity of reactants, click >REACTANT_LINK>MOL>MOLSIMILARITY in the By box.

*	To sort by the similarity of products, click >PRODUCT_LINK>MOL>MOLSIMILARITY in the By box.

*	To sort by the similarity of solvents, click >VARIATION>SOLVENT_LINK>MOL>MOLSIMILARITY in the By box.

*	To sort by the similarity of solvents, click >VARIATION>CATALYST_LINK>MOL>MOLSIMILARITY in the By box.

5.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

6.	Click Add. You see the sorting instruction in the Sorting Instructions box.

7.	(Optional) Save the sorting instructions.

8.	Click Close.

9.	Click Back (at top of help screen) to return to the previous screen and continue with Step 2 on that screen.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions. You see <MOL> in the Sort each box.

Note: In a 3D database, you see <MODEL>.

4.	In the By box, click MOLSIMILARITY.

5.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

6.	Click Add. You see the sorting instruction in the Sorting Instructions box.

7.	(Optional) Save the sorting instructions.

8.	Click Close.

9.	Click Back (at top of help screen) to return to the previous screen and continue with Step 2 on that screen.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions. You see <MODEL> in the Sort each box.

4.	In the By box, click CFS_VDW.

5.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

6.	Click Add. You see the sorting instruction in the Sorting Instructions box.

7.	(Optional) Save the sorting instructions.

8.	Click Close.

9.	Click Back (at top of help screen) to return to the previous screen and continue with Step 2 on that screen.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions. You see <MODEL> in the Sort each box.

4.	In the By box, click CFS_TDF.

5.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

6.	Click Add. You see the sorting instruction in the Sorting Instructions box.

7.	(Optional) Save the sorting instructions.

8.	Click Close.

9.	Click Back (at top of help screen) to return to the previous screen and continue with Step 2 on that screen.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions. You see <MODEL> in the Sort each box.

4.	In the By box, click CFS_RMS.

5.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

6.	Click Add. You see the sorting instruction in the Sorting Instructions box.

7.	(Optional) Save the sorting instructions.

8.	Click Close.

9.	Click Back (at top of help screen) to return to the previous screen and continue with Step 2 on that screen.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions. You see <MODEL> in the Sort each box.

4.	Decide the order of the sorting instructions.

5.	Do one of the following:

*	To sort by TDF first, choose CFS_TDF from the By box.

*	To sort by RMS deviation first, choose CFS_RMS from the By box.

6.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

7.	Click Add. You see the sorting instruction in the Sorting Instructions box.

8.	Repeat Steps 5 through 7 for the second sorting instruction.

9.	(Optional) Save the sorting instructions.

10.	Click Close.

11.	Click Back (at top of help screen) to return to the previous screen and continue with Step 2 on that screen.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions. You see <MODEL> in the Sort each box.

4.	Decide the order of the sorting instructions.

5.	Do one of the following:

*	To sort by van der Waals energy difference first, choose CFS_VDW from the By box.

*	To sort by TDF first, choose CFS_TDF from the By box.

*	To sort by RMS deviation first, choose CFS_RMS from the By box.

6.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

7.	Click Add. You see the sorting instruction in the Sorting Instructions box.

8.	Repeat Steps 5 through 7 for the second sorting instruction.

9.	(Optional) To create a third sorting instruction, repeat Steps 5 through 7.

10.	(Optional) Save the sorting instructions.

11.	Click Close.

12.	Click Back (at top of help screen) to return to the previous screen and continue with Step 2 on that screen.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions. You see <MODEL> in the Sort each box. In the By box, you see a list of database fields at lower levels of the database hierarchy.

4.	In the By box, click the field that contains the data that you want to use.

5.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

6.	Click Add. You see the sorting instruction in the Sorting Instructions box.

7.	(Optional) Save the sorting instructions.

8.	Click Close.

9.	Click Back (at top of help screen) to return to the previous screen and continue with Step 2 on that screen.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions. You see <MODEL> in the Sort each box. In the By box, you see a list of database fields at lower levels of the database hierarchy.

4.	Decide the order of the sorting instructions.

5.	In the By box, click the database field that contains the data for the first sorting instruction.

6.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

7.	Click Add. You see the sorting instruction in the Sorting Instructions box.

8.	Repeat Steps 5 through 7 for the second type of data.

9.	(Optional) To sort by a third type of data, repeat Steps 5 through 7.

8.	(Optional) Save the sorting instructions.

9.	Click Close.

10.	Click Back (at top of help screen) to return to the previous screen and continue with Step 2 on that screen.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions. You see <MODEL> in the Sort each box. In the By box, you see a list of database fields at lower levels of the database hierarchy.

4.	In the By box, click the database field that contains the data for the first sorting instruction.

5.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

6.	Click Add. You see the sorting instruction in the Sorting Instructions box.

7.	(Optional) Save the sorting instructions.

8.	Click Close.

9.	Click Back (at top of help screen) to return to the previous screen and continue with Step 2 on that screen.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions. You see <MODEL> in the Sort each box.

4.	Decide the order of the sorting instructions.

5.	In the By box, click the database field that contains the data for the first sorting instruction.

6.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

7.	Click Add. You see the sorting instruction in the Sorting Instructions box.

8.	Repeat Steps 5 through 7 for the second type of data.

9.	(Optional) To sort by a third type of data, repeat Steps 5 through 7.

10.	(Optional) Save the sorting instructions.

11.	Click Close.

12.	Click Back (at top of help screen) to return to the previous screen and continue with Step 2 on that screen.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions. In the By box, you see a list of database fields at lower levels of the database hierarchy.

4.	In the By box, click the field that contains the data that you want to use.

5.	To place records with the highest values first (ascending order), click [image] High to low. To place records with the lowest values first (ascending order), click [image] Low to high.

6.	Click Add. You see the sorting instruction in the Sorting Instructions box.

7.	(Optional) Save the sorting instructions.

8.	Click Close.

9.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


What Are Subrecords?

Click here for step-by-step instructions

A hierarchical database contains subrecords (subordinate records) that store separate sets of data within each record. You can sort these subrecords by data in any database field. For example:

*	In a reaction database, each reaction might have several variations associated with it. This information is stored in variation subrecords within each reaction record. You might want to sort variation subrecords so that those with the lowest reaction temperatures appear first within each record.

*	In a molecule database, you might have several bottles of each compound. This information is stored in subrecords within each molecule record. You might want to sort the bottle subrecords so that bottles with the largest amounts appear first within each record.


To sort subrecords within each record

This procedure assumes that the Sort dialog box is open.

1.	In the Sort each box, click the parent field that defines the subrecords that you want to sort. Examples In the By box, you see a list of database fields that are associated with the parent field that you chose.

2.	In the By box, click the field that contains the data that you want to use.

3.	To place records with the highest values first (ascending order), click [image] High to low. To place records with the lowest values first (ascending order), click [image] Low to high.

4.	Click Add. You see the sorting instruction in the Sorting Instructions box.

5.	(Optional) To create additional sorting instructions, repeat Steps 1 through 4.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions. In the By box, you see a list of database fields that you can use for sorting.

Note for local searches

4.	In the By box, click the field that contains the data that you want to use.

5.	To place records with the highest values first (ascending order), click [image] High to low. To place records with the lowest values first (ascending order), click [image] Low to high.

6.	Click Add. You see the sorting instruction in the Sorting Instructions box.

7.	(Optional) Save the sorting instructions.

8.	Click Close.

9.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions.

4.	Decide the order of the sorting instructions.

5.	In the By box, click the field that contains the data that you want to use for the first sorting instruction.

6.	To place records with the highest values first (ascending order), click [image] High to low. To place records with the lowest values first (ascending order), click [image] Low to high.

7.	Click Add. You see the sorting instruction in the Sorting Instructions box.

8.	Repeat Steps 5 through 7 for the second sorting instruction.

9.	(Optional) To create a third sorting instruction, repeat Steps 5 through 7.

10.	(Optional) Save the sorting instructions.

11.	Click Close.

12.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions.

4.	Decide the order of the sorting instructions.

5.	In the By box, click the field that contains the data that you want to use for the first sorting instruction.

Note for local searches

6.	To place records with the highest values first (ascending order), click [image] High to low. To place records with the lowest values first (ascending order), click [image] Low to high.

7.	Click Add. You see the sorting instruction in the Sorting Instructions box.

8.	Repeat Steps 5 through 7 for the second sorting instruction.

9.	(Optional) To create a third sorting instruction, repeat Steps 5 through 7.

10.	(Optional) Save the sorting instructions.

11.	Click Close.

12.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To restore a set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions.

4.	Click Restore.

5.	Click the name of the sorting instructions that you want to restore.

6.	Click OK.

7.	(Optional) You can edit the current sorting instructions.

8.	Click Close.

9.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To restore a set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions.

4.	Click Restore.

5.	Click the name of the sorting instructions that you want to restore.

6.	Click OK.

7.	(Optional) You can edit the current sorting instructions.

8.	Click Close.


To import a set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected). You see the Sort dialog box.

3.	Clear the current sorting instructions. You see the Sort dialog box.

4.	Click Close.

5.	Choose File > Import > Sorting Instructions. (To retrieve a PC-sorting instructions file on the Macintosh, press and hold the Option key while you complete this step.)

6.	Click the name of an current file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

7.	Click OK (Mac=Open).

8.	Choose List > Sort. You see the imported sorting instructions in the Sorting Instructions box.

9.	(Optional) You can edit the current sorting instructions.

10.	(Optional) Save the sorting instructions.

11.	Click Close.

12.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To import a set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions. You see the Sort dialog box.

4.	Click Close.

5.	Choose File > Import > Sorting Instructions. (To retrieve a PC-sorting instructions file on the Macintosh, press and hold the Option key while you complete this step.)

6.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

7.	Click OK (Mac=Open).

8.	Choose List > Sort. You see the imported sorting instructions in the Sorting Instructions box.

9.	(Optional) You can edit the current sorting instructions.

10.	(Optional) Save the sorting instructions.

11.	Click Close.

12.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To use the current sorting instructions

You can use sorting instructions that you created, restored, or imported earlier in your ISIS/Base session. These are the current sorting instructions.

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort. You see the current sorting instructions in the Sorting Instructions box.

3.	(Optional) You can edit the current sorting instructions.

4.	Click Close.

5.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To sort search results

Note: If you want to sort by structural similarity, transformational similarity, or both, we strongly recommend that you specify the sorting instructions before the search, and sort search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database

*	Import a set of sorting instructions from a disk file.


To sort search results

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.


To sort search results

Note: If you want to sort by structural similarity, we strongly recommend that you specify the sorting instructions before the search, and sort search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.


To sort search results

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.


To sort search results

Note: If you want to sort by structural similarity, we strongly recommend that you specify the sorting instructions before the search, and sort search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.


To sort search results

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.


To sort search results

Note: If you want to sort by derived data such as torsional degrees of freedom, van der Waals energy difference, or RMS deviation, we strongly recommend that you specify the sorting instructions before the search, and sort search results automatically after the search. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.


To sort search results

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.


To sort search results

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.


To sort search results

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.


To sort search results

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.


To sort search results

Do these steps in the order shown:

1.	Decide what you want to sort - and how to sort it.

2.	Do one of the following:

*	Use the current sorting instructions.

*	Create a new set of sorting instructions.

*	Restore a set of sorting instructions from the database.

*	Import a set of sorting instructions from a disk file.


To sort search results

The way that you sort your search results depends entirely on the ISIS search that you want to perform.

To obtain specific help, click here: The ISIS/Base Chemical Searches - and How to do Them, and click the exact search that you need. You see a help screen that contains all of the information that you need to perform your search.

Note: There are, for example, four types of substructure searches (SSS) on the ISIS/Base Chemical Searches - and How to do Them screen. Whether you search a remote or local database for molecule or reaction records is significant when you decide on a search. Thus, your choice must be accurate.

See also:

To undo sorting


Note (RSim, MSim, and CFS Searches Only)

RSim, MSim, and CFS searches generate derived data that you can use to sort your search results. If you sort by derived data, we strongly recommend that you define sorting instructions before the search and sort the search results automatically after the search. For information on defining sorting instructions for automatic sorting, see the online help for the search of your choice.


Deciding What You Want To Sort - And How To Sort It

You can sort your list of search results in the following ways:

*	If your database is flat (one level of data), you can sort your search results by data in any field of the database.

*	If your database is hierarchical (more than one level of data), you can sort your search results by data in any field at the top level of the hierarchy. You can also sort data at each level of the hierarchy.

You can also perform more complex types of sorting. For example, you can sort subrecords (subordinate records, such as data on individual bottles of a compound) within each record. To understand how to perform these tasks, we recommend that you study Local Databases: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort reaction records in the following ways:

*	By product yield. For example, place reactions with the highest yields first.

*	By reaction conditions, such as pressure, time, or temperature. For example, place reactions that require the shortest reaction times or the lowest temperatures first.

*	By several criteria. For example, place reactions with the highest yields first. If two reactions have the same yield, place the reaction with the lowest reaction temperature first.

You can also perform more complex sorting tasks. For example, you can sort by data in calculated fields. You can also sort the variation subrecords within reaction records. To understand how to perform these tasks, we recommend that you study Reactions: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort reaction records in the following ways:

*	By product yield. For example, place reactions with the highest yields first.

*	By reaction conditions, such as pressure, time, or temperature. For example, place reactions that require the shortest reaction times or the lowest temperatures first.

*	By several criteria. For example, place reactions with the highest yields first. If two reactions have the same yield, place the reaction with the lowest reaction temperature first.

You can also perform more complex sorting tasks. For example, you can sort by data in calculated fields. You can also sort the variation subrecords within reaction records. To understand how to perform these tasks, we recommend that you study Reactions: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort reaction records in the following ways:

*	By product yield. For example, place reactions with the highest yields first.

*	By reaction conditions, such as pressure, time, or temperature. For example, place reactions that require the shortest reaction times or the lowest temperatures first.

*	By several criteria. For example, place reactions with the highest yields first. If two reactions have the same yield, place the reaction with the lowest reaction temperature first.

You can also perform more complex sorting tasks. You can define calculated fields that allow you to sort search results by a calculated value (for example, the average value of a set of measurements). You can also sort the variation subrecords within each reaction record. For more information on these topics, study Reaction Components: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort reaction records in the following ways:

*	By product yield. For example, place reactions with the highest yields first.

*	By reaction conditions, such as pressure, time, or temperature. For example, place reactions that require the shortest reaction times or the lowest temperatures first.

*	By several criteria. For example, place reactions with the highest yields first. If two reactions have the same yield, place the reaction with the lowest reaction temperature first.

You can also perform more complex sorting tasks. You can define calculated fields that allow you to sort search results by a calculated value (for example, the average value of a set of measurements). You can also sort the variation subrecords within each reaction record. For more information on these topics, study Reaction Components: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort molecule records in the following ways:

*	By activity. For example, sort the list of compounds so that all thromboxane synthetase inhibitors are together.

*	By molecular weight. For example, sort the list of compounds so that compounds with the lowest molecular weight appear first.

*	By several criteria. For example, sort by activity and molecular weight.

You can also perform more complex sorting tasks. You can define calculated fields that allow you to sort search results by a calculated value (for example, the average value of a set of measurements). You can also sort subrecords within each record (for example, data on individual bottles of a compound). For more information on these topics, study Molecules: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort molecule records in the following ways:

*	By activity. For example, sort the list of compounds so that all thromboxane synthetase inhibitors are together.

*	By molecular weight. For example, sort the list of compounds so that compounds with the lowest molecular weight appear first.

*	By several criteria. For example, sort by activity and molecular weight.

You can also perform more complex sorting tasks. You can define calculated fields that allow you to sort search results by a calculated value (for example, the average value of a set of measurements). You can also sort subrecords within each record (for example, data on individual bottles of a compound). For more information on these topics, study Molecules: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort 3D structure records in the following ways:

*	By activity. For example, sort the list of compounds so that all thromboxane synthetase inhibitors are together.

*	By molecular weight. For example, sort the list of compounds so that compounds with the lowest molecular weight appear first.

*	By several criteria. For example, sort by activity and molecular weight.

You can also perform more complex sorting tasks. You can define calculated fields that allow you to sort search results by a calculated value (for example, the average value of a set of measurements). You can also sort subrecords within each record (for example, data on individual bottles of a compound). For more information on these topics, study 3D Structures: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You might want to sort 3D structure records in the following ways:

*	By activity. For example, sort the list of compounds so that all thromboxane synthetase inhibitors are together.

*	By molecular weight. For example, sort the list of compounds so that compounds with the lowest molecular weight appear first.

*	By several criteria. For example, sort by activity and molecular weight.

You can also perform more complex sorting tasks. You can define calculated fields that allow you to sort search results by a calculated value (for example, the average value of a set of measurements). You can also sort subrecords within each record (for example, data on individual bottles of a compound). For more information on these topics, study 3D Structures: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You can sort your list of search results in the following ways:

*	If your database is flat (one level of data), you can sort your search results by data in any field of the database.

*	If your database is hierarchical (more than one level of data), you can sort your search results by data in any field at the top level of the hierarchy. You can also sort data at each level of the hierarchy.

You can also perform more complex types of sorting. For example, you can sort subrecords within each record (for example, data on individual bottles of a compound). To understand how to perform these tasks, we recommend that you study Local Databases: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You can sort your list of search results in the following ways:

*	If your database is flat (one level of data), you can sort your search results by data in any field of the database.

*	If your database is hierarchical (more than one level of data), you can sort your search results by data in any field at the top level of the hierarchy. You can also sort data at each level of the hierarchy.

You can also perform more complex types of sorting. For example, you can sort subrecords within each record (for example, data on individual bottles of a compound). To understand how to perform these tasks, we recommend that you study Local Databases: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You can sort your list of search results in the following ways:

*	If your database is flat (one level of data), you can sort your search results by data in any field of the database.

*	If your database is hierarchical (more than one level of data), you can sort your search results by data in any field at the top level of the hierarchy. You can also sort data at each level of the hierarchy.

You can also perform more complex types of sorting. For example, you can sort subrecords within each record (for example, data on individual bottles of a compound). To understand how to perform these tasks, we recommend that you study Local Databases: Sorting Examples.


Deciding What You Want To Sort - And How To Sort It

You can sort your list of search results in the following ways:

*	If your database is flat (one level of data), you can sort your search results by data in any field of the database.

*	If your database is hierarchical (more than one level of data), you can sort your search results by data in any field at the top level of the hierarchy. You can also sort data at each level of the hierarchy.

You can also perform more complex types of sorting. For example, you can sort subrecords within each record (for example, data on individual bottles of a compound). To understand how to perform these tasks, we recommend that you study Local Databases: Sorting Examples.


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions.

4.	In the By box, click the field that contains the data that you want to use.

5.	To place records with the highest values first (ascending order), click [image] High to low. To place records with the lowest values first (ascending order), click [image] Low to high.

6.	Click Add. You see the sorting instruction in the Sorting Instructions box.

7.	(Optional) Save the sorting instructions.

8.	To sort search results, click Sort. To close the dialog box without sorting search results, click Close.

See also:

To undo sorting


To create a new set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions.

4.	In the By box, click the field that contains the data that you want to use.

Note for local searches

5.	To place records with the highest values first (ascending order), click [image] High to low. To place records with the lowest values first (ascending order), click [image] Low to high.

6.	Click Add. You see the sorting instruction in the Sorting Instructions box.

7.	(Optional) Save the sorting instructions.

8.	To sort search results, click Sort. To close the dialog box without sorting search results, click Close.

See also:

To undo sorting


To restore a set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions.

4.	Click Restore. You see a dialog box.

5.	Click the name of the sorting instructions that you want to restore.

6.	Click OK.

7.	(Optional) You can edit the current sorting instructions.

8.	(Optional) Save the sorting instructions.

9.	To sort search results, click Sort. To close the dialog box without sorting search results, click Close.

See also:

To undo sorting


To restore a set of sorting instructions

You can restore a set of sorting instructions that you have previously saved as an object in the remote-access file of your database.

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions.

4.	Click Restore. You see a dialog box.

5.	Click the name of the sorting instructions that you want to restore.

6.	Click OK.

7.	(Optional) You can edit the current sorting instructions.

8.	(Optional) Save the sorting instructions.

9.	To sort search results, click Sort. To close the dialog box without sorting search results, click Close.


To restore a set of sorting instructions

You can restore a set of sorting instructions that you have previously saved as an object in your database or remote-access file.

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions.

4.	Click Restore. You see a dialog box.

5.	Click the name of the sorting instructions that you want to restore.

6.	Click OK.

7.	(Optional) You can edit the current sorting instructions.

8.	(Optional) Save the sorting instructions.

9.	To sort search results, click Sort. To close the dialog box without sorting search results, click Close.


To restore a set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions.

4.	Click Restore. You see a dialog box.

5.	Click the name of the sorting instructions that you want to restore.

6.	Click OK.

7.	(Optional) You can edit the current sorting instructions.

8.	(Optional) Save the sorting instructions.

9.	To sort search results, click Sort. To close the dialog box without sorting search results, click Close.

See also:

To undo sorting


To restore a set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions.

4.	Click Restore. You see a dialog box.

5.	Click the name of the sorting instructions that you want to restore.

6.	Click OK.

7.	(Optional) You can edit the current sorting instructions.

8.	(Optional) Save the sorting instructions.

9.	To sort search results, click Sort. To close the dialog box without sorting search results, click Close.

See also:

To undo sorting


To import a set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions.

4.	Choose File > Import > Sorting Instructions. (To retrieve a PC-sorting instructions file on the Macintosh, press and hold the Option key while you complete this step.)

5.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

6.	Click OK (Mac=Open).

7.	Choose List > Sort. You see the sorting instructions that you imported in the Sorting Instructions box.

8.	(Optional) You can edit the current sorting instructions.

9.	(Optional) Save the sorting instructions.

10.	To sort search results, click Sort. To close the dialog box without sorting search results, click Close.

See also:

To undo sorting


To import a set of sorting instructions

You can import a set of sorting instructions that you have previously stored in a file.

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions.

4.	Choose File > Import > Sorting Instructions. (To retrieve a PC-sorting instructions file on the Macintosh, press and hold the Option key while you complete this step.)

5.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

6.	Click OK (Mac=Open).

7.	Choose List > Sort. You see the sorting instructions that you imported in the Sorting Instructions box.

8.	(Optional) You can edit the current sorting instructions.

9.	(Optional) Save the sorting instructions.

10.	To sort search results, click Sort. To close the dialog box without sorting search results, click Close.

See also:

To undo sorting


To import a set of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Clear the current sorting instructions.

4.	Choose File > Import > Sorting Instructions. (To retrieve a PC-sorting instructions file on the Macintosh, press and hold the Option key while you complete this step.)

5.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

6.	Click OK (Mac=Open).

7.	Choose List > Sort. You see the sorting instructions that you imported in the Sorting Instructions box.

8.	(Optional) You can edit the current sorting instructions.

9.	(Optional) Save the sorting instructions.

10.	To sort search results, click Sort. To close the dialog box without sorting search results, click Close.

See also:

To undo sorting


To use the current sorting instructions

You can use sorting instructions that you created, restored, or imported earlier in your ISIS/Base session. These are the current sorting instructions.

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort. You see the current sorting instructions in the Sorting Instructions box.

3.	(Optional) You can edit the current sorting instructions.

4.	Click Sort. ISIS sorts the search results.

See also:

To undo sorting


To export sorting instructions

You can export the current set of sorting instructions to a text file on your workstation or host computer. This allows you to save your sorting instructions if your database is read-only. Exporting sorting instructions also allows you to share exported sorting instructions with users who access a different local database, or who access the same remote database from a different remote-access file.

1.	Click the Browse mode (if not selected).

2.	Choose File > Export > Sorting Instructions. You see a dialog box.

3.	Do one of the following:

*	To create a new file that contains the current sorting instructions, enter a name in the Save As File Name text box (PC: Use the default .SRT file extension that is displayed in the text box. Mac: To save a sorting-instructions file that can be opened on the PC, press and hold the Option key while you complete this step.)

*	To overwrite an existing file with the current sorting instructions, click the name of an existing file in the Files list box, then click Yes when you see the prompt on overwriting the file.

4.	Click OK (Mac=Save).


To save sorting instructions

You can save the current set of sorting instructions as an object in your database. Saving sorting instructions allows you to sort search results without creating the sorting instructions again. To save the current sorting instructions:

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort. You see the Sort dialog box.

3.	Click Save. You see the Save Database Object dialog box.

4.	Enter a name for the sorting instructions.

5.	(Optional) To add a description to the sorting instructions, enter the description in the Description box.

6.	Click OK.

7.	Click Close.


Why Create Calculated Fields?

Click here for step-by-step instructions

A calculated field calculates a value from a set of data. For example, if your molecule database contains several activity measurements of each compound, you can create a calculated field that contains the average of those measurements. You can display data from a calculated field in a form and/or use it to sort search results, just like the data in any other database field.

To create calculated fields, you need to understand the database structure. We strongly recommend that you study Calculated Fields: Concepts/Examples before you attempt to create calculated fields.

Note: Do not confuse calculated fields with form calculations. A form calculation uses data from different database fields. For example, if your database contains a field for concentration in moles per liter and another field for molecular weight, you can use a form calculation to multiply those values to obtain the concentration in grams per liter. You can display a form calculation on your form, but you cannot use it to sort your search results.


To create a calculated field

Calculated Fields: Concepts/Examples

Note: To determine whether your database already contains a suitable calculated field, print or view a list of your database fields.

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected). You see the Sort dialog box.

3.	Click Calculated Field. You see the Calculated Fields dialog box.

4.	To choose the field that contains the data that you want to use in the calculation, click a field in the Select the field to calculate on box. You see the name of the field that you chose in the Calculated field name box.

5.	Click the Calculation type box and choose the calculation that you want.

6.	(Optional) Click the Calculated field name box and enter a new name for the calculated field.

7.	Click Add. In the Select the field to calculate on box, you see a plus sign (+) beside the name of the field that you created.

8.	Click Save.

9.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.

See also:

To delete a calculated field


To create a calculated field

Calculated Fields: Concepts/Examples

Note: To determine whether your database already contains a suitable calculated field, print or view a list of your database fields.

1.	Click the Browse mode (if not selected).

2.	Choose Database > Calculated Fields. You see a dialog box.

3.	To choose the field that contains the data that you want to use in the calculation, click a field in the Select the field to calculate on box.

4.	Click the Calculation type box and choose the calculation that you want.

5.	(Optional) Click the Calculated field name box and enter a new name for the calculated field.

6.	Click Add. In the Select the field to calculate on box, you see a plus sign (+) beside the name of the field that you created.

7.	(Optional) Repeat Steps 3 through 6 as necessary to create additional calculated fields.

8.	Click Save.

9.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.

See also:

To delete a calculated field


To create a calculated field

Calculated Fields: Concepts/Examples

Note: To determine whether your database already contains a suitable calculated field, print or view a list of your database fields.

1.	Click the Browse mode (if not selected).

2.	Choose Database > Calculated Fields. You see a dialog box.

3.	To choose the field that contains the data that you want to use in the calculation, click a field in the Select the field to calculate on box.

4.	Click the Calculation type box and choose the calculation that you want.

5.	(Optional) Click the Calculated field name box and enter a new name for the calculated field.

6.	Click Add. In the Select the field to calculate on box, you see a plus sign (+) beside the name of the field that you created.

7.	Click Save.

See also:

To delete a calculated field


To delete a calculated field

1.	Click the Browse mode (if not selected).

2.	Choose Database > Calculated Fields (if not selected). You see the Calculated Fields dialog box.

3.	Choose the field that you want to delete in the Select the field to calculate on box. You see the name of the field that you chose in the Calculated field name box at the bottom of the dialog box.

4.	Click Delete. You see a minus sign (-) beside the name of the field that you deleted.

5.	(Optional) Repeat Steps 3 and 4 for other calculated fields that you want to delete.

6.	Click Save.


Printing or Viewing a List of Your Database Fields

Click here for step-by-step instructions

Before you create a calculated field, print or view a list of database fields to see whether your database already contains a suitable field.

It is important that you print or view a list of your database fields to understand the database structure. Do not make assumptions about your database structure based on experience with other MDL programs. For example, a flat database in MACCS-II is hierarchical in ISIS.

We recommend that you print a list of database fields, because it is difficult to see the relationship of fields when scrolling through a list box.


To sort search results with the current sorting instructions

This procedure assumes that the Sort dialog box is open, and that a set of sorting instructions app[ears in the Sorting instructions box.

1.	Click Sort. ISIS sorts the search results and closes the dialog box.

See also:

To undo sorting


Modifying the Current Sorting Instructions
Editing the Current Sorting Instructions

You can use the commands in the Sort dialog box to edit the current sorting instructions.

Click one of the following:

*	Add a sorting instruction to the current set.

*	Replace a sorting instruction with a new sorting instruction.

*	Delete a sorting instruction from the current set.

*	Change the order of individual sorting instructions within the current set.


Examples

To sort records, click the first parent field from the list in the Sort each box. For example, in a remote reaction database, click <RXN>. In a local database, click <ROOT>.

To sort subrecords within each record, you need to specify the parent field that defines those subrecords. For example:

*	In an MDL reaction database, each reaction can have several variations associated with it. The <VARIATION> parent field defines variation subrecords.

*	In a molecule database, you might have several batches of each compound. You might have a parent field called <BATCH> that defines batch subrecords.

If you are not sure which parent field defines the subrecords that you want, see your ISIS Administrator.


To add a sorting instruction

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	In the Sort each box, click the parent field of the records or subrecords that you want to sort. Examples

4.	In the By box, click the field that contains the data that you want.

Note for local searches

5.	To place records with the highest values first (ascending order), click [image] High to low. To place records with the lowest values first (ascending order), click [image] Low to high.

6.	Click Add. You see the sorting instruction in the box at the bottom of the dialog box.


To replace a sorting instruction

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	In the Sorting Instructions box, click the sorting instruction that you want to replace.

4.	In the Sort each box, click the parent field of the records or subrecords that you want to sort in the new sorting instruction. Examples

5.	In the By box, click the field that contains the data that you want.

Note for local searches

6.	To place records with the highest values first (ascending order), click [image] High to low. To place records with the lowest values first (ascending order), click [image] Low to high.

7.	Click Replace. You see the new sorting instruction in the Sorting instructions box.


To delete a sorting instruction

Use this procedure to delete a sorting instruction from the current set of sorting instructions.

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	In the Sorting Instructions box, click the sorting instruction that you want to delete.

4.	Click Delete.


To change the order of sorting instructions

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected).

3.	Do one of the following:

*	To move a sorting instruction before another instruction, click the instruction in the Sorting Instructions box, and then click

*	To move a sorting instruction after another instruction, click the instruction in the Sorting Instructions box, and then click


To undo sorting

If you make a mistake in sorting your search results, you can undo the effects of sorting. When you undo sorting, ISIS places the records in the order in which ISIS retrieved them from the database.

1.	Click the Browse mode (if not selected).

2.	Choose List > Sort (if not selected). You see the Sort dialog box.

3.	Click Unsort. ISIS undoes the sorting.

4.	Click Close.


Why Specify the Most Important Data First?

You can specify up to three types of data (child fields) for each record (or subrecord) that you sort. To do this, you must decide the order in which you want ISIS to sort by each type of data. You generally want to place the most important data first. This ensures that ISIS sorts all records by that data.

For example, if you want to sort molecule records by activity and by molecular weight, you create one sorting instruction for activity and another for molecular weight. The order of the sorted records depends on the order in which you specify the sorting instructions:

*	If you place the sorting instruction for activity first, then ISIS sorts all records by activity. If several molecule records have the same activity, ISIS sorts those records (and only those records) by activity.

*	If you place the sorting instruction for molecular weight first, then ISIS sorts all records by molecular weight. If several molecule records have the same molecular weight, ISIS sorts those records (and only those records) in order by activity.


Creating a Set of Sorting Instructions

To create a new set of sorting instructions, you need to know what you want to sort, and how you want to sort it.

Click one of the following:

*	Sort your list of records by one kind of data. For example, sort molecule records by molecular weight.

*	Sort your list of records by more than one kind of data. For example, sort reaction records by reaction temperature and reaction time.

*	Sort subrecords within each record on your list (hierarchical databases only). For example, sort variation subrecords within each reaction record.


Creating a Set of Sorting Instructions

To create a new set of sorting instructions, you need to know what you want to sort, and how you want to sort it.

Click one of the following:

*	Sort your list of records by one kind of data. For example, sort molecule records by molecular weight.

*	Sort your list of records by more than one kind of data. For example, sort reaction records by reaction temperature and reaction time.

*	Sort subrecords within each record on your list (hierarchical databases only). For example, sort variation subrecords within each reaction record.


To sort the list by one kind of data

1.	Clear the current sorting instructions.

2.	(Optional) Create a calculated field as necessary (remote databases only).

3.	Click Browse (if not selected).

4.	Choose List > Sort (if not selected). You see a dialog box.

5.	In the By box, click the field that contains the data that you want to use.

Note for local searches

6.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

7.	Click Add. You see the sorting instruction in the Sorting Instructions box.

8.	(Optional) Save the sorting instructions.

9.	To sort search results, click Sort. To close the dialog box without sorting search results, click Close.


To sort the list by more than one kind of data

1.	Clear the current sorting instructions.

2.	(Optional) Create calculated fields as necessary (remote databases only).

3.	Decide the order of the sorting instructions.

4.	Click Browse (if not selected).

5.	Choose List > Sort (if not selected). You see a dialog box.

6.	In the By box, click the database field that contains the data that you want to use for the first sorting instruction.

Note for local searches

7.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

8.	Click Add. You see the sorting instruction in the Sorting Instructions box.

9.	Repeat Steps 6 through 8 for the second sorting instruction.

10.	(Optional) To create a third sorting instruction, repeat Steps 6 through 8.

11.	(Optional) Save the sorting instructions.

12.	To sort search results, click Sort. To close the dialog box without sorting search results, click Close.


To sort subrecords within each record

1.	Clear the current sorting instructions.

2.	(Optional) Create calculated fields as necessary (remote databases only).

3.	Click Browse (if not selected).

4.	Choose List > Sort (if not selected).

5.	In the Sort each box, click the parent field that defines the subrecords that you want to sort. Examples

6.	In the By box, click the field that contains the data that you want to use.

Note for local searches

7.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

8.	Click Add. You see the sorting instruction in the Sorting Instructions box.

9.	(Optional) To create additional sorting instructions, repeat Steps 5 through 8.

10.	(Optional) Save the sorting instructions.

11.	To sort search results, click Sort. To close the dialog box without sorting search results, click Close.


To sort the list by one kind of data

1.	Clear the current sorting instructions.

2.	(Optional) Create a calculated field as necessary (remote databases only).

3.	Click Browse (if not selected).

4.	Choose List > Sort (if not selected).

5.	In the By box, click the field that contains the data that you want to use.

Note for local searches

6.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

7.	Click Add. You see the sorting instruction in the Sorting Instructions box.

8.	(Optional) Save the sorting instructions.

9.	To sort search results, click Sort. To close the dialog box without sorting search results, click Close.


To sort the list by more than one kind of data

1.	Clear the current sorting instructions.

2.	(Optional) Create calculated fields as necessary (remote databases only).

3.	Decide the order of the sorting instructions.

4.	Click Browse (if not selected).

5.	Choose List > Sort (if not selected).

6.	In the By box, click the database field that contains the data that you want to use for the first sorting instruction.

Note for local searches

7.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

8.	Click Add. You see the sorting instruction in the Sorting Instructions box.

9.	Repeat Steps 6 through 8 for the second sorting instruction.

10.	(Optional) To create a third sorting instruction, repeat Steps 6 through 8.

11.	(Optional) Save the sorting instructions.

12.	To sort search results, click Sort. To close the dialog box without sorting search results, click Close.


To sort subrecords within each record

1.	Clear the current sorting instructions.

2.	(Optional) Create calculated fields as necessary (remote databases only).

3.	Click Browse (if not selected).

4.	Choose List > Sort (if not selected).

5.	In the Sort each box, click the parent field that defines the subrecords that you want to sort. Examples

6.	In the By box, click the field that contains the data that you want to use.

Note for local searches

7.	To place records with the highest values first (ascending order), click [image] High to low. Otherwise, click [image] Low to high.

8.	Click Add. You see the sorting instruction in the Sorting Instructions box.

9.	(Optional) To create additional sorting instructions, repeat Steps 5 through 8.

10.	(Optional) Save the sorting instructions.

11.	To sort search results, click Sort. To close the dialog box without sorting search results, click Close.


To clear the existing sorting instructions

Use this procedure to delete the current set of sorting instructions. You can then create a new set of sorting instructions.

1.	Click Browse (if not already selected).

2.	Choose List > Sort. You see the Sort dialog box.

3.	(Optional) Save the current sorting instructions.

4.	Click Clear All.


To save sorting instructions

Use this procedure to save the current set of sorting instructions as an object within a local database, or within the remote-access file of a remote database.

1.	Click Browse (if not already selected).

2.	Choose List > Sort (if not already selected).

3.	Do one of the following:

*	To save the new sorting instructions or the current set of sorting instructions under the same name, click Save. For new sorting instructions only, enter a name and an optional description for the sorting instructions.

*	To save the current set of sorting instructions under a new name, click Save As. Enter a name and an optional description for the sorting instructions.

4.	Click OK.


Deciding the Order of the Sorting Instructions

When you sort by more than one kind of data, the order in which you specify the sorting instructions affects how ISIS sorts the data. You generally want to place the most important data first, because ISIS sorts all records by the data in the first sorting instruction. ISIS uses the data in the remaining sorting instructions solely to specify the order of records that have the same value for the data in the first sorting instruction. For example, you might want to sort molecule records by activity and molecular weight:

*	If you place the sorting instruction for activity first, then ISIS sorts all records by activity. If several molecules have the same activity, ISIS sorts those records (and only those records) by activity.

*	If you place the sorting instruction for molecular weight first, then ISIS sorts all records by molecular weight. If several molecules have the same molecular weight, ISIS sorts those records (and only those records) in order by activity.


Deciding the Order of the Sorting Instructions

You can specify up to three types of data for each subrecord that you sort. When you sort by more than one kind of data, the order in which you specify the sorting instructions affects how ISIS sorts the data. You generally want to place the most important data first, because ISIS sorts all subrecords by the data in the first sorting instruction. ISIS uses the data in the remaining sorting instructions solely to specify the order of records that have the same value for the data in the first sorting instruction. For example, you might want to sort molecule records by activity and molecular weight:

*	If you place the sorting instruction for activity first, then ISIS sorts all records by activity. If several molecule records have the same activity, ISIS sorts those records (and only those records) by activity.

*	If you place the sorting instruction for molecular weight first, then ISIS sorts all records by molecular weight. If several molecule records have the same molecular weight, ISIS sorts those records (and only those records) in order by activity.


Why Create Calculated Fields?

Click here for step-by-step instructions

A calculated field calculates a value from a set of data. For example, if your molecule database contains several activity measurements of each compound, you can create a calculated field that contains the average of those measurements. You can display data from a calculated field in a form and/or use it to sort search results, just like the data in any other database field.

To create calculated fields, you need to understand the database structure. We strongly recommend that you study Calculated Fields: Concepts/Examples before you attempt to create calculated fields.

Note: Do not confuse calculated fields with form calculations. A form calculation uses data from different database fields. For example, if your database contains a field for concentration in moles per liter and another field for molecular weight, you can use a form calculation to multiply those values to obtain the concentration in grams per liter. You can display a form calculation on your form, but you cannot use it to sort your search results.


To export search results to a local database

Use this procedure to export your search results to a local database that has the same structure as the database from which you retrieved your search results. This procedure assumes that a database is open in the active window, and that you have retrieved a list of records.

Note: If you sort subrecords within each record on your list, then exporting your search results to a local database preserves the order of the sorted subrecords. Lists that you save or export preserve the order of sorted records, but do not preserve the order of subrecords.

1.	Click Browse (if not highlighted).

2.	Choose File > Export > Local Database.

3.	Double-click the name of the first field in the Database Fields list box. The names of all database fields appear in the Export Data list box.

4.	Click OK.

5.	Do one of the following:

*	To create a new database file that contains the exported search results, enter a name in the Save As File Name text box (PC: Use the default .DB file extension that is displayed in the text box. Mac: To save a database that can be opened on the PC, press and hold the Option key while you complete this step.)

*	To overwrite an existing database file with the exported search results, click the name of an existing file in the Files list box, then click Yes when you see the prompt on overwriting the file.

6.	Click OK (Mac=Save).


Note for local searches

For local databases, the fields that you use to sort your list of search results must be directly connected to the field at the top level of the database hierarchy (the <ROOT> parent field). If your database is hierarchical, you cannot sort your list by data at lower levels of the database hierarchy. For example, you cannot sort records in a local reaction database by product yield, because the YIELD database field is at a lower level of the hierarchy.

Similarly, if you want to sort subrecords within a hierarchical local database, the fields that you use for sorting must be directly connected to the parent field that defines the subrecord.


Printing Search Results

How you print your search results depends on whether your database is flat or hierarchical.

Note: If you are not sure whether your database is flat or hierarchical, use the procedure for printing from a hierarchical database.

Click one of the following:

*	Print search results from a flat database.

*	Print search results from a hierarchical database.


Printing Search Results

How you print your search results depends on whether your database is flat or hierarchical.

Note: If you are not sure whether your database is flat or hierarchical, use the procedure for printing from a hierarchical database.

Click one of the following:

*	Print search results from a flat database.

*	Print search results from a hierarchical database.


To print search results

Caution: It is important to understand how the currently-selected form box or table affects the amount of data that ISIS prints. If you choose the wrong box or table, you might print large amounts of irrelevant data or, worse, print incomplete data without knowing that the data is incomplete. For more information, study Printing All the Data, and Only the Data, That You Want.

1.	Click the Browse mode (if not highlighted).

2.	Click the box or table that contains the most important data.

3.	Choose File > Print. You see a dialog box.

4.	Do one of the following:

*	To print solely the record that is currently displayed, click [image] Current record.

*	To print all records in the current list, click [image] Current list.

5.	(Optional) Change headers/footers.

6.	(Optional) Preview/change page layout.

7.	(Optional) Change the starting context.

8.	Click OK. You see a dialog box.

9.	Click OK to begin printing.

10.	(Optional) To save the headers, footers, and page layout, save the form.


To print search results

Caution: It is important to understand how the currently-selected form box or table affects the amount of data that ISIS prints. If you choose the wrong box or table, you might print large amounts of irrelevant data or, worse, print incomplete data without knowing that the data is incomplete. For more information, study Printing All the Data, and Only the Data, That You Want.

1.	Click the Browse mode (if not highlighted).

2.	Click the box or table that contains the most important data.

3.	Choose File > Print. You see a dialog box.

4.	Do one of the following:

*	To print solely the record that is currently displayed, click [image] Current record.

*	To print all records in the current list, click [image] Current list.

5.	(Optional) Change headers/footers.

6.	(Optional) Preview/change page layout.

7.	(Optional) Change the starting context.

8.	Click OK. You see a dialog box.

9.	Click OK to begin printing.

10.	(Optional) To save the headers, footers, and page layout, save the form.


To print search results from a flat database

1.	Click the Browse mode (if not highlighted).

2.	Choose File > Print. You see the Print Options dialog.

3.	Do one of the following:

*	To print solely the record that is currently displayed, click [image] Current record.

*	To print all records in the current list, click [image] Current list.

4.	(Optional) Preview/change page layout.

5.	(Optional) Change headers/footers.

6.	Click OK. You see a dialog box.

7.	Click OK to begin printing.

8.	(Optional) To save the headers, footers, and page layout, save the form.


To print search results from a hierarchical database

Caution: It is important to understand how the currently-selected form box or table affects the amount of data that ISIS prints. If you choose the wrong box or table, you might print large amounts of irrelevant data or, worse, print incomplete data without knowing that the data is incomplete. For more information, study Printing All the Data, and Only the Data, That You Want.

1.	Click the Browse mode (if not highlighted).

2.	Click the box or table that contains the most important data.

3.	Choose File > Print. You see a dialog box.

4.	Do one of the following:

*	To print solely the record that is currently displayed, click [image] Current record.

*	To print all records in the current list, click [image] Current list.

5.	(Optional) Change headers/footers.

6.	(Optional) Preview/change page layout.

7.	(Optional) Change the starting context.

8.	Click OK. You see a dialog box.

9.	Click OK to begin printing.

10.	(Optional) To save the headers, footers, and page layout, save the form.


To print search results from a flat database

1.	Click the Browse mode (if not highlighted).

2.	Choose File > Print. You see the Print Options dialog.

3.	Do one of the following:

*	To print solely the record that is currently displayed, click [image] Current record.

*	To print all records in the current list, click [image] Current list.

4.	(Optional) Preview/change page layout.

5.	(Optional) Change headers/footers.

6.	Click OK. You see a dialog box.

7.	Click OK to begin printing.

8.	(Optional) To save the headers, footers, and page layout, save the form.


To print search results from a hierarchical database

Caution: It is important to understand how the currently-selected form box or table affects the amount of data that ISIS prints. If you choose the wrong box or table, you might print large amounts of irrelevant data or, worse, print incomplete data without knowing that the data is incomplete. For more information, study Printing All the Data, and Only the Data, That You Want.

1.	Click the Browse mode (if not highlighted).

2.	Click the box or table that contains the most important data.

3.	Choose File > Print. You see a dialog box.

4.	Do one of the following:

*	To print solely the record that is currently displayed, click [image] Current record.

*	To print all records in the current list, click [image] Current list.

5.	(Optional) Change headers/footers.

6.	(Optional) Preview/change page layout.

7.	(Optional) Change the starting context.

8.	Click OK. You see a dialog box.

9.	Click OK to begin printing.

10.	(Optional) To save the headers, footers, and page layout, save the form.


Why Choose the Most Important Data?

You generally want to print all the data that is most important, and only that data. For example:

*	If you are primarily interested in literature references, click the box or table that contains literature references. This ensures that ISIS/Base prints all the literature references for every variation of every reaction.

*	If you are primarily interested in the reaction structure, click the box or table that is connected to the RXNSTRUCTURE field. This ensures that ISIS/Base prints the reactions that you want, but does not print large amounts of data from lower levels of the database hierarchy.

Caution: If you click the wrong box or table, you might print large amounts of irrelevant data or, worse, print incomplete data without knowing that the data is incomplete. For more information, study Printing All the Data, and Only the Data, That You Want.


Why Choose the Most Important Data?

You generally want to print all the data that is most important, and only that data. For example:

*	If you are primarily interested in test results, click the box or table that contains the test results. This ensures that ISIS/Base prints all the test results for every batch of every compound.

*	If you are primarily interested in molecular structures, click the box or table that is connected to the MOLSTRUCTURE field. This ensures that ISIS/Base prints the structures that you want, but does not print large amounts of data from lower levels of the database hierarchy.

Caution: If you click the wrong box or table, you might print large amounts of irrelevant data or, worse, print incomplete data without knowing that the data is incomplete. For more information, study Printing All the Data, and Only the Data, That You Want.


Why Choose the Most Important Data?

You generally want to print all the data that is most important to you. For example:

*	If you are primarily interested in test results, click the box or table that contains the test results. This ensures that ISIS/Base prints all the test results for every 3D structure.

*	If you are primarily interested in 3D structures, click the box or table that is connected to the MODELSTRUCTURE field. This ensures that ISIS/Base prints the 3D structures that you want, but does not print large amounts of data from lower levels of the database hierarchy.

Caution: If you click the wrong box or table, you might print large amounts of irrelevant data or, worse, print incomplete data without knowing that the data is incomplete. For more information, study Printing All the Data, and Only the Data, That You Want.


Why Choose the Most Important Data?

You generally want to print all the data that is most important to you:

*	In a reaction database, you might want the literature references for each reaction. In that case, click the box or table that contains literature references. On the other hand, if you are interested solely in the structure of the reaction, click the RXNSTRUCTURE box.

*	In a 2D or 3D molecule database, you might want test results for each compound. In that case, click the box or table that contains the test results. On the other hand, if you are interested solely in the 2D structures of each compound, click the MOLSTRUCTURE box.

Caution: If you click the wrong box or table, you might print large amounts of irrelevant data or, worse, print incomplete data without knowing that the data is incomplete. For more information, study Printing All the Data, and Only the Data, That You Want.


Changing the Text of Headers and Footers

Click here for step-by-step instructions

You can change the text that is printed in the headers and footers on each page of search results. ISIS can automatically print the following text in headers and footers:

*	Current page number

*	Database name

*	Time of day

*	Date

*	Ending context (from currently-selected box or table)

*	Starting context

You can also change the color and font of the text in headers and footers.

Notes: The default text for headers and footers is stored with the form. If you want to change the default text, you need to save the form after you make the changes.


To change the text of headers and footers

This procedure assumes that the Print Options or Page Layout dialog is open.

1.	Click Header/Footer (if not selected). You see a dialog box.

2.	Click one of the six boxes that corresponds to the position where you want the text to appear.

3.	Do one of the following:

*	Type your own text.

*	Insert a header/footer code.

Caution: Do not change the text of the header/footer codes. If you do so, ISIS prints the codes as ordinary text.

4.	(Optional) Change the color of the text in the header or footer.

5.	(Optional) Change the font, size, or text style of the text in the header or footer.

6.	(Optional) Repeat Steps 2 through 5 as necessary.

7.	Click OK.


To change the text of headers and footers

This procedure assumes that the Header/Footer dialog is open.

1.	Click one of the six boxes that corresponds to the position where you want the text to appear.

2.	Do one of the following:

*	Type your own text.

*	Insert a header/footer code.

Caution: Do not change the text of the header/footer codes. If you do so, ISIS will print the codes as ordinary text. To type a header/footer code as ordinary text, precede it with an ampersand. For example: &&[Page].

3.	(Optional) Change the color of the text in the header or footer.

4.	(Optional) Change the font, size, or text style of the text in the header or footer.

5.	(Optional) Repeat Steps 1 through 4 as necessary.

6.	Click OK.


To change the text of headers and footers

1.	Choose File > Page Layout (if not selected).

2.	Click Header/Footer. You see a dialog box.

3.	Click one of the six boxes that corresponds to the position where you want the text to appear.

4.	Do one of the following:

*	Type your own text.

*	Insert a header/footer code.

Caution: Do not change the text of the header/footer codes. If you do so, ISIS will print the codes as ordinary text. To type a header/footer code as ordinary text, precede it with an ampersand. For example: &&[Page].

5.	(Optional) Change the color of the text in the header or footer.

6.	(Optional) Change the font, size, or text style of the text in the header or footer.

7.	(Optional) Repeat Steps 3 through 6 as necessary.

8.	Click OK.


To change the text of headers and footers

This procedure assumes that the Form Defaults settings dialog is open and that the Header/Footer tab is selected.

1.	Click one of the six boxes that corresponds to the position where you want the text to appear.

2.	Do one of the following:

*	Type your own text.

*	Insert a header/footer code.

Caution: Do not change the text of the header/footer codes. If you do so, ISIS will print the codes as ordinary text. To type a header/footer code as ordinary text, precede it with an ampersand. For example: &&[Page].

3.	(Optional) Change the color of the text in the header or footer.

4.	(Optional) Change the font, size, or text style of the text in the header or footer.

5.	(Optional) Repeat Steps 1 through 4 as necessary.

6.	Click OK.


To insert a header/footer code

Use this procedure to insert codes into a header or footer. The procedure assumes that the Header/Footer dialog is open.

1.	Do one of the following:

*	To insert the current page number, click

*	To insert the current date, click

*	To insert the current time, click

*	To insert any other header/footer code, choose the code from the list box and click Apply.

Note: To print a header/footer code as text, insert an ampersand (&) before the code. For example: &&[Page].

2.	Click Back (at top of help screen) to return to the previous screen and continue with Step 5 on that screen.


To insert a header/footer code

Use this procedure to insert codes into a header or footer. The procedure assumes that the Header/Footer dialog is open.

1.	Do one of the following:

*	To insert the current page number, click

*	To insert the current date, click

*	To insert the current time, click

*	To insert any other header/footer code, choose the code from the list box and click Apply.

Note: To print a header/footer code as text, insert an ampersand (&) before the code. For example: &&[Page].

2.	Click Back (at top of help screen) to return to the previous screen and continue with Step 4 on that screen.


To insert a header/footer code

Use this procedure to insert codes into a header or footer. The procedure assumes that the Header/Footer dialog is open.

1.	Do one of the following:

*	To insert the current page number, click

*	To insert the current date, click

*	To insert the current time, click

*	To insert any other header/footer code, choose the code from the list box and click Apply.

Note: To print a header/footer code as text, insert an ampersand (&) before the code. For example: &&[Page].

2.	Click Back (at top of help screen) to return to the previous screen and continue with Step 3 on that screen.


To change the color of text in a header or footer

The following procedure assumes that the Header/Footer dialog is open.

1.	Select the text that you want to change.

2.	Choose the color that you want from the Color list box.

3.	Click Back (at top of help screen) to return to the previous screen and continue with Step 5 on that screen.


To change the color of text in a header or footer

The following procedure assumes that the Header/Footer dialog is open.

1.	Select the text that you want to change.

2.	Choose the color that you want from the Color list box.

3.	Click Back (at top of help screen) to return to the previous screen and continue with Step 6 on that screen.


To change the color of text in a header or footer

The following procedure assumes that the Header/Footer dialog is open.

1.	Select the text that you want to change.

2.	Choose the color that you want from the Color list box.

3.	Click Back (at top of help screen) to return to the previous screen and continue with Step 4 on that screen.


To change the color of text in a header or footer

1.	Choose File > Page Layout (if not selected).

2.	Click Header/Footer. You see a dialog box.

3.	Select the text that you want to change.

4.	Choose the color that you want from the Color list box.

5.	Click OK.


To change the font, size, and text style in a header or footer

The following procedure assumes that the Header/Footer dialog is open.

1.	Select the text that you want to change.

2.	Click Font. You see a dialog box..

3.	Choose the font, style, and size that you want. The sample text changes according to the choices that you make.

4.	Click OK.

5.	Click Back (at top of help screen) to return to the previous screen and continue with Step 7 on that screen.


To change the font, size, and text style in a header or footer

The following procedure assumes that the Header/Footer dialog is open.

1.	Select the text that you want to change.

2.	Click Font. You see a dialog box..

3.	Choose the font, style, and size that you want. The sample text changes according to the choices that you make.

4.	Click OK.

5.	Click Back (at top of help screen) to return to the previous screen and continue with Step 6 on that screen.


To change the font, size, and text style in a header or footer

The following procedure assumes that the Header/Footer dialog is open.

1.	Select the text that you want to change.

2.	Click Font. You see a dialog box..

3.	Choose the font, style, and size that you want. The sample text changes according to the choices that you make.

4.	Click OK.

5.	Click Back (at top of help screen) to return to the previous screen and continue with Step 5 on that screen.


To change the font, size, and text style in a header or footer

1.	Choose File > Page Layout (if not selected).

2.	Click Header/Footer. You see a dialog box.

3.	Select the text that you want to change.

4.	Click Font. You see a dialog box.

5.	Choose the font, style, and size that you want. The sample text changes according to the choices that you make.

6.	Click OK.


Previewing and Changing Page Layout

Click here for step-by-step instructions

You can preview how forms, headers, and footers will appear on the page (page layout) when you print your search results. You can use the following options to change the page layout:

*	Number of forms per page

*	Amount of space between forms (interform spacing)

*	Margins

*	Print forms at actual size or enlarge them to fit the area that you define

*	Location of headers and footers on the page

Note: The default page layout is stored with the form. If you want to change the default page layout, you need to save the form after you make the changes.


To preview and change page layout

This procedure assumes that the Print Options dialog is open.

1.	Click Page Layout. You see a dialog box. The diagram on the right side of the dialog box shows how forms, headers, and footers will be arranged on the printed page.

2.	Change the page layout as desired. You see the outline of the new layout of forms in the diagram on the right side of the dialog box.

3.	(Optional) To see a more detailed picture of the layout of forms on the page, click Update Preview.

4.	(Optional) Change the text of headers/footers.

5.	Click Print.


Previewing and Changing Page Layout

Click here for step-by-step instructions

You can preview how forms, headers, and footers will appear on the page (page layout) when you print your search results. You can use the following options to change the page layout:

*	Number of forms per page

*	Amount of space between forms (interform spacing)

*	Margins

*	Print forms at actual size or enlarge them to fit the area that you define

*	Location of headers and footers on the page

Note: The default page layout is stored with the form. If you want to change the default page layout, you need to save the form after you make the changes.


To preview and change page layout

1.	Choose File > Page Layout. You see a dialog box. The diagram on the right side of the dialog box shows how forms, headers, and footers will be arranged on the printed page.

2.	Change the page layout as desired. You see the outline of the new layout of forms in the diagram on the right side of the dialog box.

3.	(Optional) To see a more detailed picture of the layout of forms on the page, click Update Preview.

4.	(Optional) Change the text of headers/footers.

5.	Do one of the following:

*	To print the form, click Print.

*	To remove the dialog box and keep the changes that you made, click Close.

6.	(Optional) To store the changes with the form, save the form.


What Is the Ending Context?

The ending context is the level and branch of the database hierarchy from which you want to print all data. You choose the ending context by clicking the box or table that contains the data that you want to print.

For more information on printing from hierarchical databases, see Printing All the Data, and Only the Data, That You Want.


Why Change the Starting Context?

Click here for step-by-step instructions

Changing the starting context allows you to restrict the number of subrecords that you print within each record. For example, you might want to print data from only the first variation of each reaction, or the first batch of each compound.

Caution: If you are not sure how to use the starting context, we strongly recommend that you not change the starting context. If you choose the wrong starting context, you might print incomplete data without knowing that the data is incomplete.

By default, the starting context is set to the highest parent field in the database. This ensures that ISIS prints all data from every level of the database for the box or table that you chose. For more information on starting and ending contexts, study Printing All the Data, and Only the Data, That You Want.


To change the starting context

This procedure assumes that the Print Options dialog is open. For more information on choosing the starting context, see Printing All the Data, and Only the Data, That You Want.

1.	Click Customize. You see the Customized Data Selection dialog box.

2.	Click the Starting Context box and choose the parent field that is immediately below the level for which you want to print solely the first set of data.

3.	Click OK. In the Print Options dialog box, the Settings box specifies the starting context that you chose in Step 2.

4.	(Optional) Change the text of the header or footer to print the starting context with your search results.

5.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To change the starting context

This procedure assumes that the Print Options dialog is open. For more information on starting and ending context, see Printing All the Data, and Only the Data, That You Want.

1.	Click Customize. You see the Customized Data Selection dialog box.

2.	Click the Starting Context box and choose the parent field that is immediately below the level for which you want to print solely the first set of data.

3.	Click OK. In the Print Options dialog box, the Data To Be Printed box specifies the starting context that you chose in Step 2.


Text/Numeric Query Strings in 3D Queries

A text/numeric string in a 3D data constraint is a phrase that specifies the retrieval of data. The phrase contains:

*	A search operator that specifies the type of search (such as an equal sign, =, to specify a search that finds solely the exact target text in the query).

*	The text or numeric target value (specific data) that you want to find.

For example, to find an atom-pair with a proton spin-spin coupling constant greater than 1.5, enter > 1.5 as the query (where > is the search operator and 1.5 is the target value).


Filtering Search Results

You can filter your search results so that you view only the subrecords that match your query.

For example, you might want to find literature references in a reaction database by an author named R. L. Smith. To do this, you can conduct a Search By Form (SBF) with the query LIKE "%R. L. SMITH%" in a box or table that is connected to the field RXN>VARIATION>LITTEXT>littext_ref. Each reaction record can have several variation subrecords, and each variation subrecord can contain multiple literature-reference (LITTEXT) subrecords. ISIS retrieves all reactions that contain at least one literature reference that matches your query. However, the reactions that you retrieve might also contain subrecords that do not match your query. To display only the variations and literature references that match your query, you must filter the search results.

For more information on filtering search results, see:

Molecule records: SBF in a remote database or SBF in a local database

Reaction records: SBF in a remote database or SBF in a local database

3D Structure records: SBF in a remote database or SBF in a local database


To conduct a remote MEXACT search for molecules

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote MEXACT search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Current Mol.

5.	Click [image] Exact Match (if not selected).

6.	Click OK.

See also:

To abandon the search


To conduct a local MEXACT search for molecules

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export,

7.	(Optional) Query: Save, revise, print, or export.


To execute the local MEXACT search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Current Mol.

See also:

To abandon the search


To conduct a remote REXACT/Comp search for reaction components

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Find records that are related to the reaction on display.

8.	(Optional) Query: Save, revise, print, or export.


To execute the remote REXACT/Comp search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Subset Rxn.

See also:

To abandon the search


To conduct a remote 3DEXACT search for 3D structures

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	(Optional) Change fixed-atom tolerances.

5.	Execute the search (includes automatic sorting).

6.	View the search results.

7.	(Optional) Search results: Sort, save, manipulate, print, or export.

8.	(Optional) Query: Save, revise, print, or export.


Changing Fixed-Atom Tolerances

Click here for step-by-step instructions.

Fixed-atom tolerances specify how closely the spatial arrangement of the atoms in your 3D query must fit the spatial arrangement of the matching atoms in the 3D structures that you retrieve. Your ISIS administrator sets default fixed-atom tolerances that your site uses for registering 3D structures to molecule databases. You might want to increase the tolerances so that your query retrieves more 3D structures. If you are not sure whether to change fixed-atom tolerances, we recommend that you not change the default tolerances.

Caution: If you change the default fixed-atom tolerances for searching, you must restore the default fixed-atom tolerances before you register 3D structures.

For more information on fixed-atom tolerances, see Searching Concepts/Examples.


To execute the remote 3DEXACT search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Current Mol. A dialog box appears.

5.	Click [image] Exact Match (if not selected).

6.	Click OK.

See also:

To abandon the search

To restore default fixed-atom tolerances


To conduct a local 3DEXACT search for 3D structures

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the local 3DEXACT search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query.

4.	Choose Search > Current Mol.

See also:

To abandon the search


To conduct a remote MEXACT search for reaction components

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote MEXACT search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Current Mol.

5.	Click [image] Exact Match (if not selected).

6.	Click OK.

See also:

To abandon the search


To conduct a local MEXACT search for reaction components

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the local MEXACT search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Current Mol.

See also:

To abandon the search


To conduct a remote REXACT/Rxn search for reactions

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Find records that are related to the reaction on display.

8.	(Optional) Query: Save, revise, print, or export.


To execute the remote REXACT/Rxn search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Current Rxn.

See also:

To abandon the search


To conduct a local REXACT/Rxn search for reactions

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Find records that are related to the reaction on display.

8.	(Optional) Query: Save, revise, print, or export.


To execute the local REXACT/Rxn search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Current Rxn.

See also:

To abandon the search


To conduct a remote SSS search for molecules

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote SSS search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > SSS.

See also:

To abandon the search


To conduct a local SSS search for molecules

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the local SSS search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > SSS.

See also:

To abandon the search


To conduct a remote RGROUP search for molecules

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote Rgroup search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > SSS.

See also:

To abandon the search


To conduct a remote SSS search for reaction components

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote SSS search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > SSS.

See also:

To abandon the search


To conduct a local SSS search for reaction components

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the local SSS search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > SSS.

See also:

To abandon the search


To conduct a remote RSS/Rxn search for reactions

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Find records that are related to the reaction on display.

8.	(Optional) Query: Save, revise, print, or export.


To execute the remote RSS/Rxn search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > RSS.

See also:

To abandon the search


To conduct a local RSS/Rxn search for reactions

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Find records that are related to the reaction on display.

8.	(Optional) Query: Save, revise, print, or export.


To execute the local RSS/Rxn search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > RSS.

See also:

To abandon the search


To conduct a remote RSS/Comp search for reaction components

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Find records that are related to the reaction on display.

8.	(Optional) Query: Save, revise, print, or export.


To execute the remote RSS/Comp search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > RSS.

See also:

To abandon the search


To conduct a local RSS/Comp search for reaction components

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Find records that are related to the reaction on display.

8.	(Optional) Query: Save, revise, print, or export.


To execute the local RSS/Comp search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > RSS.

See also:

To abandon the search


To conduct a remote SBF search for molecule records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, or print.


To execute the search
To execute the remote SBF search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Choose Search > By Form.

See also:

To abandon the search


To conduct a local SBF search for molecule records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, or print.


To execute the search
To execute the local SBF search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Choose Search > By Form.

See also:

To abandon the search


To conduct a remote SBF search for reaction records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Find records that are related to the reaction on display.

8.	(Optional) Query: Save, revise, or print.


To execute the search
To execute the remote SBF search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Choose Search > By Form.

See also:

To abandon the search


To conduct a local SBF search for reaction records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Find records that are related to the reaction on display.

8.	(Optional) Query: Save, revise, or print.


To execute the search
To execute the local SBF search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Choose Search > By Form.

See also:

To abandon the search


To conduct a remote SSS/Biopoly search for molecules
To conduct a remote SSS/Biopoly search for biopolymer records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote SSS/Biopoly search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > SSS.

See also:

To abandon the search


To conduct a remote SSS3D/Biopoly search for biopolymer records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	(Optional) Change fixed-atom tolerances.

5.	Execute the search (includes automatic sorting).

6.	(Optional) Remove flexible structures.

7.	View the search results.

8.	(Optional) Search results: Sort, save, manipulate, print, or export.

9.	(Optional) Query: Save, revise, print, or export.


To conduct a local SSS/Biopoly search for molecules
To conduct a local SSS/Biopoly search for biopolymer records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the local SSS/Biopoly search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > SSS.

See also:

To abandon the search


To conduct a remote CFS/Biopoly search for molecules
To conduct a remote CFS/Biopoly search for biopolymer records

Searching Concepts/Examples

You generally conduct a CFS/Biopoly search in two phases: An initial CFS search followed by a bump-checking CFS search.

Note: CFS/Biopoly searching provides many options that allow you to control how ISIS fits 3D structures to your query. These options subtly interact with each other and can produce undesirable results if improperly used. We strongly recommend that you study the Request-A-Document CFS/Biopoly Searching Concepts/Examples before you attempt a CFS/Biopoly search.

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	(Optional) Change fixed-atom tolerances.

5.	Sprout hydrogens and lone pairs for the initial CFS search.

6.	Execute the initial CFS search (includes sorting, CFS options, and search cutoffs).

7.	Sprout hydrogens and lone pairs for bump checking.

8.	(Optional) Execute the bump-checking CFS search.

9.	View the search results.

10.	(Optional) Search results: Sort, save, manipulate, print, or export.

11.	(Optional) Query: Save, revise, print, or export.


To execute the remote CFS/Biopoly search

1.	(Optional) Specify default CFS options.

2.	(Optional) Choose automatic sorting.

2.	Do one of the following:

*	Do not sort search results.

*	Sort by torsional degrees of freedom (TDF).

*	Sort by RMS deviation (RMS).

*	Sort by both TDF and RMS deviation.

*	Sort by data in a single database field.

*	Sort by more than one kind of data.

3.	Click the Query mode (if not highlighted).

4.	Click the box that contains the query (if not selected).

5.	Choose Search > CFS. You see the CFS Options dialog box.

6.	(Optional) Specify search cutoffs.

7.	(Optional) Change other CFS options.

8.	Click OK.

9.	(Optional) To repeat the search with different CFS options, repeat Steps 1 through 8.

See also:

To abandon the search


To conduct a remote RSim search for reactions

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Find records that are related to the reaction on display.

8.	(Optional) Query: Save, revise, print, or export.


To execute the remote RSim search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Similarity.

5.	Enter a number between 0 and 100 into the Structure text box and into the Reacting Centers text box. The higher the numbers, the more the records that you retrieve resemble your query.

6.	Do one of the following:

*	To retrieve reaction components with the same structural complexity as your query, click [image] Normal.

*	To retrieve reaction components with greater structural complexity than your query, click [image] Subsimilar.

*	To retrieve reaction components with less structural complexity than your query, click [image] Supersimilar.

7.	Click OK.

See also:

To abandon the search


To conduct a remote MSim search for molecules

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote MSim search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Similarity.

5.	Enter a number between 0 and 100 into the Structure text box. The higher the number, the more the records that you retrieve resemble your query.

6.	Do one of the following:

*	To retrieve molecules with the same structural complexity as your query, click [image] Normal.

*	To retrieve molecules with greater structural complexity than your query, click [image] Subsimilar.

*	To retrieve molecules with less structural complexity than your query, click [image] Supersimilar.

7.	Click OK.

See also:

To abandon the search


To conduct a remote FLEX search for molecules

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote FLEX search

Do these steps in the order shown:

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Current Mol.

5.	Click [image] Flexmatch.

6.	(Optional) Do one of the following:

*	Retrieve structures that are salts of your query.

*	Retrieve structures with different isotopic labels than your query.

*	Retrieve different structural representations of your query. Example

7.	(Optional) To change Flexmatch parameters for polymers, ordered mixtures, unordered mixtures, and/or attached data, enter the three-letter codes to specify the features that must match your query.

8.	Click OK.

See also:

To abandon the search


What are Flexmatch Parameters?

Click here for step-by-step instructions

Flexmatch parameters define the features of retrieved molecules that must match the query molecule. Changing the default values of these parameters loosens the definition of an exact match. This allows you to find structures that:

*	Match your query, but have different isotopic labels

*	Match your query, but might be represented differently in the database. For example, the pi-metal bonds in ferrocene can be represented in different ways:


What are Flexmatch Parameters?

Click here for step-by-step instructions

Flexmatch parameters define the features of retrieved reaction components that must match the query. Changing the default values of these parameters loosens the definition of an exact match. This allows you to find structures that:

*	Match your query, but have different isotopic labels

*	Match your query, but might be represented differently in the database. For example, the pi-metal bonds in ferrocene can be represented in different ways:


To change Flexmatch parameters

1.	Click Flexmatch. You see a dialog box.

2.	Do one of the following:

*	To retrieve salts with different counterions than your query, you require these settings:

Fragments must match

Salts must match

*	To retrieve different isotopes than your query, you require this setting:

Isotopes must match

*	To retrieve different structural representations than your query that are also the loosest definition of an exact match, you require these settings:

Type of Bond Match: Both Off

Type of Charge Match: Both Off

Fragments must match

Hydrogen count must match

Isotopes must match

Metal bonds must match

Radicals must match

Salts must match

Stereo bonds must match

Valences must match

Note: If you want to set Flexmatch parameters that are different from any of these, you need to know which parameters require other parameters to function correctly. To learn these requirements and to see some searching examples, click here.

3.	Click OK. You see the Current Mol dialog.

4.	(Optional) To change Flexmatch parameters for polymers, ordered mixtures, unordered mixtures, and/or attached data, enter the three-letter codes for the features that must match your query.

5.	Click Back (at top of help screen) to return to the previous screen and continue with Step 7 on that screen.


Entering 3-Letter Codes
Entering Three-Letter Codes

Click here for step-by-step instructions

If your Flexmatch query contains polymers, mixtures, or attached data, you might want to specify that some or all of these features must match your query. To specify that these features must match your query, you must enter the three-letter codes for the corresponding flexmatch parameters.

 Caution: The Flexmatch parameters are interactive. To obtain the correct results, you need to know which flexmatch parameters require other flexmatch parameters to function correctly. Thus, we recommend that you use another search where possible! For a list of ISIS/Base searches, click here.


To enter 3-letter codes
To enter three-letter codes

1.	Click the Flexmatch codes box in the Current Mol dialog.

2.	Press the End key. You see the cursor at the end of the current string of flexmatch parameters.

3.	(Optional) To specify that both the type of mixture (ordered or unordered) and the order of components in an ordered mixture, must match the corresponding structures in your query, type /MIX.

4.	(Optional) To specify that attached data must match the attached data in your query, type /DAT.

5.	(Optional) To specify that that all polymer definitions must match the corresponding structures in your query, type /POL. (The polymer definition is the set of atoms and bonds that is associated with a set of polymer brackets).

6.	(Optional) To specify that the polymer bracket type (for example, monomer, SRU, or copolymer) and polymer connectivity must match the corresponding structures in your query, type /TYP.

7.	(Optional) To specify that the source-based and structure-based representations of the same polymer  do not match (that is, source-based and structure-based representations are considered distinct structures), type /MSU.

8.	(Optional) To specify that polymer end groups must match the corresponding structures in your query, type /END.

9.	Click Back (at top of help screen) to return to the previous screen and continue with Step 7 on that screen.


To retrieve salts of your query

1.	Choose Search > Current Mol (if not selected).

2.	Click [image] Flexmatch.

3.	Click Flexmatch. You see a dialog box.

4.	Do one of the following:

*	To retrieve salts that contain different counterions than your query, you require these settings:

Fragments

Salts

Example

*	To retrieve salts that contain a specific counterion, you require these settings:

Fragments

Salts

Example

Note: If you want to set Flexmatch parameters that are different from any of these, you need to know which parameters require other parameters to function correctly. To learn these requirements and to see some searching examples, click here.

5.	Click OK.

6.	Click Back (at top of help screen) to return to the previous screen and continue with Step 7 on that screen.


Example


Example


To retrieve molecules with different isotopic labels

1.	Choose Search > Current Mol (if not selected).

2.	Click [image] Flexmatch.

3.	Click Flexmatch. You see a dialog box.

4.	To retrieve different isotopes than your query, you require this setting:

Isotopes

Note: If you want to set Flexmatch parameters that are different from any of these, you need to know which parameters require other parameters to function correctly. To learn these requirements and to see some searching examples, click here.

5.	Click OK.

6.	Click Back (at top of help screen) to return to the previous screen and continue with Step 7 on that screen.


To retrieve different structural representations

To retrieve structures that match your query, but might be represented differently in the database, use the loosest possible definition of an exact match.

1.	Choose Search > Current Mol (if not selected).

2.	Click [image] Flexmatch.

3.	Click Flexmatch. You see a dialog box.

4.	To retrieve different structural representations than your query, you require the following settings:

Type of Bond Match: Both Off

Type of Charge Match:  Both Off

Fragments

Hydrogen count

Isotopes

Metal bonds

Radicals

Salts

Stereo bonds

Valences

Note: If you want to set Flexmatch parameters that are different from any of these, you need  to know which parameters require other parameters to function correctly. To learn these requirements and to see some searching examples, click here.

5.	Click OK.

6.	Click Back (at top of help screen) to return to the previous screen and continue with Step 7 on that screen.


To change Flexmatch parameters

1.	Choose Search > Current Mol (if not selected).

2.	Click [image] Flexmatch.

3.	Click Flexmatch. You see a dialog box.

4.	Do one of the following:

*	To retrieve salts with different counterions than your query, you require these settings:

Fragments must match

Salts must match

*	To retrieve different isotopes than your query, you require this setting:

Isotopes must match

*	To retrieve different structural representations than your query that are also the loosest definition of an exact match, you require these settings:

Type of Bond Match: Both Off

Type of Charge Match: Both Off

Fragments must match

Hydrogen count must match

Isotopes must match

Metal bonds must match

Radicals must match

Salts must match

Stereo bonds must match

Valences must match

Note: If you want to set Flexmatch parameters that are different from any of these, you need to know which parameters require other parameters to function correctly. To learn these requirements and to see some searching examples, click here.

5.	Click OK.

6.	Click Back (at top of help screen) to return to the previous screen and continue with Step 7 on that screen.


To change Flexmatch parameters

Note: Flexmatch parameters interact with each other. For more information on these interactions, see the Searching Examples.

1.	Click Query (if not highlighted).

2.	Click the box that contains the query (if not selected).

3.	Choose Search > Current Mol (if not selected).

4.	Click [image] Flexmatch.

5.	Click Flexmatch. You see a dialog box.

6.	To obtain more information on Flexmatch parameters, click Help.

7.	Change the Flexmatch parameters of your choice.

8.	Click OK.


To conduct a remote TAUT search for molecules

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote TAUT search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Current Mol.

5.	Click [image] Tautomers.

6.	Click OK.

See also:

To abandon the search


To conduct a remote ISOMER search for molecules

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote ISOMER search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Current Mol.

5.	Click [image] Isomers.

6.	Click OK.

See also:

To abandon the search


To conduct a remote PARENT search for molecules

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the PARENT search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Current Mol.

5.	Click [image] Parent Molecule.

6.	Click OK.

See also:

To abandon the search


To conduct a remote MSim search for reaction components

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote MSim search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Enter a number between 0 and 100 into the Structure text box. The higher the number, the more the records that you retrieve resemble your query.

5.	Do one of the following:

*	To retrieve molecules with the same structural complexity as your query, click [image] Normal.

*	To retrieve molecules with greater structural complexity than your query, click [image] Subsimilar.

*	To retrieve molecules with less structural complexity than your query, click [image] Supersimilar.

6.	Click OK.

See also:

To abandon the search


To conduct a remote FLEX search for reaction components

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote FLEX search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Current Mol.

5.	Click [image] Flexmatch.

6.	(Optional) Change Flexmatch parameters.

7.	Click OK.

See also:

To abandon the search


To retrieve salts of your query

1.	Choose Search > Current Mol (if not selected).

2.	Click [image] Flexmatch.

3.	Click Flexmatch. You see a dialog box.

4.	Do one of the following:

*	To retrieve salts with different counterions than your query, you require these settings:

Fragments

Salts

Example

*	To retrieve salts with a specific counterion in your query, you require these settings:

Fragments

Salts

Example

Note: If you want to set Flexmatch parameters that are different from any of these, you need to know which parameters require other parameters to function correctly. To learn these requirements and to see some searching examples, click here.

5.	Click OK.

6.	Click Back (at top of help screen) to return to the previous screen and continue with Step 7 on that screen.


To retrieve molecules with different isotopic labels

1.	Choose Search > Current Mol (if not selected).

2.	Click [image] Flexmatch.

3.	Click Flexmatch. You see a dialog box.

4.	To retrieve different isotopes than your query, you require this setting:

Isotopes

Note: If you want to set Flexmatch parameters that are different from any of these, you need to know which parameters require other parameters to function correctly. To learn these requirements and to see some searching examples, click here.

5.	Click OK.

6.	Click Back (at top of help screen) to return to the previous screen and continue with Step 7 on that screen.


To retrieve different structural representations

To retrieve structures that match your query, but might be represented differently in the database, use the loosest possible definition of an exact match.

1.	Choose Search > Current Mol (if not selected).

2.	Click [image] Flexmatch.

3.	Click Flexmatch. You see a dialog box.

4.	To retrieve different structural representations than your query, you require the following settings:

Type of Bond Match: Both Off

Type of Charge Match:  Both Off

Fragments

Hydrogen count

Isotopes

Metal bonds

Radicals

Salts

Stereo bonds

Valences

Note: If you want to set Flexmatch parameters that are different from any of these, you need  to know which parameters require other parameters to function correctly. To learn these requirements and to see some searching examples, click here.

5.	Click OK.

6.	Click Back (at top of help screen) to return to the previous screen and continue with Step 7 on that screen.


To conduct a remote TAUT search for reaction components

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote TAUT search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Current Mol.

5.	Click [image] Tautomers.

6.	Click OK.

See also:

To abandon the search


To conduct a remote ISOMER search for reaction components

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote ISOMER search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Current Mol.

5.	Click [image] Isomers.

6.	Click OK.

See also:

To abandon the search


To conduct a remote PARENT search for reaction components

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote PARENT search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Current Mol.

5.	Click [image] Parent Molecule.

6.	Click OK.

See also:

To abandon the search


To conduct a remote RGROUP search for reaction components

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote RGROUP search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > SSS.

See also:

To abandon the search


Choosing Automatic Sorting

To sort search results automatically after the search, you must define sorting instructions before the search. The sorting instructions that you define depend on the data that you want to use to sort your search results.

Note: If you sort by transformational similarity and/or structural similarity, we strongly recommend that you sort search results automatically. If you sort your search results manually after the search, ISIS must repeat the search to calculate similarity data.

Click one of the following:

*	Do not sort search results.

*	Sort by structural similarity.

*	Sort by transformational similarity.

*	Sort by both structural and transformational similarity.

*	Sort by data in a single database field.

*	Sort by more than one kind of data.


Choosing Automatic Sorting

To sort search results automatically after the search, you must define sorting instructions before the search. The sorting instructions that you define depend on the data that you want to use to sort your search results.

Click one of the following:

*	Do not sort search results.

*	Sort by data in a single database field.

*	Sort by data in more than one database field.


Choosing Automatic Sorting

To sort search results automatically after the search, you must define sorting instructions before the search. The sorting instructions that you define depend on the data that you want to use to sort your search results.

Note: If you sort by similarity, we strongly recommend that you sort search results automatically. If you sort your search results manually after the search, ISIS must repeat the search to calculate similarity data.

Click one of the following:

*	Do not sort search results.

*	Sort by structural similarity.

*	Sort by data in a single database field.

*	Sort by more than one kind of data.


Choosing Automatic Sorting

To sort search results automatically after the search, you must define sorting instructions before the search. The sorting instructions that you define depend on the data that you want to use to sort your search results.

Click one of the following:

*	Do not sort search results.

*	Sort by data in a single database field.

*	Sort by data in more than one database field.


Choosing Automatic Sorting

To sort search results automatically after the search, you must define sorting instructions before the search. The sorting instructions that you define depend on the data that you want to use to sort your search results.

Note: If you sort by similarity, we strongly recommend that you sort search results automatically. If you sort your search results manually after the search, ISIS must repeat the search to calculate similarity data.

Click one of the following:

*	Do not sort search results.

*	Sort by similarity.

*	Sort by data in a single database field.

*	Sort by more than one kind of data.


Choosing Automatic Sorting

To sort search results automatically after the search, you must define sorting instructions before the search. The sorting instructions that you define depend on the data that you want to use to sort your search results.

Click one of the following:

*	Do not sort search results.

*	Sort by data in a single database field.

*	Sort by data in more than one database field.


Choosing Automatic Sorting

To sort search results automatically after the search, you must define sorting instructions before the search. The sorting instructions that you define depend on the data that you want to use to sort your search results.

Click one of the following:

*	Do not sort search results.

*	Sort by data in a single database field.

*	Sort by data in more than one database field.


Choosing Automatic Sorting

To sort search results automatically after the search, you must define sorting instructions before the search. The sorting instructions that you define depend on the data that you want to use to sort your search results.

Click one of the following:

*	Do not sort search results.

*	Sort by data in a single database field.

*	Sort by data in more than one database field.


Choosing Automatic Sorting

To sort search results automatically after the search, you must define sorting instructions before the search. The sorting instructions that you define depend on the data that you want to use to sort your search results.

Click one of the following:

*	Do not sort search results.

*	Sort by data in a single database field.

*	Sort by data in more than one database field.


Choosing Automatic Sorting

To sort search results automatically after the search, you must define sorting instructions before the search. The sorting instructions that you define depend on the data that you want to use to sort your search results.

Click one of the following:

*	Do not sort search results.

*	Sort by data in a single database field.

*	Sort by data in more than one database field.


Choosing Automatic Sorting

To sort search results automatically after the search, you must define sorting instructions before the search. The sorting instructions that you define depend on the data that you want to use to sort your search results.

Click one of the following:

*	Do not sort search results

*	Sort by data in a single database field

*	Sort by data in more than one database field


Choosing Automatic Sorting

To sort search results automatically after the search, you must define sorting instructions before the search. The sorting instructions that you define depend on the data that you want to use to sort your search results.

Note: If you sort by torsional degrees of freedom (TDF) and/or RMS deviation, we strongly recommend that you sort search results automatically. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.

Click one of the following:

*	Do not sort search results.

*	Sort by torsional degrees of freedom (TDF).

*	Sort by RMS deviation (RMS).

*	Sort by both TDF and RMS deviation.

*	Sort by data in a single database field.

*	Sort by more than one kind of data.


Choosing Automatic Sorting

To sort search results automatically after the search, you must define sorting instructions before the search. The sorting instructions that you define depend on the data that you want to use to sort your search results.

Note: If you sort by torsional degrees of freedom (TDF), van der Waals energy difference, and/or RMS deviation, we strongly recommend that you sort search results automatically. If you sort your search results manually after the search, ISIS must repeat the search to calculate the data.

Click one of the following:

*	Do not sort search results.

*	Sort by van der Waals energy difference (VDW).

*	Sort by torsional degrees of freedom (TDF).

*	Sort by RMS deviation (RMS).

*	Sort by a combination of CFS data.

*	Sort by data in a single database field.

*	Sort by more than one kind of data.


To conduct a remote QB search for molecule records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	(Optional) Choose automatic sorting.

4.	Obtain a query and execute the search.

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save or revise.


To choose automatic sorting

1.	Do one of the following:

*	Do not sort search results.

*	Sort by data in a single database field.

*	Sort by data in more than one database field.

2.	Click Query (if not selected).

3.	Set Search > [image] Sort on Search (not Sort on Search).


To conduct a local QB search for molecule records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	(Optional) Choose automatic sorting.

4.	Obtain a query and execute the search.

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save or revise.


To choose automatic sorting

1.	Do one of the following:

*	Do not sort search results

*	Sort by data in a single database field.

*	Sort by data in more than one database field.

2.	Click Query (if not selected).

3.	Set Search > [image] Sort on Search (not Sort on Search).


To conduct a remote QB search for reaction records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search

3.	(Optional) Choose automatic sorting.

4.	Obtain a query and execute the search.

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Find records that are related to the reaction on display.

8.	(Optional) Query: Save or revise.


To choose automatic sorting

1.	Do one of the following:

*	Do not sort search results.

*	Sort by data in a single database field.

*	Sort by data in more than one database field.

2.	Click Query (if not selected).

3.	Set Search > [image] Sort on Search (not Sort on Search).


To conduct a local QB search for reaction records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	(Optional) Choose automatic sorting.

4.	Obtain a query and execute the search.

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Find records that are related to the reaction on display.

8.	(Optional) Query: Save or revise.


To choose automatic sorting

1.	Do one of the following:

*	Do not sort search results.

*	Sort by data in a single database field.

*	Sort by data in more than one database field.

2.	Click Query (if not selected).

3.	Set Search > [image] Sort on Search (not Sort on Search).


To conduct a remote QB search for 3D structure records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Choose automatic sorting.

4.	Obtain a query and execute the search.

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save or revise.


To choose automatic sorting

1.	Do one of the following:

*	Do not sort search results.

*	Sort by data in a single database field.

*	Sort by data in more than one database field.

2.	Click Query (if not selected).

3.	Set Search > [image] Sort on Search (not Sort on Search).


To conduct a local QB search for 3D structure records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	(Optional) Choose automatic sorting.

4.	Obtain a query and execute the search.

5.	View the search results.

6.	(Optional) Search results: Save, manipulate, print, or export.

7.	(Optional) Query: Save or revise.


To choose automatic sorting

1.	Do one of the following:

*	Do not sort search results.

*	Sort by data in a single database field.

*	Sort by data in more than one database field.

2.	Click Query (if not selected).

3.	Set Search > [image] Sort on Search (not Sort on Search).


To conduct a remote ALL search for all molecule records

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Execute the search.

4.	View the search results.

5.	(Optional) Search results: Save, manipulate, print, or export.


To execute the remote ALL search

1.	Click Query (if not highlighted).

2.	Choose Search > Retrieve All.

See also:

To abandon the search


To conduct a remote ID search for molecule records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, or print.


To execute the remote ID search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Choose Search > By Form.

See also:

To abandon the search


To conduct a remote FMLA search for molecules

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	(Optional) Choose automatic sorting.

4.	Obtain a query and execute the search.

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save or revise.


To choose automatic sorting

1.	Do one of the following:

*	Do not sort search results.

*	Sort by data in a single database field.

*	Sort by data in more than one database field.

2.	Click Query (if not selected).

3.	Set Search > [image] Sort on Search (not Sort on Search).


To conduct a local FMLA search for molecules

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	(Optional) Choose automatic sorting.

4.	Obtain a query and execute the search.

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save or revise.


To choose automatic sorting

1.	Do one of the following:

*	Do not sort search results.

*	Sort by data in a single database field.

*	Sort by data in more than one database field.

2.	Click Query (if not selected).

3.	Set Search > [image] Sort on Search (not Sort on Search).


To conduct a remote FMLA search for reaction components

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	(Optional) Choose automatic sorting.

4.	Obtain a query and execute the search.

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save or revise.


To choose automatic sorting

1.	Do one of the following:

*	Do not sort search results.

*	Sort by data in a single database field.

*	Sort by data in more than one database field.

2.	Click Query (if not selected).

3.	Set Search > [image] Sort on Search (not Sort on Search).


To conduct a local FMLA search for reaction components

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	(Optional) Choose automatic sorting.

4.	Obtain a query and execute the search.

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save or revise.


To choose automatic sorting

1.	Do one of the following:

*	Do not sort search results.

*	Sort by data in a single database field.

*	Sort by data in more than one database field.

2.	Click Query (if not selected).

3.	Set Search > [image] Sort on Search (not Sort on Search).


To conduct a remote ID search for reaction records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, or print.


To execute the remote ID search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Choose Search > By Form.

See also:

To abandon the search


To conduct a remote ID search for 3D records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, or print.


To execute the remote ID search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Choose Search > By Form.

See also:

To abandon the search


To conduct a local ALL search for all molecule records

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Execute the search.

4.	View the search results.

5.	(Optional) Search results: Save, manipulate, print, or export.


To execute the local ALL search

1.	Click Query (if not highlighted).

2.	Choose Search > Retrieve All.

See also:

To abandon the search


To conduct a local ID search for molecule records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, or print.


To execute the local ID search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Choose Search > By Form.

See also:

To abandon the search


To conduct a local ID search for reaction records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, or print.


To execute the local ID search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Choose Search > By Form.

See also:

To abandon the search


To conduct a local ID search for 3D records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, or print.


To execute the local ID search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Choose Search > By Form.

See also:

To abandon the search


To conduct a remote ALL search for all reaction records

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Execute the search (includes automatic sorting).

4.	View the search results.

5.	(Optional) Search results: Save, manipulate, print, or export.


To conduct a local ALL search for all reaction records

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Execute the search.

4.	View the search results.

5.	(Optional) Search results: Save, manipulate, print, or export.


To conduct a remote ALL search for all 3D structure records

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Execute the search.

4.	View the search results.

5.	(Optional) Search results: Save, manipulate, print, or export.


To conduct a local ALL search for all 3D structure records

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Execute the search.

4.	View the search results.

5.	(Optional) Search results: Save, manipulate, print, or export.


To execute the SSS3D search

1.	(Optional) Choose automatic sorting.

2.	Click the Query mode (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > SSS.

See also:

To abandon the search


To remove flexible structures

To remove 3D structures that are flexible in the region that matches the query, conduct a CFS search with a search cutoff of 1 for torsional degrees of freedom. The search cutoff removes structures that contain more than one rotatable bond in the region that matches the query.

1.	Choose Search > Set Search Domain > Current. This sets the search domain to the results of the SSS3D search.

2.	Click the Query mode (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Click Search > CFS. You see the CFS Options dialog box.

5.	Click Defaults.

6.	You require this setting:

7.	Click OK.

See also:

To abandon the search


To conduct a remote SSS3D search for 3D structures

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	(Optional) Change fixed-atom tolerances.

5.	Execute the search (includes automatic sorting).

6.	(Optional) Remove flexible structures.

7.	View the search results.

8.	(Optional) Search results: Sort, save, manipulate, print, or export.

9.	(Optional) Query: Save, revise, print, or export.


Removing Flexible Structures

Click here for step-by-step instructions

If you want to use the results of your SSS3D search in structure-activity studies, you might want only structures that are rigid in the region that matches the query. For example:

However, an SSS3D search retrieves both rigid and flexible 3D structures from the database. (Some 3D structures might be flexible, but happen to have the correct conformation to fit the query). You can use a CFS search to remove flexible structures.


To execute the remote SSS3D search

1.	(Optional) Choose automatic sorting.

2.	Click the Query mode (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > SSS.

See also:

To abandon the search


To conduct a remote CFS search for 3D structures

Searching Concepts/Examples

You generally conduct a CFS search in two phases: An initial CFS search followed by a bump-checking CFS search.

Note: CFS searching provides many options that allow you to control how ISIS fits 3D structures to your query. These options subtly interact with each other and can produce undesirable results if improperly used. We strongly recommend that you study the Request-A-Document CFS Searching Concepts/Examples before you attempt a CFS search.

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	(Optional) Change fixed-atom tolerances.

5.	Sprout hydrogens and lone pairs for the initial CFS search.

6.	Execute the initial CFS search (includes sorting, CFS options, and search cutoffs).

7.	Sprout hydrogens and lone pairs for bump checking.

8.	(Optional) Execute the bump-checking CFS search.

9.	View the search results.

10.	(Optional) Search results: Sort, save, manipulate, print, or export.

11.	(Optional) Query: Save, revise, print, or export.


To execute the initial CFS search

For fastest search speeds, the initial CFS search ignores nonbonded (van der Waals) interactions between parts of the molecule that ISIS rotates to fit the query. The bump-checking CFS search that you perform later calculates nonbonded interactions.

1.	(Optional) Specify default CFS options.

2.	(Optional) Choose automatic sorting.

3.	Click the Query mode (if not highlighted).

4.	Click the box that contains the query (if not selected).

5.	Choose Search > CFS. You see the CFS Options dialog box.

6.	(Optional) Specify search cutoffs.

7.	(Optional) Change other CFS options.

8.	Click OK.

See also:

To abandon the search


To specify default CFS options

1.	Click the Query mode (if not highlighted).

2.	Choose Options > CFS.

3.	Click Defaults.

4.	Click OK.

5.	Click Back (at top of help screen) to return to the previous screen and continue with Step 2 on that screen.


To specify default CFS options

1.	Click the Query mode (if not highlighted).

2.	Choose Options > CFS Options. You see a dialog box.

3.	Click Defaults.

4.	Click OK.


What Are Default CFS Options?

Click here for step-by-step instructions

If you are not sure how to use the CFS options, we strongly recommend that you specify the default CFS options as the first step in the initial CFS search.

The default CFS options provide a good balance between achieving fast search speeds and retrieving the maximum number of 3D structures. The default options also serve as a useful starting point if you want to change CFS options that are required for sorting and search cutoffs.

For more information on the default CFS options, study CFS Searching Concepts/Examples.


Default CFS Options

Click here for step-by-step instructions

If you are not sure how to use the CFS options, we strongly recommend that you specify the default CFS options as the first step in the initial CFS search.

The default CFS options provide a good balance between achieving fast search speeds and retrieving the maximum number of 3D structures. The default options also serve as a useful starting point if you want to change CFS options that are required for sorting and search cutoffs.

For more information on the default CFS options, study CFS Searching Concepts/Examples.


What Is a Search Cutoff?

In the initial CFS search, you can specify search cutoffs that exclude fitted 3D structures that do not meet your criteria:

*	Torsional degrees of freedom (TDF) is the number of rotatable bonds in the fitted 3D structure in the region that matches the query. Use a TDF cutoff to eliminate highly flexible structures.

*	RMS deviation (RMS) measures how closely a fitted 3D structure matches the query (goodness-of-fit).

Note: To specify a search cutoff for RMS deviation, your query can contain solely the following 3D components: atoms, ring centroids, distances, and angles that are defined by three points.

Click one of the following:

*	Specify a search cutoff for torsional degrees of freedom (TDF)

*	Specify a search cutoff for RMS deviation

*	Specify search cutoffs for both torsional degrees of freedom (TDF) and RMS deviation


Specifying a Search Cutoff for Torsional Degrees of Freedom (TDF)

Click here for step-by-step instructions

To eliminate highly flexible molecules and increase search speed, you can specify a search cutoff for torsional degrees of freedom (TDF). TDF is the number of rotatable bonds on the paths that connect the mapped atoms in the fitted 3D structure (Mapped atoms are the atoms in the fitted 3D structure that correspond to atoms in the query). The higher the TDF value, the more flexible is the portion of the 3D structure that maps to your query.

If you specify a search cutoff for TDF, ISIS excludes fitted structures with TDF values that are greater than the value that you specify. This improves search speed by eliminating highly flexible molecules before ISIS performs the slower calculations of the CFS search.

Note: If you want to specify a search cutoff for RMS deviation, your query can contain only the following 3D components: atoms, ring centroids, distances, and angles defined by three points.

For more information on search cutoffs, see CFS Searching Concepts/Examples.


To specify a search cutoff for torsional degrees of freedom

This procedure assumes that the CFS Options dialog box is displayed.

1.	Enter a value in the box that corresponds to the TDF search cutoff:

2.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To specify a search cutoff for torsional degrees of freedom

This procedure assumes that the CFS Options dialog box is displayed.

1.	Enter a value in the box that corresponds to the TDF search cutoff:


Specifying a Search Cutoff for RMS Deviation (RMS)

Click here for step-by-step instructions

RMS deviation is measures how closely a fitted 3D structure fits the constraints of the query. When you specify a search cutoff for RMS deviation, ISIS calculates the RMS deviation for each fitted 3D structure. If the RMS value is greater than the value that you specify, ISIS eliminates any fitted 3D structure for which the calculated RMS value is greater than the search cutoff.

Note: To specify a search cutoff for RMS deviation, your query can contain solely the following 3D components: atoms, ring centroids, distances, and angles defined by three points.

For more information on RMS deviation, see CFS Searching Concepts/Examples.


To specify a search cutoff for RMS deviation

This procedure assumes that the CFS Options dialog box is displayed.

1.	Enter a value in the box that corresponds to the search cutoff for RMS deviation:

2.	To specify the derivative fitter, click [image] Derivative.

3.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To specify a search cutoff for RMS deviation

This procedure assumes that the CFS Options dialog box is displayed.

1.	Enter a value in the box that corresponds to the search cutoff for RMS deviation:

2.	To specify the derivative fitter, click [image] Derivative.


Specifying a Search Cutoff for both RMS Deviation and TDF

Click here for step-by-step instructions

Torsional degrees of freedom (TDF) is the number of rotatable bonds in the region of the 3D structure that matches your query. The higher the TDF, the more flexible is the molecule in the region that matches the query. Use a TDF cutoff to eliminate highly flexible structures and to increase search speed.

RMS deviation (RMS). RMS deviation measures how closely a fitted 3D structure matches the query. The lower the RMS deviation, the better the fitted 3D structure matches the query. Use an RMS cutoff to eliminate structures that fit the query poorly.

Note: To specify a search cutoff for RMS deviation, your query can contain solely the following 3D components: atoms, ring centroids, distances, and angles defined by three points.

For more information on search cutoffs for TDF and RMS deviation, see CFS Searching Concepts/Examples.


To specify a search cutoff for both RMS deviation and TDF

This procedure assumes that the CFS Options dialog box is displayed.

1.	Enter values into the boxes that correspond to the TDF and RMS deviation search cutoffs:

2.	To specify the derivative fitter, click [image] Derivative.

3.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To specify a search cutoff for both RMS deviation and TDF

This procedure assumes that the CFS Options dialog box is displayed.

1.	Enter values into the boxes that correspond to the TDF and RMS deviation search cutoffs:

2.	To specify the derivative fitter, click [image] Derivative.


Changing Other CFS Options

Steps 2 and 6 of this procedure contain instructions for changing the CFS options that are required for sorting and search cutoffs. If you are not sure how to use the other CFS options, we strongly recommend that you not change any other CFS options. The CFS options subtly interact with each other and can produce undesirable results if improperly used. In most cases, the default values of the other CFS options provide the best balance between accuracy and search speed for the initial CFS search.

After you have more experience with CFS searching, you might want to experiment with the other CFS options. To learn how to make meaningful choices, study CFS Searching Concepts/Examples.


Executing the Bump Checking CFS Search

Click here for step-by-step instructions

Bump checking eliminates fitted 3D structures with unfavorable nonbonded interactions (that is, structures that contain atoms that bump into one another). The bump-checking CFS search checks all fitted structures that you obtain from the initial CFS search. You must execute the bump-checking CFS search when you want to:

*	Specify a search cutoff for van der Waals energy difference.

*	Sort your search results by van der Waals energy difference.

Also, we strongly recommend that you execute the bump-checking CFS search when you want to export fitted 3D structures to a CFS SDfile for use in a modeling software program.

For more information on bump checking, see CFS Searching Concepts/Examples.


To execute the bump-checking CFS search

This procedure assumes that the current list is a list of search results from a CFS search.

1.	Choose Search > Set Search Domain > Current. This sets the search domain to the results of the initial CFS search.

2.	(Optional) Choose automatic sorting.

3.	Click the Query mode (if not highlighted).

4.	Click the box that contains the query (if not selected).

5.	Choose Search > CFS.

6.	To perform bump checking during the search, you require these settings:

Bump Checking at: View Time [image] Search Time

Caution: Make no other changes in CFS options dialog box, with the possible exception of the options in Steps 7 and 8 below.

7.	(Optional) To perform global relaxation during bump checking, you require this setting:

Global relaxation

8.	(Optional) To specify a search cutoff for van der Waals energy difference, enter a value in the box that corresponds to that search cutoff:

9.	Click OK.

See also:

To abandon the search


What Is a Search Cutoff for van der Waals Energy Difference?

Van der Waals energy difference (vdW) is the difference in nonbonded (van der Waals) interaction energy between the fitted conformation and the conformation that is stored in the database. When you specify a search cutoff for vdW, ISIS eliminates any fitted 3D structure for which the calculated vdW is greater than the vdW that you specify.

Notes: (1) Calculations for van der Waals energy difference are meaningful solely when bump checking is active and hydrogens are sprouted at all sites. Therefore, you can specify this cutoff in the bump-checking CFS search. (2) If you specified search cutoffs for torsional degrees of freedom (TDF), RMS deviation, or both in the initial CFS search, use them in the bump-checking CFS search also.

For more information on  van der Waals energy difference, see CFS Searching Concepts/Examples.


To sprout hydrogens and lone pairs for the initial CFS search

3D structures in a molecule database generally do not contain explicit hydrogen atoms and lone-pair electrons. For the initial CFS search, you want to sprout hydrogens solely at sites where hydrogens and lone pairs appear on the query. This produces faster search speeds.

Note: If the 3D structures in your database already contain explicit hydrogens and lone pairs, sprouting hydrogens and lone pairs does not affect your search results.

1.	Choose Options > Settings > Session.

2.	Click the Search tab (if not selected).

3.	Click the Sprout hydrogens and lone pairs box and choose Query Atoms Only.

4.	Click OK.


To sprout hydrogens for bump checking

When you perform bump checking, you want to sprout hydrogens at all sites that can have hydrogen (If your query contains lone pairs, ISIS also sprouts lone pairs at the corresponding sites on structures that you retrieve.). Sprouting all hydrogens provides a more realistic representation of the 3D structure and helps eliminate unrealistic conformations.

1.	Click Options > Settings > Session.

2.	Click the Search tab (if not selected).

3.	Click the Sprout hydrogens and lone pairs box and choose All.

4.	Click OK.


To sprout hydrogens and lone pairs at all sites

3D structures in a molecule database generally do not contain explicit hydrogen atoms and lone-pair electrons. Consequently, if you want to export 3D structures from your CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search to a modeling software program that cannot sprout hydrogens, you must sprout hydrogen atoms on the 3D structures. Hydrogens appear at all sites on the structures that can have hydrogens.

Notes: (1) If your query contains lone pairs, ISIS also sprouts lone pairs at the corresponding sites on structures that you retrieve. (2) If your database already contains structures with explicit hydrogen atoms, ISIS does not change these structures.

1.	Click Options > Settings > Session.

2.	Click the Search tab (if not selected).

3.	Click the Sprout hydrogens and lone pairs box and choose All.

4.	Click OK.


To sprout hydrogens and lone pairs on query atoms

3D structures in a molecule database generally do not contain explicit hydrogen atoms and lone-pair electrons. When you view the structures the you retrieve from a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search, you can sprout hydrogen atoms and lone pairs at atoms where they are explicitly shown on the query.

Note: If your database already contains structures with explicit hydrogen atoms, ISIS does not change these structures.

1.	Click Options > Settings > Session.

2.	Click the Search tab (if not selected).

3.	Click the Sprout hydrogens and lone pairs box and choose Query.

4.	Click OK.


Changing Fixed-Atom Tolerances

Click here for step-by-step instructions

If your query contains a submodel, you need to specify fixed-atom tolerances. Your ISIS administrator provides default fixed-atom tolerances that your site uses for registering 3D structures to molecule databases. You might want to change these tolerance values for searching. For example, you might want to increase the tolerances so that your query retrieves more 3D structures.

If you are not sure whether to change fixed-atom tolerances, we recommend that you not change fixed-atom tolerances.


To restore default fixed-atom tolerances

Your ISIS administrator sets default fixed-atom tolerances that your site uses for registering 3D structures to molecule databases. The ISIS/Base Session Settings file that your ISIS Administrator provides you specifies these tolerances. If you change fixed-atom tolerances for searching, you must restore the default tolerances before you register 3D structures.

Use the following procedure to restore the ISIS/Base Settings file that contains the default fixed-atom tolerances:

1.	Choose Options > Settings > Session.

2.	Click Read.

3.	Navigate to where the file that contains the general settings file is located on your disk, and click the name of the settings file in the Files list box.

4.	Click OK (Mac=Open).

5.	Click OK.


To change fixed-atom tolerances

1.	Choose Options > Settings > Session.

2.	Click the Search tab (if not already selected).

3.	Do one of the following:

*	To specify maximum atomic displacement only, you require the following settings:

Max. atomic displacement

Max. RMS deviation

*	To specify maximum RMS deviation only, you require the following settings:

Max. atomic displacement

Max. RMS deviation

*	To specify both fixed-atom tolerances, you require the following settings:

Max. atomic displacement

Max. RMS deviation

4.	Enter value(s) into the corresponding box(es) for the fixed-atom tolerance(s) that you specified in Step 4.

5.	Click OK.

See also:

To restore default fixed-atom tolerances


To conduct a remote SBF search for 3D structure records

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search.

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, or print.


To execute the search

1.	(Optional) Choose automatic sorting.

2.	Click the Query mode (if not selected).

3.	Choose Search > By Form.

See also:

To abandon the search


Transfer to ISIS/Base

Note: If you are in ISIS/Draw and do not see the icon pictured above, do the following: Switch to ISIS/Base and open a database. Click the Query button, then click the appropriate structure box or column on the form.


To conduct a remote SSS/Poly search for molecules

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote SSS/Poly search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > SSS.

See also:

To abandon the search


To conduct a remote POLY/Exact search for molecules

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote POLY/Exact search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Polymer.

5.	Click [image] Find this exact polymer (if not selected).

6.	(Optional) To specify that the attached data in the molecules that you retrieve must match the attached data in your query exactly, set [image] Attached data must match.

7.	(Optional) To specify that the polymer end groups in the molecules that you retrieve must match the polymer end groups in your query exactly, set [image] End groups must match.

8.	Click OK.

See also:

To abandon the search


To conduct a remote POLY/Both search for molecules

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote POLY/Both search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Polymer.

5.	Click [image] Find the monomer or SRU representation of this polymer (if not selected).

6.	(Optional) To specify that the attached data in the molecules that you retrieve must match the attached data in your query exactly, set [image] Attached data must match.

7.	(Optional) To specify that the polymer end groups in the molecules that you retrieve must match the polymer end groups in your query exactly, set [image] End groups must match.

8.	Click OK.

See also:

To abandon the search


To conduct a remote POLY/Co search for molecules

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote POLY/Co search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Polymer.

5.	Click [image] Find all copolymers that contain this monomer or SRU (if not selected).

6.	(Optional) To specify that the attached data in the molecules that you retrieve must match the attached data in your query exactly, set [image] Attached data must match.

7.	(Optional) To specify that the polymer end groups in the molecules that you retrieve must match the polymer end groups in your query exactly, set [image] End groups must match.

8.	Click OK.

See also:

To abandon the search


To conduct a remote POLY/Sub search for molecules

Searching Concepts/Examples

Do these steps in the order shown:

1.	Define a search domain.

2.	Obtain a suitable form that contains boxes or tables that are linked to the database fields that you want to search.

3.	Obtain a query.

4.	Execute the search (includes automatic sorting).

5.	View the search results.

6.	(Optional) Search results: Sort, save, manipulate, print, or export.

7.	(Optional) Query: Save, revise, print, or export.


To execute the remote POLY/Sub search

1.	(Optional) Choose automatic sorting.

2.	Click Query (if not highlighted).

3.	Click the box that contains the query (if not selected).

4.	Choose Search > Polymer.

5.	Click [image] Find all polymers that contain this polymer substructure (if not selected).

6.	Click OK.

See also:

To abandon the search


ISIS/Desktop 2.3 Help -- Table of Contents

This help file contains information on how to use the unmodified versions of ISIS/Draw 2.3 and ISIS/Base 2.3.

 How To Use ISIS/Desktop Help

 Using ISIS/Draw

 Using ISIS/Base

 ISIS Licensing/Documentation

 Customer Support

Note: We assume that you understand basic concepts for your system, such as how to move and scroll windows, select objects, and choose menu commands.


Unmodified ISIS

If you have modified ISIS/Draw or ISIS/Base, some of the information in this help file will not be accurate. Such modifications include:

*	Installing some ISIS Add-ins (with the Add-in Manager)

*	Installing some ISIS applications

*	Opening the ACD or Metabolite databases

*	Customizing ISIS/Draw or ISIS/Base (with ISIS/ADK)

See your ISIS Administrator if you do not know which (if any) Add-ins or applications are installed, or which databases are open.

For help on ISIS Add-ins, applications, or databases, choose the appropriate command from the Help menu.


MDL Help Files: Overview

 Help for ISIS/Desktop, Applications, and Add-ins

 Help for MDL Databases


 Help for ISIS/Desktop, Applications, and Add-ins

ISIS/Draw and ISIS/Base ("ISIS/Desktop") share one help file and a common Index. You can access their Tables of Contents and their Index directly from the Help menu.

Note: The Index shown on the Help menu is the Index for ISIS/Draw and ISIS/Base only.

ISIS applications and Add-ins have their own separate help files with separate help Indexes. To obtain help for these products, choose the name (for example, ISIS/Base Add-ins) on the Help menu. You see the Table of Contents specific to that product.

To access the Index specific to that product, click Search.


 Help for MDL Databases

MDL has two types of database documentation that are available online-only.

*	The databases are described in Portable Document Format (PDF) for online viewing and printing. Use Adobe Acrobat Reader to read and print the books. Adobe Acrobat Reader is included in the Document folder of the ISIS installation CD. You can also download it for free from Adobe’s web site at http://www.adobe.com.

*	The database applications, and how to use them, are described in online help. You access the online help for database applications from the ISIS/Base Help menu. For example, if you use the Metabolite database applications, Metabolite Browser and Metabolite Registrar, you see Metabolite Registrar and Metabolite Browser on the Help menu. Choose the name to access the help file for that application. To access the index specific to Metabolite Browser or Metabolite Registrar, click Search in the Help window.

Note: The Index (Draw + Base only) item shown on the Help menu is for ISIS/Draw and ISIS/Base only.

See also:

Information on MDL Databases


 Using ISIS/Base

 SEARCHING with ISIS/Base

 Creating and Editing FORMS

 Database Creation & Registration

 Information on MDL Databases

Tools, Menus, Settings (Program Defaults)


 Searching with ISIS/Base

New MDL Customers:

(Click this item.)

How to Choose the Best Type of Search -- and How to Do It

Experienced MACCS-II, REACCS, CPSS Users:

(Click these items in the order shown.)

1.	Differences Between ISIS and Other MDL Products

2.	How to Choose the Best Type of Search -- and How to Do It

Existing ISIS 1.1/1.2 Users:

What is new in searching in ISIS/Base?

The ISIS/Base Chemical Searches-- and How to Do Them


The ISIS/Base Chemical Searches -- and How to Do Them
The ISIS/Base Search Types

The ISIS/Base Chemical Searches -- and How to Do Them

New users: If you do not know exactly which search you need, see How To Choose the Best Type of Search -- and How to Do It.

Molecule Record (Remote Searches):

ALL    FLEX    FMLA    ID    ISOMER    MEXACT    MSim    PARENT    QB    POLY/Exact    POLY/Both    POLY/Co    POLY/Sub    RGROUP    SBF    SSS    SSS/Biopoly    SSS/Poly    TAUT

Molecule Record (Local Searches):

ALL    FMLA    ID    MEXACT    QB    SBF    SSS    SSS/Biopoly

Reaction Records (Remote Searches):

ALL    FLEX    FMLA    ID    ISOMER    MEXACT    MSim    PARENT    QB    RELATED    REXACT/Comp    REXACT/Rxn    RGROUP    RSim    RSS/Comp    RSS/Rxn    SBF    SSS    TAUT

Reaction Records (Local Searches):

ALL    FMLA    ID    MEXACT    QB    RELATED    REXACT/Rxn    RSS/Comp    RSS/Rxn    SBF    SSS

3D Structure Records (Remote Searches):

3DEXACT    ALL    CFS    CFS/Biopoly    ID    MSim    QB    SBF    SSS3D    SSS3D/Biopoly

3D Structure Records (Local Searches):

3DEXACT    ALL    ID    QB    SBF


Database Creation/Registration and Importing/Exporting Data
 Database Creation/Registration, Importing/Exporting Data

Information on:

*	Creating local databases

*	Registering and updating database records

*	Conventions for representing polymers, organometallics, and other structures

*	Importing and exporting database data

is available online in the ISIS/Base Database Maintenance 2.0 manual, in the PDF file Dbmaint.pdf. This PDF file is located in the Documents subdirectory within the ISIS directory (Mac=Documents folder).


What is an MEXACT Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Molecule Exact Match (MEXACT) search finds molecule records that match your structure query exactly. Your structure query is a two-dimensional representation of a molecule (a 2D structure). For example:


What is an MEXACT Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Molecule Exact Match (MEXACT) search finds molecule records that match your structure query exactly. Your structure query is a two-dimensional representation of a molecule (a 2D structure). For example:


What is an REXACT/Comp Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Reaction Exact Match for Reaction Components (REXACT/Comp) search finds reaction records that match your reaction component query exactly. Your reaction component query is a two-dimensional representation of a reaction component (a 2D structure with a reaction arrow). For example, a reactant query is as follows:


What is an MEXACT Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Molecule Exact Match (MEXACT) search finds reaction records that match your reaction component query exactly. Your reaction component query is a two-dimensional representation of a reaction component (a 2D structure without a reaction arrow). For example, a reactant query is as follows:


What is an MEXACT Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Molecule Exact Match (MEXACT) search finds reaction records that match your reaction component query exactly. Your reaction component query is a two-dimensional representation of a reaction component (a 2D structure without a reaction arrow). For example, a reactant query is as follows:


What is an REXACT/Rxn Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Reaction Exact Match for Reactions (REXACT/Rxn) search finds reaction records that match your reaction query exactly. Your reaction query is a reaction with two-dimensional representations of reactants and products (a 2D reaction structure). For example:


What is an REXACT/Rxn Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Reaction Exact Match for Reactions (REXACT/Rxn) search finds reaction records that match your reaction query exactly. Your reaction query is a reaction with two-dimensional representations of reactants and products (a 2D reaction structure). For example:


What is an SSS Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Molecule Substructure (SSS) search finds molecule records that contain your query as a substructure wholly within a larger structure. Your substructure query is a two-dimensional representation of a portion of a molecule (a 2D substructure). For example:

You can also increase the power of an SSS search by the addition of specific restrictions (called query features) on atoms and/or bonds. There are a number of query features available for use. Example


An Example of the Use of Query Features

In the following example, the ISIS atom-query feature (H0) prohibits the attachment of hydrogens on a specific atom in the records retrieved:

In addition, the hydrogens block substitutions at the specified positions.


What is an SSS Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Molecule Substructure (SSS) search finds molecule records that contain your query as a substructure wholly within a larger structure. Your substructure query is a two-dimensional representation of a portion of a molecule (a 2D substructure). For example:

You can also increase the power of an SSS search by the addition of specific restrictions (called query features) on atoms and/or bonds. There are a number of query features available for use. Example


What is an RGROUP Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

An Rgroup (RGROUP) search finds molecule records that contain your query as a substructure wholly within a larger structure with additional restrictions. For example, you can:

*	Specify the structural fragments (such as functional groups or atoms) of your choice at specific sites within a molecule.

*	Exclude structural fragments of your choice at specific sites within a molecule.

*	Specify that the presence of one structural fragment requires the presence of another (Rgroup conditions).

You can also increase the power of an RGROUP search by the addition of specific restrictions (called query features) on atoms and/or bonds. There are a number of query features available for use. Example


What is an SSS Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Molecule Substructure (SSS) search finds reaction records that contain your query as a substructure wholly within a larger reaction component. Your substructure query is a two-dimensional representation of a portion of a reaction component (a 2D substructure without a reaction arrow). For example, a product query is as follows:

You can also increase the power of an SSS search by the addition of specific restrictions (called query features) on atoms and/or bonds. There are a number of query features available for use. Example


An Example of the Use of Query Features

In the following example, the ISIS atom-query feature (H0) prohibits the attachment of hydrogens on a specific atom in the records retrieved:

In addition, the hydrogens block substitutions at the specified positions.


What is an SSS Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Molecule Substructure (SSS) search finds reaction records that contain your query as a substructure wholly within a larger reaction component. Your substructure query is a two-dimensional representation of a portion of a reaction component (a 2D substructure without a reaction arrow). For example, a product query is as follows:

You can also increase the power of an SSS search by the addition of specific restrictions (called query features) on atoms and/or bonds. There are a number of query features available for use. Example


What is an RSS/Rxn Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Reaction Substructure for Reactions (RSS/Rxn) search finds reaction records that contain your query as a reaction substructure wholly within a larger reaction. Your reaction substructure query is a two-dimensional representation of a portion of a reaction (a 2D reaction substructure). For example:

Your query can also contain query features on atoms and/or bonds and on the reaction. The reaction query feature CHANGE (/) specifies that the bond order in the reactant must change in the product at the specified position. The atom-atom maps (numbers) specify which atoms in the reactants correspond to the atoms in the products.


What is an RSS/Rxn Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Reaction Substructure for Reactions (RSS/Rxn) search finds reaction records that contain your query as a reaction substructure wholly within a larger reaction. Your reaction substructure query is a two-dimensional representation of a portion of a reaction (a 2D reaction substructure). For example:

Your query can also contain query features on atoms and/or bonds. For example, you can use the ISIS atom-query feature HO to prohibit the attachment of hydrogens on a specific atom in the records retrieved.


What is an RSS/Comp Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Reaction Substructure for Reaction Components (RSS/Comp) search finds reaction records that contain your query as a substructure (with a reaction arrow) wholly within a larger reactant or product. Your reaction component substructure query is a two-dimensional representation of a portion of a reactant or a product (a 2D reaction component substructure). For example, a reactant substructure query is as follows:

Note


Note

The reaction query feature CHANGE (/) specifies that the bond order in the reactant must change in the product at the specified position.


What is an RSS/Comp Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Reaction Substructure for Reaction Components (RSS/Comp) search finds reaction records that contain your query as a substructure (with a reaction arrow) wholly within a larger reactant or product. Your reaction component substructure query is a two-dimensional representation of a portion of a reactant or a product (a 2D reaction component substructure). For example, a reactant substructure query is as follows:


What is an SBF Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Search By Form (SBF) search finds molecule records that contain your text/numeric query exactly as you specify it or your graphical query as a substructure wholly within a larger structure.

In addition, you can combine text/numeric and graphical queries. For example, you can specify the text/numeric query > 350 molecular weight AND the graphical substructure query benzene.


What is an SBF Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Search By Form (SBF) search finds molecule records that contain your text/numeric query exactly as you specify it or your graphical query as a substructure wholly within a larger structure.

In addition, you can combine text/numeric and graphical queries. For example, you can specify the text/numeric query > 350 molecular weight AND the graphical substructure query benzene.


What is an SBF Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Search By Form (SBF) search finds reaction records that contain your text/numeric query exactly as you specify it or your graphical query as a substructure (or a reaction substructure) wholly within a larger structure (or a reaction).

In addition, you can combine text/numeric and graphical queries. For example, you can specify in a single search both the text/numeric query > 80% yield AND the graphical product substructure query oxirane.


What is an SBF Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Search By Form (SBF) search finds reaction records that contain your text/numeric query exactly as you specify it or your graphical query as a substructure (or a reaction substructure) wholly within a larger structure (or a reaction).

In addition, you can combine text/numeric and graphical queries. For example, you can specify in a single search both the text/numeric query > 80% yield AND the graphical product substructure query oxirane.


What is an RSim Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Reaction Similarity (RSim) search finds reaction records that are similar to your query. You can define both the type and degree of similarity in your query. The type of similarity can be:

a)	Structural -- physical resemblance to the substrate molecules in your query

b)	Transformational -- similar reacting centers

The degree of similarity can be an arbitrary value between 0 and 100 (these are not actual units). The higher the value, the more similarity.


What is an MSim Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Molecule Similarity (MSim) search finds molecules that are structurally similar to your query. You can define the degree of similarity in your query to be an arbitrary value between 0 and 100 (these are not actual units). The higher the value, the more similarity. For example:

3D Database Users: An MSim search uses solely the 2D information on a molecule, such as atom types, bond types, and connectivity.


What is an FLEX Search?
What is a FLEX Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Flexmatch (FLEX) search finds records that are an exact match of your query, except in the ways that you specify. Use FLEX to find structures that match your query, but might be represented differently in the database. For example:

You can also use FLEX to find structures that contain different counterions than the salt in your query, or that match your query, but have different isotopic labels.


What is a TAUT Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Tautomer (TAUT) search finds molecule records that are tautomers of your structure query. For example:


What is an ISOMER Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

An Isomer (ISOMER) search finds molecule records that are geometric stereoisomers or optical stereoisomers of your query. For example:


What is a PARENT Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Parent (PARENT) search finds molecule records that are the parent molecules of your salt query. For example:


What is an MSim Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Molecule Similarity (MSim) search finds reaction records that are structurally similar to your query. You can define the degree of similarity in your query to be an arbitrary value between 0 and 100 (these are not actual units). The higher the value, the more similarity. For example, a reactant query:


What is an FLEX Search?
What is a FLEX Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Flexmatch (FLEX) search finds records that are an exact match of your query, except in the ways that you specify. Use FLEX to find structures that match your query, but might be represented differently in the database. For example:

You can also use FLEX to find structures that contain different counterions than the salt in your query, or that match your query, but have different isotopic labels.


What is a TAUT Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Tautomer (TAUT) search finds reaction records that contain reaction components that are tautomers of your structure query. For example, a reactant query:


What is an ISOMER Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

An Isomer (ISOMER) search finds reaction records with reaction components that are geometric isomers or stereoisomers of your query. For example, a reactant query:


What is a PARENT Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Parent (PARENT) search finds reaction records with reaction components that are the parent molecules of your salt query. For example, a salt query that is a reactant:


What is an RGROUP Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

An Rgroup (RGROUP) search finds reaction records that contain your query as a substructure wholly within a larger structure with additional restrictions. For example, you can:

*	Specify the structural fragments (such as functional groups or atoms) of your choice at specific sites within a reaction component.

*	Exclude structural fragments of your choice at specific sites within a reaction component.

*	Specify that the presence of one structural fragment requires the presence of another (Rgroup conditions).

You can also increase the power of an RGROUP search by the addition of specific restrictions (called query features) on atoms and/or bonds. There are a number of query features available for use. Example


What is a QB Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

You can use the Query Builder (QB) search to create any of the other searches in ISIS. However, you must use an all-text search query.

Thus, we recommend that you use another search where possible!

This search does have one unique feature: You can combine AND, OR and NOT boolean operators in a search query.


What is a QB Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

You can use the Query Builder (QB) search to create any of the other searches in ISIS. However, you must use an all-text search query.

Thus, we recommend that you use another search where possible!

This search does have one unique feature: You can combine AND, OR and NOT boolean operators in a search query.


What is a QB Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

You can use the Query Builder (QB) search to create any of the other searches in ISIS. However, you must use an all-text search query.

Thus, we recommend that you use another search where possible!

This search does have one unique feature: You can combine AND, OR and NOT boolean operators in a search query.


What is a QB Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

You can use the Query Builder (QB) search to create any of the other searches in ISIS. However, you must use an all-text search query.

Thus, we recommend that you use another search where possible!

This search does have one unique feature: You can combine AND, OR and NOT boolean operators in a search query.


What is a QB Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

You can use the Query Builder (QB) search to create any of the other searches in ISIS. However, you must use an all-text search query.

Thus, we recommend that you use another search where possible!

This search does have one unique feature: You can combine AND, OR and NOT boolean operators in a search query.


What is a QB Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

You can use the Query Builder (QB) search to create any of the other searches in ISIS. However, you must use an all-text search query.

Thus, we recommend that you use another search where possible!

This search does have one unique feature: You can combine AND, OR and NOT boolean operators in a search query.


What is an ALL Search?

Click here for step-by-step instructions

An ALL search finds every record in the database. You do not use a query for this search.


What is an ID Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

An ID search finds the records that contain the corporate identification numbers that you specify in your query. To do this type of search, you need:

*	An ID field in your database. This is a field in the database that contains corporate identification numbers for the records in your database.

*	A box or table in a form that is linked to the ID field. A form is the set of boxes and/or tables that you use to hold your query and to view the results of a search.

If you do not have these items, see your ISIS Administrator.


What is an FMLA Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Formula (FMLA) search finds molecule records that contain the formula that you specify in your query. Your formula query can be:

*	An exact formula and no other atoms, such as C17 H19 N O3

*	A subformula and any additional atoms, such as C5 H10

*	A subformula and any additional atoms except a specific atom, such as C5 H10 N0, where N0 represents zero nitrogens.

Note1: If you enter a single atom within your query but you do not include spaces, you must also enter a value of 1 for the single atom. For example:  and [image] are equivalent.

Note2: To specify more than one formula in a single query, or to combine a formula search with a search for other data, use Search By Form (SBF).


What is an FMLA Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Formula (FMLA) search finds molecule records that contain the formula that you specify in your query. Your formula query can be:

*	An exact formula and no other atoms, such as C17 H19 N O3, or

*	A subformula and any additional atoms, such as C5 H10, or

*	A subformula and any additional atoms except a specific atom, such as C5 H10 N0, where N0 represents zero nitrogens.

Note1: If you enter a single atom within your query but you do not include spaces, you must also enter a value of 1 for the single atom. For example:  and [image] are equivalent.

Note2: To specify more than one formula in a single query, or to combine a formula search with a search for other data, use Search By Form (SBF).


What is an FMLA Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Formula (FMLA) search finds reaction records with a specific reaction component that contains the formula that you specify in your query. Your formula query can be:

*	An exact formula and no other atoms, such as C17 H19 N O3, or

*	A subformula and any additional atoms, such as C5 H10, or

*	A subformula and any additional atoms except a specific atom, such as C5 H10 N0, where N0 represents zero nitrogens.

Note1: If you enter a single atom within your query but you do not include spaces, you must also enter a value of 1 for the single atom. For example:  and [image] are equivalent.

Note2: To specify more than one formula in a single query, or to combine a formula search with a search for other data, use Search By Form (SBF).


What is an FMLA Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Formula (FMLA) search finds reaction records with a specific reaction component that contains the formula that you specify in your query. Your formula query can be:

*	An exact formula and no other atoms, such as C17 H19 N O3, or

*	A subformula and any additional atoms, such as C5 H10, or

*	A subformula and any additional atoms except a specific atom, such as C5 H10 N0, where N0 represents zero nitrogens.

Note1: If you enter a single atom within your query but you do not include spaces, you must also enter a value of 1 for the single atom. For example:  and [image] are equivalent.

Note2: To specify more than one formula in a single query, or to combine a formula search with a search for other data, use Search By Form (SBF).


What is an ID Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

An ID search finds the records that contain the corporate identification numbers that you specify in your query. To do this type of search, you need:

*	An ID field in your database. This is a field in the database that contains corporate identification numbers for the records in your database.

*	A box or table in a form that is linked to the ID field. A form is the set of boxes and/or tables that you use to hold your query and to view the results of a search.

If you do not have these items, see your ISIS Administrator.


What is an ID Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

An ID search finds the records that contain the corporate identification numbers that you specify in your query. To do this type of search, you need:

*	An ID field in your database. This is a field in the database that contains corporate identification numbers for the records in your database.

*	A box or table in a form that is linked to the ID field. A form is the set of boxes and/or tables that you use to hold your query and to view the results of a search.

If you do not have these items, see your ISIS Administrator.


What is an ALL Search?

Click here for step-by-step instructions

An ALL search finds every record in the database. You do not use a query for this search.


What is an ID Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

An ID search finds the records that contain the corporate identification numbers that you specify in your query. To do this type of search, you need:

*	An ID field in your database. This is a field in the database that contains corporate identification numbers for the records in your database.

*	A box or table in a form that is linked to the ID field. A form is the set of boxes and/or tables that you use to hold your query and to view the results of a search.

If you do not have these items, see your ISIS Administrator.


What is an ID Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

An ID search finds the records that contain the corporate identification numbers that you specify in your query. To do this type of search, you need:

*	An ID field in your database. This is a field in the database that contains corporate identification numbers for the records in your database.

*	A box or table in a form that is linked to the ID field. A form is the set of boxes and/or tables that you use to hold your query and to view the results of a search.

If you do not have these items, see your ISIS Administrator.


What is an ID Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

An ID search finds the records that contain the corporate identification numbers that you specify in your query. To do this type of search, you need:

*	An ID field in your database. This is a field in the database that contains corporate identification numbers for the records in your database.

*	A box or table in a form that is linked to the ID field. A form is the set of boxes and/or tables that you use to hold your query and to view the results of a search.

If you do not have these items, see your ISIS Administrator.


What is an SSS/Biopoly Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Biopolymer Substructure (SSS/Biopoly) search finds biopolymer records that contain your query as a fragment (a set of residues of your choice) wholly within a larger, rigid biopolymer. The matching residues might be anywhere within the biopolymer.


What is an SSS/Biopoly Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Biopolymer Substructure (SSS/Biopoly) search finds biopolymer records that contain your query as a fragment (a set of residues of your choice) wholly within a larger, rigid biopolymer. The matching residues might be anywhere within the biopolymer.


What is a CFS/Biopoly Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Conformationally Flexible Substructure (CFS/Biopoly) search finds 3D structures that contain your query as a fragment (a set of residues of your choice) wholly within a larger, unrigid biopolymer.

A CFS search attempts to fit residues to the query by rotating their single bonds. Consequently, the 3D structures that you obtain from a CFS search are not necessarily in the same conformations as the 3D structures in the database.


What is an SSS3D/Biopoly Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A 3D Substructure for Biopolymers (SSS3D/Biopoly) search finds biopolymers that contain your query as a sub-sequence wholly within a larger sequence. (Conduct an SSS3D/Biopoly search rather than an SSS/Biopoly search if you need to specify 3D geometric or 3D data constraints in your query.)

An SSS3D/Biopoly search retrieves solely biopolymers that are stored in the database and does not change the conformations of the biopolymers that you retrieve.

In contrast, a CFS/Biopoly search derives additional conformations by rotating single bonds within the residues of biopolymers that you retrieve. Consequently, CFS/Biopoly can find structures that SSS3D might miss. Use SSS3D/Biopoly when fast search speed is more important than retrieving all possible structures or you want to find biopolymers that are rigid in the region that matches your query.


What is an SBF Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Search By Form (SBF) search finds molecule records that contain your graphical query as a substructure wholly within a larger structure or your text/numeric query exactly as you specify it.

In addition, you can combine graphical and text/numeric queries. Do this by using the boolean algebraic operator AND to conduct a single search with this multiple-component query. For example, you can specify a graphical substructure query AND the text/numeric query < 100 molecular weight.


What is an ALL Search?

Click here for step-by-step instructions

An ALL search finds every record in the database. You do not use a query for this search.


What is an ALL Search?

Click here for step-by-step instructions

An ALL search finds every record in the database. You do not use a query for this search.


What is an ALL Search?

Click here for step-by-step instructions

An ALL search finds every record in the database. You do not use a query for this search.


What is an ALL Search?

Click here for step-by-step instructions

An ALL search finds every record in the database. You do not use a query for this search.


What is a Remote Exact Match Search for 3D Structures?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

An Exact 3D Search (3DEXACT) retrieves 3D structures that are duplicates of your 3D search query. The atoms in a duplicate 3D structure have the same 3D coordinates within allowed deviations. Two fixed-atom tolerances specify the allowed deviations:

*	Maximum atomic displacement specifies the allowed deviation (in Angstroms) of individual atoms in a 3D structure from the atoms in the query.

*	Maximum RMS deviation specifies allowed root-mean-square (RMS) deviation of all the atoms in a 3D structure from the atoms in the query.

Caution: Your ISIS Administrator establishes default fixed-atom tolerances for 3D structure registration. If you change the default fixed-atom tolerances for searching, you must restore the default values before you register 3D structures.


What is a Local Exact Match Search for 3D Structures?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

An Exact 3D Search (3DEXACT) retrieves 3D structures that exactly match your 3D search query.

Note: A 3DEXACT search in a local database uses solely information on the number, type, and connectivity of atoms in a molecule (2D information), and ignores the spatial arrangement of atoms.


What is an SSS3D Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A 3D Substructure (SSS3D) search finds 3D structures that contain your query as a substructure wholly within a larger structure. An SSS3D search:

*	Retrieves solely 3D structures that are stored in the database.

*	Does not change the conformations of the 3D structures that you retrieve.

In contrast, a CFS search derives additional conformations by rotating single bonds in the structures that you retrieve. Consequently, CFS can find structures that SSS3D might miss. Use SSS3D when:

*	Fast search speed is more important than retrieving all possible structures. For example, if you conduct a series of searches to refine your query, you might want to use SSS3D in the early stages of query refinement.

*	You want to find 3D structures that are rigid in the region that matches your query.


What is a CFS Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Conformationally Flexible Substructure (CFS) search finds 3D structures that contain your query as a substructure wholly within a larger structure. A CFS search attempts to fit 3D structures to the query by rotating single bonds. Consequently, the 3D structures that you obtain from a CFS search are not necessarily in the same conformations as the 3D structures in the database. For example:

Note: CFS searches can require a long time. If fast search speed is more important than finding all possible 3D structures that fit the query, use an SSS3D search.


What is an SBF Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Search By Form (SBF) search finds 3D structure records that contain your graphical query as a substructure wholly within a larger structure or your text/numeric query exactly as you specify it.

In addition, you can combine graphical and text/numeric queries. Do this by using the boolean algebraic operator AND to conduct a single search with this multiple-component query. For example, you can specify a graphical substructure query AND the text/numeric query < 100 molecular weight.


What is an SSS/Poly Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Substructure Search for Polymers (SSS/Poly) search finds molecule records that contain your polymer query as a substructure wholly within another molecule:

You can also increase the power of an SSS/Poly search by the addition of specific restrictions (called query features) on atoms, bonds, and/or brackets. There are a number of query features available for use. Example


An Example of the Use of Query Features

In the following example, the ISIS bond query feature S/D finds both single and double bonds. In addition, the anypolymer (anyp) polymer brackets specify the retrieval of any polymer type (mon, SRU, co, or mer) that contains the substructure:


What is a POLY/Exact Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Exact Polymer (POLY/Exact) search finds molecule records that match your polymer query exactly and that also match any text/numeric search criteria on your form. For example:


What is a POLY/Both Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Polymer Search for Both Structure- and Source-Based Polymer Structures (POLY/Both) finds molecules that match both source-based and structure-based representations of your polymer query and that also match any text/numeric search criteria on your form. For example:


What is a POLY/Co Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Polymer Search for Copolymers (POLY/Co) search finds molecule records that are copolymers of your polymer query, and that also match any text/numeric search criteria on your form. For example:


What is a POLY/Sub Search?

Click: Step-by-Step Instructions

          Searching Concepts/Examples

A Polymer Substructure (POLY/Sub) search finds molecule records that contain your polymer query as a substructure wholly within another molecule and that also match any text/numeric search criteria on your form. For example:

You can increase the power of a POLY/Sub search by adding specific restrictions (called query features) to atoms and bonds. Example


I Want to Search a Remote Molecule Database

For a remote molecule database, there are 13 possible searches that you can conduct.

Click any item to see a definition of that search:

*	Retrieve All

*	ID

*	Search By Form (SBF)

*	Query Builder (QB)

*	3D Structure Exact (3DEXACT)

*	Conformationally Flexible Substructure (CFS)

*	Static 3D Substructure Search (SSS3D)


I Want to Search a Local Molecule Database

For a local molecule database, there are 5 possible searches that you can conduct.

Click any item to see a definition of that search:

*	Retrieve All

*	ID

*	Search By Form (SBF)

*	Query Builder (QB)

*	3D Structure Exact (3DEXACT)


Request-A-Documents available in the ISIS/Desktop 2.3 Helps

You can view Request-A-Documents online, however we recommend that you print them out. To do so, click the Printer icon at the top of the Request-A-Document screen.

Click any of the following items:

Differences Between ISIS and Other MDL Products

How to use ISIS/Desktop Help

Calculated Fields

Printing All the Data, and Only the Data, that you Want

Sorting

Forms

Drawing Sketch Tables

ISIS/Draw "Quick Start"

Predefined Abbreviated Structures Available Via the Keyboard

Drawing Polymers: MDL Requirements for Database Searching and Registration

Drawing Mixtures: MDL Requirements for Database Searching and Registration

Searching: To see a Request-A-Document on a specific ISIS/Base search, click The ISIS/Base Search Types, then click the search of your choice, and then click Searching Concepts/Examples.


Sorting: Concepts/Examples

Click any of the following items:

3D Structures: Sorting Examples

Local Databases: Sorting Examples

Molecules: Sorting Examples

Reaction Components: Sorting Examples

Reactions: Sorting Examples


Forms: Concepts/Examples

Click any of the following items:

Determine the type of form that you need

Determine the type of table that you need

Box Creation Exercise

Table Creation Exercise


Substructure Search

Click any item to see a definition of that search:

*	Local SSS search for molecules

*	Remote SSS search for molecules

*	Local SSS search for reaction components

*	Remote SSS search for reaction components


Tracking Changes for ISIS 2.2.1 Release

Dave Krause

March 2, 1999

Nicki Davis and I made the following changes for the ISIS 2.2.1 release.  This is the first release for which we used the Documentation Building Block (DBB) methodology.  This page tracks the changes that we made.

1.	The major change is that we included the Functional Groups information, which was developed for Reagent Selector 1.0.  The Functional Groups information is taken from the DBB Fxgrp.doc and modified for ISIS.  For example, the words “reagent core” were replaced by “query”, and “Reagent Selector” was replaced by “ISIS”, in all occurrences.

2.	The Functional Groups RAD was assigned the number 150, and this number was used in all topic headings.

3.	The bitmap images that contain the word “query”, rather than “reagent core”, were used. I created two new necessary bitmap images.  I created DKPCD005.bmp starting with NDRG004.bmp, and DKDRG003.bmp starting with NDRG003.bmp.

4.	Functional group index entries were changed to read “query” rather than “reagent core”.

5.	The Functional Groups information is included at the end of the file DRAW.doc, pages 706 – 746.

6.	Links were added to access this Functional Groups information.  Links were added in the help topics for the Edit Atom, Edit Bond, and Edit Query Atom dialog boxes, in the file DRAWCS.doc.

7.	Links from the DBB Fxgrp.doc material were adapted for ISIS.  For example, links were modified to point to the ISIS/Draw Quick Start RAD and to the Rgroups RAD and metaprocedure.

8.	Index entries were added for the Functional Groups material (“functional groups, queries for common”).  More index entries for Rgroup procedures were added (“Rgroup query features, drawing”).

9.	Because ISIS does not have filters, the information in the DBB Fxgrp.doc on filtering functional groups was blended with the material on drawing queries for each functional group, as appropriate.

10.	In Draw.doc, I cleaned up the Rgroup topics, making the same corrections as in the DBB Rgroup.doc.  Specifically, I changed “continue with Step 5” to “continue with Step 4” twice, and also the title of the topic to which you return is now “Specifying Rgroup Query Features”.  These edits are given as comments in Rgroup.doc.

Notes added by Nicki Davis, 3/5/1999:

I made minor corrections to the RAD "Queries for Common Compound Classes" in DRAW.DOC, as agreed by Dave and me. These corrections were reflected in the DBB from which it originated, FXGRP.DOC, and which were incorporated into the DBB on 3/3/1999. Therefore, the ISIS RAD reflects only corrections made to the DBB through 3/3/1999.


To obtain an MEXACT query

MEXACT queries contain a 2D structure (a molecule that is drawn without regard to its 3D spatial arrangement). You search for molecules that match your query exactly. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the MOLSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a 2D Structure or

Specifying Stereochemistry

Drawing Mixtures: MDL Requirements for Database Searching and Registration

3.	Transfer the query back to ISIS/Base.


Drawing a 2D Structure

A 2D structure is a molecule that is drawn without regard to its 3D spatial arrangement. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Drawing Mixtures: MDL Requirements for Database Searching and Registration

*	Verifying the Chemistry of Sketches


To import an existing query from a molfile

Use this procedure to import a structure query from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a structure query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a 2D Structure or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an MEXACT query

MEXACT queries contain a 2D structure (a molecule that is drawn without regard to its 3D spatial arrangement). You search for molecules that match your query exactly. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the MOLSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a 2D Structure or

Specifying Stereochemistry

3.	Transfer the query back to ISIS/Base.


Drawing a 2D Structure

A 2D structure is a molecule that is drawn without regard to its 3D spatial arrangement. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a molfile

Use this procedure to import a structure query from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a structure query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a 2D Structure or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an REXACT/Comp query

REXACT/Comp queries contain either one or more reactants with a reaction arrow or one or more products with a reaction arrow. Each reaction component is a 2D structure (a molecule that is drawn without regard to its 3D spatial arrangement). You search for reaction components that match your query exactly. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the RXNSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a rxnfile.

*	Restore a query that you previously saved as an object in the database.


Examples


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a Reaction Component Structure or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Component Structure

A reaction component structure is a 2D structure (molecule) from a reaction without regard to its 3D spatial arrangement. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a rxnfile

Use this procedure to import a reaction component query (with the reaction arrow) from a rxnfile that was created in CPSS, ISIS, or REACCS.

1.	Click Query (if not highlighted).

2.	Select the RXNSTRUCTURE box (if not highlighted).

3.	Choose File > Import > Rxnfile. (To retrieve a PC-rxnfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure or reaction is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

Use this procedure to restore a reaction component query (with the reaction arrow) from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the RXNSTRUCTURE box (if not highlighted).

3.	Choose Database > Restore Reaction.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected reaction component is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing reaction component (with a reaction arrow) that you see in a box or table cell in ISIS/Base.

1.	Select the RXNSTRUCTURE box that contains the structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Reaction Component Structure or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an MEXACT query

MEXACT queries contain a reaction component (without a reaction arrow). Each reaction component is a 2D structure (a molecule that is drawn without regard to its 3D spatial arrangement). You search for reaction components that match your query exactly. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the box or table cell on the form that will hold your MEXACT query. In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples

Examples of reactants:


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a Reaction Component Structure or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Component Structure

A reaction component structure is a 2D structure (molecule) from a reaction without regard to its 3D spatial arrangement. For example, a product:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a molfile

Use this procedure to import a reaction component query (without the reaction arrow) from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a reaction component query (without the reaction arrow) that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing reaction component (without a reaction arrow) that you see in a box or table cell in ISIS/Base.

1.	Select the box or table cell that contains the reaction component that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Reaction Component Structure or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an MEXACT query

MEXACT queries contain a reaction component (without a reaction arrow). Each reaction component is a 2D structure (a molecule that is drawn without regard to its 3D spatial arrangement). You search for reaction components that match your query exactly. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the box or table cell on the form that will hold your MEXACT query. In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples

Examples of reactants:


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a Reaction Component Structure or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Component Structure

A reaction component structure is a 2D structure (molecule) from a reaction without regard to its 3D spatial arrangement. For example, a product:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a molfile

Use this procedure to import a reaction component query (without the reaction arrow) from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a reaction component query (without the reaction arrow) that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing reaction component (without a reaction arrow) that you see in a box or table cell in ISIS/Base.

1.	Select the box or table cell that contains the reaction component that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Reaction Component Structure or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an REXACT/Rxn query

REXACT/Rxn queries contain an entire reaction. Each reaction component in the reaction is a 2D structure (a molecule that is drawn without regard to its 3D spatial arrangement). You search for reactions that match your query exactly. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the RXNSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a rxnfile.

*	Restore a query that you previously saved as an object in the database.


Examples

The following reaction is both the query and the reaction retrieved:


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a Reaction Structure or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Structure

A reaction structure is a transformation that contains 2D structures (molecules) as components without regard to their 3D spatial arrangement. For example, the following reaction is both the query and the reaction record retrieved:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a rxnfile

Use this procedure to import a reaction query from a rxnfile that was created in CPSS, ISIS, or REACCS.

1.	Click Query (if not highlighted).

2.	Select the RXNSTRUCTURE box (if not highlighted).

3.	Choose File > Import > Rxnfile. (To retrieve a PC-rxnfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure or reaction is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

Use this procedure to restore a reaction query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the RXNSTRUCTURE box (if not highlighted).

3.	Choose Database > Restore Reaction.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected reaction component is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing reaction that you see in a box or table cell in ISIS/Base.

1.	Select the RXNSTRUCTURE box that contains the reaction that you want to edit. An ISIS/Draw window opens that contains the reaction.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Reaction Structure or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an REXACT/Rxn query

REXACT/Rxn queries contain an entire reaction. Each reaction component in the reaction is a 2D structure (a molecule that is drawn without regard to its 3D spatial arrangement). You search for reactions that match your query exactly. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the RXNSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a rxnfile.

*	Restore a query that you previously saved as an object in the database.


Examples

The following reaction is both the query and the reaction retrieved:


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a Reaction Structure or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Structure

A reaction structure is a transformation that contains 2D structures (molecules) as components without regard to their 3D spatial arrangement. For example, the following reaction is both the query and the reaction record retrieved:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a rxnfile

Use this procedure to import a reaction query from a rxnfile that was created in CPSS, ISIS, or REACCS.

1.	Click Query (if not highlighted).

2.	Select the RXNSTRUCTURE box (if not highlighted).

3.	Choose File > Import > Rxnfile. (To retrieve a PC-rxnfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure or reaction is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

Use this procedure to restore a reaction query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the RXNSTRUCTURE box (if not highlighted).

3.	Choose Database > Restore Reaction.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected reaction component is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing reaction that you see in a box or table cell in ISIS/Base.

1.	Select the RXNSTRUCTURE box that contains the reaction that you want to edit. An ISIS/Draw window opens that contains the reaction.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Reaction Structure or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an SSS query

SSS queries contain your query as a 2D substructure. You search for molecules that contain your query wholly within a larger structure. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the MOLSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a 2D Substructure or

Specifying Query Features or

Specifying Stereochemistry

Drawing Mixtures: MDL Requirements for Database Searching and Registration

3.	Transfer the query back to ISIS/Base.


Drawing a 2D Substructure

A 2D substructure is a fragment of a molecule that is drawn without regard to its 3D spatial arrangement. You retrieve molecules that contain your 2D substructure query embedded wholly within them. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Drawing Mixtures: MDL Requirements for Database Searching and Registration

*	Verifying the Chemistry of Sketches


To import an existing query from a molfile

Use this procedure to import a structure query from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a structure query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing substructure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the molecule substructure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the substructure. You see the substructure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a 2D Substructure or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an SSS query

SSS queries contain your query as a 2D substructure. You search for molecules that contain your query wholly within a larger structure. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the MOLSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a 2D Substructure or

Specifying Query Features or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a 2D Substructure

A 2D substructure is a fragment of a molecule that is drawn without regard to its 3D spatial arrangement. You retrieve molecules that contain your 2D substructure query embedded wholly within them. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a molfile

Use this procedure to import a structure query from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a structure query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing substructure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the molecule substructure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the substructure. You see the substructure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a 2D Substructure or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an RGROUP query

RGROUP queries contain your query as a root structure with defined Rgroup substituents attached to it at any position. You can also specify Rgroup conditions for your Rgroup query. You search for molecules that contain your query wholly within a larger structure. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the MOLSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples

You can specify that the Rgroup label R1 on the root structure allows a carboxyl group at its position and that R2 allows either a chlorine atom or a sulfonic acid group at its position.


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) Do the following steps in order:

a.	Draw the root structure.

b.	Draw Rgroup substituents.

c.	Specify attachment points for Rgroup substituents.

d.	Specify the members of each Rgroup.

e.	Specify Rgroup conditions.

3.	Transfer the query back to ISIS/Base.


Specifying Atom and/or Bond Query Features

A query feature on a molecule is a restriction on an atom and/or a bond that specifies the retrieval of certain types of molecule records from an ISIS/Base database.

Click one of the following:

*	Specifying atom query features

*	Specifying bond query features


Drawing the Root Structure

Click here for step-by-step instructions

A root structure contains that portion of a molecule that does not vary among the molecules retrieved. In the following example, the phenyl ring is the invariant portion of the structure:

Each Rgroup label represents a list of Rgroup substituents that you allow to be attached to the root structure. You draw the root structure by drawing the invariant portion of the structure, drawing bonds for Rgroup labels, then specifying Rgroup labels:


To draw the root structure

You draw the root structure of an Rgroup by drawing the invariant portion of the structure, adding bonds to the atoms that you want to be Rgroup labels, then specifying Rgroup labels. For example:

1.	Draw the invariant portion of the root structure.

2.	Draw bonds for Rgroup labels.

3.	Specify Rgroup labels on the root structure.


To import an existing query from a molfile

Use this procedure to import a structure query from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a structure query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing the Root Structure or

Specifying the Rgroup labels on the root structure. or

Drawing an Rgroup Substituent or

Specifying Attachment Points or

Specifying the Members of an Rgroup or

Specifying Rgroup Conditions or

Specifying Query Features or

Specifying Stereochemistry.

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To import an existing graphical query from a list

Use this procedure to import a list of 3D substructures from an SDfile that was created in a CPSS, ISIS, REACCS, or MACCS-II database and to retrieve an existing 3D substructure query from that list.

1.	Click Browse (if not highlighted).

2.	Select the MODELSTRUCTURE box. It highlights.

3.	Choose File > Import > List. (To retrieve a PC-list file on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). The name of the file appears in the Open File Name text box.

5.	Click OK (Mac=Open). The selected list is imported into your form and you see the first record in the boxes and tables.

6.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

7.	Choose Edit > Copy.

8.	Click Query.

9.	Choose Edit > Paste.

10.	(Optional) You can edit the existing graphical query.


Editing an Existing Text and/or Numeric Query on the Form

Click one of the following items:

*	To delete characters from the query

*	To edit the characters of an existing query


To delete characters from the query

1.	Select the text that you want to delete.

2.	Press the Back Space key.


To edit the characters of an existing query

Use this procedure to edit text or numeric characters in a box or a table cell.

1.	Select the box or table cell that contains an existing query.

2.	(Optional) You cannot add a second search operator to the same box or table cell, but you can replace the existing one. To replace a search operator, select it, and then type in the search operator that you want.

3.	(Optional) To edit text or numeric characters, select them and type in the characters that you want.

4.	(Optional) To add additional text or numeric characters, place the cursor in the position of your choice and type in the characters that you want.

Note: You can also enter partial text and/or numeric values and at least one wildcard.


To edit the characters of an existing query

Use this procedure to edit text or numeric characters in a box or a table cell.

1.	Select the box or table cell that contains an existing query.

2.	(Optional) You cannot add a second search operator to the same box or table cell, but you can replace the existing one. To replace a search operator, select it, and then type in the search operator that you want.

3.	(Optional) To edit text or numeric characters, select them and type in the characters that you want.

4.	(Optional) To add additional text or numeric characters, place the cursor in the position of your choice and type in the characters that you want.

Note: You can also enter partial text and/or numeric values and at least one wildcard.


Obtaining an Existing Text/Numeric Query

You can either paste a text/numeric query from the Clipboard or you can restore a text/numeric query from the database that is open currently.

Click one of the following:

*	Paste a query from the Clipboard

*	Restore a query from the current database


To paste an existing text/numeric query from the Clipboard

This procedure assumes that you have a text/numeric query from any ASCII text editor on the Clipboard.

Caution: You can only enter a single text/numeric query into a single box or table cell on your form.

1.	Select the box or table cell on the form in ISIS/Base that will hold your SBF query (if not selected).

2.	Choose Edit > Paste.

3.	Repeat Steps 1 and 2 as needed. You can enter a maximum of 25 queries into individual table cells on the form. Examples

4.	(Optional) You can edit the existing query.


To restore an existing text/numeric query from the current database

1.	Click Query (if not highlighted).

2.	Choose Search > Restore Query.

3.	Click the name of an existing query in the Select Object list box.

4.	Click OK (Mac=Open). The selected query is restored.

5.	(Optional) You can edit the existing query.


To obtain an SSS query

SSS queries contain your query as a 2D substructure. You search for reactions with reaction components that contain your query wholly within a larger structure. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the box or table cell on the form that will hold your SSS query. In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a Reaction Component Substructure or

Specifying Query Features on a Reaction Component or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Component Substructure

A reaction component substructure is a fragment of a molecule from a reaction that is drawn without regard to its 3D spatial arrangement. You retrieve reactions that contain your 2D substructure query embedded wholly within the reaction components. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a molfile

Use this procedure to import a reaction component query (without the reaction arrow) from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a reaction component query (without the reaction arrow) that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing reaction substructure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the reaction component substructure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the substructure. You see the substructure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Reaction Component Substructure or

Specifying Query Features on a Reaction Component or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an SSS query

SSS queries contain your query as a 2D substructure. You search for reactions with reaction components that contain your query wholly within a larger structure. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the box or table cell on the form that will hold your SSS query. In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a Reaction Component Substructure or

Specifying Query Features on a Reaction Component or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Component Substructure

A reaction component substructure is a fragment of a molecule from a reaction that is drawn without regard to its 3D spatial arrangement. You retrieve reactions that contain your 2D substructure query embedded wholly within the reaction components. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a molfile

Use this procedure to import a reaction component substructure query (without the reaction arrow) from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a reaction component substructure query (without the reaction arrow) that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing substructure (without the reaction arrow) that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the reaction component substructure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the substructure. You see the substructure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Reaction Component Substructure or

Specifying Query Features on a Reaction Component or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an RSS query
To obtain an RSS/Rxn query

RSS/Rxn queries contain your query as a reaction substructure with atom-atom maps and your choice of restrictions on the reacting centers. You search for reactions that contain your query wholly within a larger reaction structure. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the RXNSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a rxnfile.

*	Restore a query that you previously saved as an object in the database.


Examples

The atom-atom maps specify which atoms in the reactants correspond to the atoms in the products. The reaction query feature CHANGE (/) specifies that the bond order in the reactant must change in the product at the specified position.


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a Reaction Substructure or

Specifying Query Features on a Reaction Component or

Specifying Query Features on a Reaction or

Specifying Atom-Atom Maps on a Reaction or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Substructure

A reaction substructure is a fragment of a reaction that is drawn without regard to its 3D spatial arrangement. You retrieve reactions that contain your reaction substructure query embedded wholly within them. For example:

Note: When you search a remote reaction database, always atom-atom map your query. This example displays the mapped atoms and reacting centers.

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a rxnfile

Use this procedure to import a reaction substructure query from a rxnfile that was created in CPSS, ISIS, or REACCS.

1.	Click Query (if not highlighted).

2.	Select the RXNSTRUCTURE box (if not highlighted).

3.	Choose File > Import > Rxnfile. (To retrieve a PC-rxnfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure or reaction is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

Use this procedure to restore a reaction substructure query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the RXNSTRUCTURE box (if not highlighted).

3.	Choose Database > Restore Reaction.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected reaction component is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing substructure that you see in a box or table cell in ISIS/Base.

1.	Select the RXNSTRUCTURE box that contains the reaction substructure that you want to edit. An ISIS/Draw window opens that contains the reaction substructure.

2.	Click the substructure. You see the substructure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Reaction Substructure or

Specifying Query Features on a Reaction Component or

Specifying Query Features on a Reaction or

Specifying Stereochemistry or

Specifying Atom-Atom Maps on a Reaction or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an RSS query

RSS/Rxn queries contain your query as a reaction substructure. A reaction substructure contains fragments that are reactants and fragments that are products. You search for reactions that contain your query wholly within a larger reaction structure. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the RXNSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a rxnfile.

*	Restore a query that you previously saved as an object in the database.


Examples


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a Reaction Substructure or

Specifying Query Features on a Reaction Component or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Substructure

A reaction substructure is a fragment of a reaction that is drawn without regard to its 3D spatial arrangement. You retrieve reactions that contain your reaction substructure query embedded wholly within them. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a rxnfile

Use this procedure to import a reaction substructure query from a rxnfile that was created in CPSS, ISIS, or REACCS.

1.	Click Query (if not highlighted).

2.	Select the RXNSTRUCTURE box (if not highlighted).

3.	Choose File > Import > Rxnfile. (To retrieve a PC-rxnfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure or reaction is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

Use this procedure to restore a reaction substructure query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the RXNSTRUCTURE box (if not highlighted).

3.	Choose Database > Restore Reaction.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected reaction component is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing substructure that you see in a box or table cell in ISIS/Base.

1.	Select the RXNSTRUCTURE box that contains the reaction substructure that you want to edit. An ISIS/Draw window opens that contains the reaction substructure.

2.	Click the substructure. You see the substructure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Reaction Substructure or

Specifying Query Features on a Reaction Component or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an RSS/Comp query

RSS/Comp queries contain your query as a reaction component substructure with a reaction arrow and your choice of restrictions on the reacting centers. (Your query is a fragment that is a reactant or a fragment that is a product.) You search for reactions with reaction components that contain your query wholly within a larger reaction component structure. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the RXNSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a rxnfile.

*	Restore a query that you previously saved as an object in the database.


Examples

The reaction query feature CHANGE (/) specifies that the bond order in the reactant must change in the product at the specified position.


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a Reaction Component Substructure or

Specifying Query Features on a Reaction Component or

Specifying Query Features on a Reaction or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Component Substructure

A reaction component substructure is a fragment of a molecule from a reaction that is drawn without regard to its 3D spatial arrangement. You retrieve reactions that contain your 2D substructure query embedded wholly within the reaction components. For example:

Note: This example displays the reacting centers.

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a rxnfile

Use this procedure to import a reaction component substructure query (with the reaction arrow) from a rxnfile that was created in CPSS, ISIS, or REACCS.

1.	Click Query (if not highlighted).

2.	Select the RXNSTRUCTURE box (if not highlighted).

3.	Choose File > Import > Rxnfile. (To retrieve a PC-rxnfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure or reaction is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

Use this procedure to restore a reaction component substructure query (with the reaction arrow) from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the RXNSTRUCTURE box (if not highlighted).

3.	Choose Database > Restore Reaction.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected reaction component is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing substructure that you see in a box or table cell in ISIS/Base.

1.	Select the RXNSTRUCTURE box that contains the reaction component substructure that you want to edit. An ISIS/Draw window opens that contains the reaction component substructure.

2.	Click the substructure. You see the substructure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Reaction Component Substructure or

Specifying Query Features on a Reaction Component or

Specifying Query Features on a Reaction or

Specifying Stereochemistry.

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an RSS/Comp query

RSS/Comp queries contain your query as a reaction component substructure with a reaction arrow. (Your query is a fragment that is a reactant or a fragment that is a product.) You search for reactions with reaction components that contain your query wholly within a larger reaction component structure. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the RXNSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a rxnfile.

*	Restore a query that you previously saved as an object in the database.


Examples


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a Reaction Component Substructure or

Specifying Query Features on a Reaction Component or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Component Substructure

A reaction component substructure is a fragment of a molecule from a reaction that is drawn without regard to its 3D spatial arrangement. You retrieve reactions that contain your 2D substructure query embedded wholly within the reaction components. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a rxnfile

Use this procedure to import a reaction component substructure query (with the reaction arrow) from a rxnfile that was created in CPSS, ISIS, or REACCS.

1.	Click Query (if not highlighted).

2.	Select the RXNSTRUCTURE box (if not highlighted).

3.	Choose File > Import > Rxnfile. (To retrieve a PC-rxnfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure or reaction is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

Use this procedure to restore a reaction component substructure query (with the reaction arrow) from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the RXNSTRUCTURE box (if not highlighted).

3.	Choose Database > Restore Reaction.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected reaction component is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing substructure that you see in a box or table cell in ISIS/Base.

1.	Select the RXNSTRUCTURE box that contains the reaction component substructure that you want to edit. An ISIS/Draw window opens that contains the reaction component substructure.

2.	Click the substructure. You see the substructure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Reaction Component Substructure or

Specifying Query Features on a Reaction Component or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an SBF query

SBF queries can contain any combination of text/numeric strings and/or structures in different boxes and tables on the form. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	(Optional) To enter text or numeric data, do one of the following:

*	Enter a new text/numeric query

*	Obtain an existing text/numeric query.

4.	(Optional) Click a box or cell on the form that will hold a structure, and then do one of the following:

*	Draw a new graphical query.

*	Import a graphical query from a molfile.

*	Restore a graphical query that you previously saved as an object in the database.

5.	(Optional) Repeat Steps 3 and 4 as needed. You can conduct a single search with a maximum of 25 queries.

Note: The placement of multiple queries within a table in an SBF search might produce different search results. For more information, see Obtaining Different Search Results with Multiple Queries in Tables.


Examples

In this example, you want to find all molecules with a specific steroid substructure wholly within them and that have a melting point that is greater than 220 degrees Centigrade and that contain the term "one" at the end of their compound name:

Note: The percent sign (%) is a wildcard. (Do not use wildcards with a partial formula query.)


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a 2D Substructure or

Specifying Query Features or

Specifying Stereochemistry

Drawing Mixtures: MDL Requirements for Database Searching and Registration

3.	Transfer the query back to ISIS/Base.


Drawing a 2D Substructure

A 2D substructure is a fragment of a molecule that is drawn without regard to its 3D spatial arrangement. You retrieve molecules that contain your 2D substructure query embedded wholly within them. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Drawing Mixtures: MDL Requirements for Database Searching and Registration

*	Verifying the Chemistry of Sketches


To enter a new text/numeric query

Use this procedure to enter a new text/numeric string (a query) to the boxes and table cells on the form. If you enter more than one query into a single form, ISIS joins your query strings automatically with the boolean algebraic operator AND. Examples

1.	Select the box or table cell of your choice (if not highlighted).

2.	Enter the search operator.

3.	Enter a space.

4.	Enter the text and/or numeric values that you want to find. You can enter a maximum of 25 queries into the same table. Examples

Notes: (1) You can also enter a partial query with at least one wildcard. (Do not use wildcards with a partial formula query.) (2) Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

5.	(Optional) Repeat Steps 1 through 4 as needed.

See also:

To delete characters from the query

To edit the characters of an existing query


Examples

To find compounds with the term methane in their name and a molecular weight that is greater than 350:

Note: The percent sign (%) is a wildcard. (Do not use wildcards with a partial formula query.)


To edit an existing text and/or numeric query on the form

Searching Concepts/Examples

1.	(Optional) To delete unwanted text from a box or table cell, select the text, and then press the Back Space key.

2.	(Optional) To add text to the current query, click the box or table cell that contains a query string, and then enter the characters of your choice in the correct format for text/numeric strings.

3.	(Optional) To add another query string to a different box or a different table cell, click the box or table cell of your choice (if not highlighted), enter a search operator, enter a space, and then enter the target text and/or numeric values of your choice. (You can also enter partial text and/or numeric values and at least one wildcard.) Examples


Obtaining an Existing Text/Numeric Query

You can either paste a text/numeric query from the Clipboard or you can restore a text/numeric query from the database that is open currently.

Click one of the following:

*	Paste a query from the Clipboard

*	Restore a query from the current database


To paste an existing text/numeric query from the Clipboard

This procedure assumes that you have a text/numeric query from any ASCII text editor on the Clipboard.

Caution: You can only enter a single text/numeric query into a single box or table cell on your form.

1.	Select the box or table cell on the form in ISIS/Base that will hold your SBF query (if not selected).

2.	Choose Edit > Paste.

3.	Repeat Steps 1 and 2 as needed. You can enter a maximum of 25 text/numeric query strings into individual table cells on the form. Examples

4.	(Optional) You can edit the existing query.


To restore an existing text/numeric query from the current database

1.	Click Query (if not highlighted).

2.	Choose Search > Restore Query.

3.	Click the name of an existing query in the Select Object list box.

4.	Click OK (Mac=Open). The selected query is restored.

5.	(Optional) You can edit the existing query.


To import an existing graphical query from a molfile

Use this procedure to import a graphical query from a molfile that was created in CPSS, ISIS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing graphical query from a database

You can restore a graphical query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query
To edit an existing graphical query

Searching Concepts/Examples

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the substructure that you want to edit. An ISIS/Draw window opens that contains the substructure .

2.	Click the substructure. You see the substructure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a 2D Substructure or

Specifying Query Features or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an SBF query

SBF queries can contain any combination of text/numeric strings and/or structures in different boxes and tables on the form. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	(Optional) To enter text or numeric data, do one of the following:

*	Enter a new text/numeric query

*	Obtain an existing text/numeric query.

4.	(Optional) Click a box or cell on the form that will hold a structure, and then do one of the following:

*	Draw a new graphical query.

*	Import a graphical query from a molfile.

*	Restore a graphical query that you previously saved as an object in the database.

5.	(Optional) Repeat Steps 3 and 4 as needed. You can conduct a single search with a maximum of 25 queries.

Note: The placement of multiple queries within a table in an SBF search might produce different search results. For more information, see Obtaining Different Search Results with Multiple Queries in Tables.


Examples

In this example, you want to find all molecules with a specific steroid substructure wholly within them and that have a melting point that is greater than 220 degrees Centigrade and that have the term aspirin as a portion of the total compound name:

Note: The percent sign (%) is a wildcard. (Do not use wildcards with a partial formula query.)


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a 2D Substructure or

Specifying Query Features or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a 2D Substructure

A 2D substructure is a fragment of a molecule that is drawn without regard to its 3D spatial arrangement. You retrieve molecules that contain your 2D substructure query embedded wholly within them. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To enter a new text/numeric query

Use this procedure to enter a new text/numeric string (a query) to the boxes and table cells on the form. If you enter more than one query into a single form, ISIS joins your query strings automatically with the boolean algebraic operator AND. Examples

1.	Select the box or table cell of your choice (if not highlighted).

2.	Enter the search operator.

3.	Enter a space.

4.	Enter the text and/or numeric values that you want to find. You can enter a maximum of 25 queries into the same table. Examples

Notes: (1) You can also enter a partial query with at least one wildcard. (Do not use wildcards with a partial formula query.) (2) Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

5.	(Optional) Repeat Steps 1 through 4 as needed.

See also:

To delete characters from the query

To edit the characters of an existing query


Examples

To find compounds with the term methane in their name and a molecular weight that is greater than 350:

Note: The percent sign (%) is a wildcard. (Do not use wildcards with a partial formula query.)


To edit an existing text and/or numeric query on the form

Searching Concepts/Examples

1.	(Optional) To delete unwanted text from a box or table cell, select the text, and then press the Back Space key.

2.	(Optional) To add text to the current query, click the box or table cell that contains a query string, and then enter the characters of your choice in the correct format for text/numeric strings.

3.	(Optional) To add another query string to a different box or a different table cell, click the box or table cell of your choice (if not highlighted), enter a search operator, enter a space, and then enter the target text and/or numeric values of your choice. (You can also enter partial text and/or numeric values and at least one wildcard.) Examples


Obtaining an Existing Text/Numeric Query

You can either paste a text/numeric query from the Clipboard or you can restore a text/numeric query from the database that is open currently.

Click one of the following:

*	Paste a query from the Clipboard

*	Restore a query from the current database


To paste an existing text/numeric query from the Clipboard

This procedure assumes that you have a text/numeric query from any ASCII text editor on the Clipboard.

Caution: You can only enter a single text/numeric query into a single box or table cell on your form.

1.	Select the box or table cell on the form in ISIS/Base that will hold your SBF query (if not selected).

2.	Choose Edit > Paste.

3.	Repeat Steps 1 and 2 as needed. You can enter a maximum of 25 text/numeric query strings into individual table cells on the form. Examples

4.	(Optional) You can edit the existing query.


To restore an existing text/numeric query from the current database

1.	Click Query (if not highlighted).

2.	Choose Search > Restore Query.

3.	Click the name of an existing query in the Select Object list box.

4.	Click OK (Mac=Open). The selected query is restored.

5.	(Optional) You can edit the existing query.


To import an existing graphical query from a molfile

Use this procedure to import a graphical query from a molfile that was created in CPSS, ISIS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing graphical query from a database

You can restore a graphical query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing graphical query

Searching Concepts/Examples

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the substructure that you want to edit. An ISIS/Draw window opens that contains the substructure .

2.	Click the substructure. You see the substructure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a 2D Substructure or

Specifying Query Features or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an SBF query

SBF queries can contain any combination of text/numeric strings and/or structures in different boxes and tables on the form. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	(Optional) To enter text or numeric data, do one of the following:

*	Enter a new text/numeric query

*	Obtain an existing text/numeric query.

4.	(Optional) Click a box or cell on the form that will hold a structure, and then do one of the following:

*	Draw a new graphical query.

*	Import a graphical query from a molfile or a rxnfile.

*	Restore a graphical query that you previously saved as an object in the database.

5.	(Optional) Repeat Steps 3 and 4 as needed. You can conduct a single search with a maximum of 25 queries.

Note: The placement of multiple queries within a table in an SBF search might produce different search results. For more information, see Obtaining Different Search Results with Multiple Queries in Tables.


Examples

In this example, you want to find all transformations with a specific reaction substructure wholly within them and that have a product yield that is greater than 95 percent and that have a REGNO that begins with the letter T:

In the graphical query component, the atom-atom maps specify which atoms in the reactants correspond to the atoms in the products. In addition, the reaction query feature CHANGE (/) specifies that the bond order in the reactant must change in the product at the specified position. The percent sign (%) is a wildcard. (Do not use wildcards with a partial formula query.)


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a Reaction Component Substructure or

Drawing a Reaction Substructure or

Specifying Query Features on a Reaction Component or

Specifying Query Features on a Reaction or

Specifying Atom-Atom Maps on a Reaction or

Specifying Rgroup Query Features or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Component Substructure

A reaction component substructure is a fragment of a molecule from a reaction that is drawn without regard to its 3D spatial arrangement. You retrieve reactions that contain your 2D substructure query embedded wholly within the reaction components. For example:

Note: This example displays the reacting centers.

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


Drawing a Reaction Substructure

A reaction substructure is a fragment of a reaction that is drawn without regard to its 3D spatial arrangement. You retrieve reactions that contain your reaction substructure query embedded wholly within them. For example:

Note: When you search a remote reaction database, always atom-atom map your query. This example displays the mapped atoms and reacting centers.

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To enter a new text/numeric query

Use this procedure to enter a new text/numeric string (a query) to the boxes and table cells on the form. If you enter more than one query into a single form, ISIS joins your query strings automatically with the boolean algebraic operator AND. Examples

1.	Select the box or table cell of your choice (if not highlighted).

2.	Enter the search operator.

3.	Enter a space.

4.	Enter the text and/or numeric values that you want to find. You can enter a maximum of 25 queries into the same table. Examples

Notes: (1) You can also enter a partial query with at least one wildcard. (Do not use wildcards with a partial formula query.) (2) Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

5.	(Optional) Repeat Steps 1 through 4 as needed.

See also:

To delete characters from the query

To edit the characters of an existing query


Examples

To find compounds with two or three oxygens in their molecular formula and a product yield that is greater than 95 percent:

Note: Do not use wildcards with a partial formula query.


To edit an existing text and/or numeric query on the form

Searching Concepts/Examples

1.	(Optional) To delete unwanted text from a box or table cell, select the text, and then press the Back Space key.

2.	(Optional) To add text to the current query, click the box or table cell that contains a query string, and then enter the characters of your choice in the correct format for text/numeric strings.

3.	(Optional) To add another query string to a different box or a different table cell, click the box or table cell of your choice (if not highlighted), enter a search operator, enter a space, and then enter the target text and/or numeric values of your choice. (You can also enter partial text and/or numeric values and at least one wildcard.) Examples


Obtaining an Existing Text/Numeric Query

You can either paste a text/numeric query from the Clipboard or you can restore a text/numeric query from the database that is open currently.

Click one of the following:

*	Paste a query from the Clipboard

*	Restore a query from the current database


To paste an existing text/numeric query from the Clipboard

This procedure assumes that you have a text/numeric query from any ASCII text editor on the Clipboard.

Caution: You can only enter a single text/numeric query into a single box or table cell on your form.

1.	Select the box or table cell on the form in ISIS/Base that will hold your SBF query (if not selected).

2.	Choose Edit > Paste.

3.	Repeat Steps 1 and 2 as needed. You can enter a maximum of 25 text/numeric query strings into individual table cells on the form. Examples

4.	(Optional) You can edit the existing query.


To restore an existing text/numeric query from the current database

1.	Click Query (if not highlighted).

2.	Choose Search > Restore Query.

3.	Click the name of an existing query in the Select Object list box.

4.	Click OK (Mac=Open). The selected query is restored.

5.	(Optional) You can edit the existing query.


To import an existing graphical query from a molfile or a rxnfile

Use this procedure to import a graphical query from a molfile or a rxnfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Do one of the following:

*	If you selected a table cell or box that holds a structure without a reaction arrow, choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

*	If you selected a table cell or box that holds a reaction or a reaction component with a reaction arrow, choose File > Import > Rxnfile. (To retrieve a PC-rxnfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing graphical query from a database

You can restore a graphical query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Do one of the following:

*	If you selected a table cell or box that holds a structure without a reaction arrow, choose Database > Restore Molecule.

*	If you selected a table cell or box that holds a reaction or a reaction component with a reaction arrow, choose Database > Restore Reaction.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing graphical query

Searching Concepts/Examples

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the reaction substructure that you want to edit. An ISIS/Draw window opens that contains the reaction substructure .

2.	Click the substructure. You see the substructure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Reaction Component Substructure or

Drawing a Reaction Substructure or

Specifying Query Features on a Reaction Component or

Specifying Query Features on a Reaction or

Specifying Rgroup Query Features or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an SBF query

SBF queries can contain any combination of text/numeric strings and/or structures in different boxes and tables on the form. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	(Optional) To enter text or numeric data, do one of the following:

*	Enter a new text/numeric query

*	Obtain an existing text/numeric query.

4.	(Optional) Click a box or cell on the form that will hold a structure, and then do one of the following:

*	Draw a new graphical query.

*	Import a graphical query from a molfile or a rxnfile.

*	Restore a graphical query that you previously saved as an object in the database.

5.	(Optional) Repeat Steps 3 and 4 as needed. You can conduct a single search with a maximum of 25 queries.

Note: The placement of multiple queries within a table in an SBF search might produce different search results. For more information, see Obtaining Different Search Results with Multiple Queries in Tables.


Examples

In this example, you want to find all transformations with a specific product substructure wholly within them and that have a product yield that is greater than 95 percent and that contain the author Smythe:

Note: The percent signs (%) and underscore (_) are wildcards. (Do not use wildcards with a partial formula query.)


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a Reaction Component Substructure or

Drawing a Reaction Substructure or

Specifying Query Features on a Reaction Component or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Component Substructure

A reaction component substructure is a fragment of a molecule from a reaction that is drawn without regard to its 3D spatial arrangement. You retrieve reactions that contain your 2D substructure query embedded wholly within the reaction components. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


Drawing a Reaction Component Substructure
Drawing a Reaction Substructure

A reaction substructure is a fragment of a reaction that is drawn without regard to its 3D spatial arrangement. You retrieve reactions that contain your reaction substructure query embedded wholly within them. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To enter a new text/numeric query

Use this procedure to enter a new text/numeric string (a query) to the boxes and table cells on the form. If you enter more than one query into a single form, ISIS joins your query strings automatically with the boolean algebraic operator AND. Examples

1.	Select the box or table cell of your choice (if not highlighted).

2.	Enter the search operator.

3.	Enter a space.

4.	Enter the text and/or numeric values that you want to find. You can enter a maximum of 25 queries into the same table. Examples

Notes: (1) You can also enter a partial query with at least one wildcard. (Do not use wildcards with a partial formula query.) (2) Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

5.	(Optional) Repeat Steps 1 through 4 as needed.

See also:

To delete characters from the query

To edit the characters of an existing query


Examples

To find compounds with two or three oxygens in their molecular formula and a product yield that is greater than 95 percent:

Note: Do not use wildcards with a partial formula query.


To edit an existing text and/or numeric query on the form

Searching Concepts/Examples

1.	(Optional) To delete unwanted text from a box or table cell, select the text, and then press the Back Space key.

2.	(Optional) To add text to the current query, click the box or table cell that contains a query string, and then enter the characters of your choice in the correct format for text/numeric strings.

3.	(Optional) To add another query string to a different box or a different table cell, click the box or table cell of your choice (if not highlighted), enter a search operator, enter a space, and then enter the target text and/or numeric values of your choice. (You can also enter partial text and/or numeric values and at least one wildcard.) Examples


Obtaining an Existing Text/Numeric Query

You can either paste a text/numeric query from the Clipboard or you can restore a text/numeric query from the database that is open currently.

Click one of the following:

*	Paste a query from the Clipboard

*	Restore a query from the current database


To paste an existing text/numeric query from the Clipboard

This procedure assumes that you have a text/numeric query from any ASCII text editor on the Clipboard.

Caution: You can only enter a single text/numeric query into a single box or table cell on your form.

1.	Select the box or table cell on the form in ISIS/Base that will hold your SBF query (if not selected).

2.	Choose Edit > Paste.

3.	Repeat Steps 1 and 2 as needed. You can enter a maximum of 25 text/numeric query strings into individual table cells on the form. Examples

4.	(Optional) You can edit the existing query.


To restore an existing text/numeric query from the current database

1.	Click Query (if not highlighted).

2.	Choose Search > Restore Query.

3.	Click the name of an existing query in the Select Object list box.

4.	Click OK (Mac=Open). The selected query is restored.

5.	(Optional) You can edit the existing query.


To import an existing graphical query from a molfile or a rxnfile

Use this procedure to import a graphical query from a molfile or a rxnfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Do one of the following:

*	If you selected a table cell or box that holds a structure without a reaction arrow, choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

*	If you selected a table cell or box that holds a reaction or a reaction component with a reaction arrow, choose File > Import > Rxnfile. (To retrieve a PC-rxnfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing graphical query from a database

You can restore a graphical query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Do one of the following:

*	If you selected a table cell or box that holds a structure without a reaction arrow, choose Database > Restore Molecule.

*	If you selected a table cell or box that holds a reaction or a reaction component with a reaction arrow, choose Database > Restore Reaction.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing graphical query

Searching Concepts/Examples

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the reaction substructure that you want to edit. An ISIS/Draw window opens that contains the reaction substructure .

2.	Click the substructure. You see the substructure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Reaction Component Substructure or

Drawing a Reaction Substructure or

Specifying Query Features on a Reaction Component or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an RSim query

RSim queries contain a reaction, a structural similarity value for the set of reaction components, and/or a transformational similarity value for the reacting centers. (If you enter a transformational similarity value, you must also mark the reacting centers.) You search for records that are similar to your query structurally (with varying structural complexities) and/or transformationally. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the RXNSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a rxnfile.

*	Restore a query that you previously saved as an object in the database.


Examples

You create a reaction, transfer it to ISIS/Base, and then you are prompted to enter similarity values. For example:


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click Drawing a Reaction Structure.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Structure

A reaction structure is a transformation that contains 2D structures (molecules) as components without regard to their 3D spatial arrangement. For example:

Note: Do not use query features in an RSim query.

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


Drawing a Reaction Component Structure

A reaction component structure is a 2D structure (molecule) from a reaction without regard to its 3D spatial arrangement. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a rxnfile

Use this procedure to import a reaction query from a rxnfile that was created in CPSS, ISIS, or REACCS.

1.	Click Query (if not highlighted).

2.	Select the RXNSTRUCTURE box (if not highlighted).

3.	Choose File > Import > Rxnfile. (To retrieve a PC-rxnfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure or reaction is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

Use this procedure to restore a reaction query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the RXNSTRUCTURE box (if not highlighted).

3.	Choose Database > Restore Reaction.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected reaction component is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing reaction that you see in a box or table cell in ISIS/Base.

1.	Select the RXNSTRUCTURE box that contains the query that you want to edit. An ISIS/Draw window opens that contains the query.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Reaction Structure or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an MSim query

MSim queries contain a 2D structure and a structural similarity value. You search for molecules that are structurally similar to your query. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the MOLSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples

You create the 2D structure, enter it into the form in ISIS/Base, and then you are prompted to assign a structural similarity value:


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click Drawing a 2D Structure.

3.	Transfer the query back to ISIS/Base.


Drawing a 2D Structure

A 2D structure is a molecule that is drawn without regard to its 3D spatial arrangement. For example:

Note: Do not use query features in an MSim query.

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a molfile

Use this procedure to import a structure query from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a structure query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a 2D Structure or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain a FLEX query

FLEX queries contain a  2D structure and one or more Flexmatch parameters that you specify. You search for molecules that match your query exactly, but with a looser definition of an exact match. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the MOLSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples

You create a 2D structure and transfer it to ISIS/Base. For example:

In ISIS/Base, you are prompted to check the Flexmatch Parameters of your choice. For example:

*	You can specify that the stereo configuration must match.

*	You can specify that the isotopes must match.


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a 2D Structure or

Specifying Stereochemistry

Drawing Mixtures: MDL Requirements for Database Searching and Registration

3.	Transfer the query back to ISIS/Base.


Drawing a 2D Structure

A 2D structure is a molecule that is drawn without regard to its 3D spatial arrangement. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Drawing Mixtures: MDL Requirements for Database Searching and Registration

*	Verifying the Chemistry of Sketches


To import an existing query from a molfile

Use this procedure to import a structure query from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a structure query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the molecule component of the FLEX query. If you need help, click:

Drawing a 2D Structure or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain a TAUT query

TAUT queries contain a 2D structure (molecule). You search for molecules that match your query exactly and molecules that are the tautomer of your query. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the MOLSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click Drawing a 2D Structure.

3.	Transfer the query back to ISIS/Base.


Drawing a 2D Structure

A 2D structure is a molecule that is drawn without regard to its 3D spatial arrangement. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a molfile

Use this procedure to import a structure query from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a structure query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a 2D Structure or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an ISOMER query

ISOMER queries contain a 2D structure (molecule). You search for molecules that are geometric stereoisomers or optical stereoisomers of your query. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the MOLSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click Drawing a 2D Structure.

3.	Transfer the query back to ISIS/Base.


Drawing a 2D Structure

A 2D structure is a molecule that is drawn without regard to its 3D spatial arrangement. For example:

Note: An ISOMER search ignores any stereochemistry that you add to your query.

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Drawing Mixtures: MDL Requirements for Database Searching and Registration

*	Verifying the Chemistry of Sketches


To import an existing query from a molfile

Use this procedure to import a structure query from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a structure query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a 2D Structure or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain a PARENT query

PARENT queries contain the salt form of a 2D structure (a molecule that is drawn without regard to its 3D spatial arrangement). You search for molecules that are the parent structure of your salt query. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the MOLSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a 2D Structure or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a 2D Structure

A 2D structure is a molecule from a reaction that is drawn without regard to its 3D spatial arrangement. Your query is the salt form of a 2D structure. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a molfile

Use this procedure to import a structure query from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a structure query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a 2D Structure or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an MSim query

MSim queries contain a reaction component structure (without a reaction arrow), such as a reactant, and a structural similarity value. You search for reactions with reaction components that are structurally similar to the reaction component in your query. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the box or table on the form that will hold your MSim query. In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples

You create the 2D structure, enter it into the form in ISIS/Base, and then you are prompted to assign a structural similarity value:


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click Drawing a Reaction Component Structure.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Component Structure

A reaction component structure is a 2D structure (molecule) from a reaction without regard to its 3D spatial arrangement. For example, a product:

Note: Do not use query features in an MSim query.

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a molfile

Use this procedure to import a reaction component query (without the reaction arrow) from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a reaction component query (without the reaction arrow) that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Click the box that contains the structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Reaction Component Structure or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain a FLEX query

FLEX queries contain a reaction component structure (without a reaction arrow), such as a reactant, and one or more Flexmatch parameters that you specify. You search for reactions with reaction components that match your query exactly, but with a looser definition of an exact match. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the box or table cell on the form that will hold your FLEX query. In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples

You create a reaction component and transfer it to ISIS/Base. For example:

In ISIS/Base, you are prompted to check the Flexmatch Parameters of your choice. For example:

*	You can specify that the stereo configuration must match.

*	You can specify that the isotopes must match.


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a Reaction Component Structure or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Component Structure

A reaction component structure is a 2D structure (molecule) from a reaction without regard to its 3D spatial arrangement. For example, a product:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a molfile

Use this procedure to import a reaction component query (without the reaction arrow) from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a reaction component query (without the reaction arrow) that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Click the box that contains the structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the molecule component of the FLEX query. If you need help, click:

Drawing a Reaction Component Structure or

Specifying Stereochemistry.

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain a TAUT query

TAUT queries contain a reaction component structure (without a reaction arrow), such as a reactant. You search for reactions with reaction components that match your query exactly and for reaction components that are the tautomer of your query. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the box or table cell on the form that will hold your TAUT query. In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click Drawing a Reaction Component Structure.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Component Structure

A reaction component structure is a 2D structure (molecule) from a reaction without regard to its 3D spatial arrangement. For example, a product:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a molfile

Use this procedure to import a reaction component query (without the reaction arrow) from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a reaction component query (without the reaction arrow) that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Click the box that contains the structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Reaction Component Structure or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an ISOMER query

ISOMER queries contain a reaction component structure (without a reaction arrow), such as a reactant. You search for molecules that are geometric stereoisomers or optical stereoisomers of your query. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the box or table cell on the form that will hold your ISOMER query. In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click Drawing a Reaction Component Structure.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Component Structure

A reaction component structure is a 2D structure (molecule) from a reaction without regard to its 3D spatial arrangement. For example, the product cis-2-butene:

Note: An ISOMER search ignores any stereochemistry that you add to your query.

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a molfile

Use this procedure to import a reaction component query (without the reaction arrow) from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a reaction component query (without the reaction arrow) that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Click the box that contains the structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Reaction Component Structure or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain a PARENT query

PARENT queries contain the salt form of a reaction component structure (without a reaction arrow), such as a reactant. You search for reactions with reaction components that are the parent structure of your salt query. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the box or table cell on the form that will hold your PARENT query. In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a Reaction Component Structure or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Component Structure

A 2D structure is a molecule from a reaction that is drawn without regard to its 3D spatial arrangement. Your query is the salt form of a 2D structure. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To import an existing query from a molfile

Use this procedure to import a reaction component query (without the reaction arrow) from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a reaction component query (without the reaction arrow) that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Click the box that contains the structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Reaction Component Structure or

Specifying Stereochemistry.

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an RGROUP Query

RGROUP queries contain a root structure with defined Rgroup substituents attached to it at any position. You can also specify Rgroup conditions for your Rgroup query. You search for reactions that contain your Rgroup query wholly within a larger reaction component. Examples

Note: You can only create an Rgroup query with a reaction component without a reaction arrow.

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the box or table cell on the form that will hold your RGROUP query. In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples

You can specify that the Rgroup label R1 on the root structure allows a carboxyl group at its position and that R2 allows either a chlorine atom or a sulfonic acid group at its position.


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) Do the following steps in order:

a.	Draw the root structure.

b.	Draw Rgroup substituents.

c.	Specify attachment points for Rgroup substituents.

d.	Specify the members of each Rgroup.

e.	Specify Rgroup conditions.

3.	Transfer the query back to ISIS/Base.


Specifying Atom and/or Bond Query Features

A query feature on a reaction component is a restriction on an atom and/or a bond that specifies the retrieval of certain types of reaction records from the database.

Click one of the following:

*	Specifying atom query features

*	Specifying bond query features


To import an existing query from a molfile

Use this procedure to import a reaction component query (without the reaction arrow) from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a reaction component query (without the reaction arrow) that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the reaction component (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Click the box that contains the structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing the Root Structure or

Specifying the Rgroup labels on the root structure. or

Drawing an Rgroup Substituent or

Specifying Attachment Points or

Specifying the Members of an Rgroup or

Specifying Rgroup Conditions or

Specifying Query Features on a Reaction Component or

Specifying Stereochemistry.

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an ID query

ID queries contain either one text/numeric string in a box or one or more text/numeric strings in a table on the form. (Enter solely one text/numeric string per table cell to a maximum of 25). Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the box or table cell on the form that will hold the query.

4.	Either enter a new query

      or obtain an existing query.

See also:

Viewing More Than Twenty-Five ID Numbers in a Single Search


Viewing More Than Twenty-Five ID Numbers in a Single Search

An ID search allows you to enter a maximum of 25 queries into different boxes or table cells on the form in ISIS/Base when you conduct a single ID search. If you require more than 25 ID numbers per search, you can alternatively export a list of search results (that contains more than 25 records), and then view the list in any ASCII text editor. You see the ID numbers that are associated with each record in a special list file format.

The list file format: On Line 1, you see the number 1 if the ID contains text or you see the number 3 if the ID is an integer. On Line 2, you see the total number of ID numbers in the list. On each successive line, you see the ID numbers for each record on the list. Example


Example

In this example, a value of 3 on Line 1 indicates that the ID numbers are integers. A value of 6 on Line 2 indicates that there are a total of 6 ID numbers. Lines 3 through 8 contain the 6 ID numbers (integers):

3

6

1

4

5

7

9

10


Examples

To find all records with the ID number 81157, enter:

= 81157

To find all records with ID numbers greater than 11250, enter:

> 11250

To find all records between and including 11250 and 81157, enter:

BETWEEN 11250 81157


Entering a New Query

You can enter a query that contains a single ID number, a set of ID numbers, or a specific range of ID numbers.

Notes: (1) You can enter a partial query with at least one wildcard. (2) Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

Click one of the following:

*	Single ID number or

*	Any set of ID numbers or

*	A specific range of ID numbers.


Obtaining an Existing Text/Numeric Query

You can either paste a text/numeric query from the Clipboard or you can restore a text/numeric query from the database that is open currently.

Click one of the following:

*	Paste a query from the Clipboard

*	Restore a query from the current database


To paste an existing text/numeric query from the Clipboard

This procedure assumes that you have a text/numeric query from any ASCII text editor on the Clipboard.

Caution: You can only enter a single text/numeric query into a single box or table cell on your form.

1.	Select the box or table cell on the form in ISIS/Base that will hold your ID query (if not selected).

2.	Choose Edit > Paste.

3.	Repeat Steps 1 and 2 as needed. You can enter a maximum of 25 ID numbers into individual table cells on the form. Examples

4.	(Optional) You can edit the existing query.


To restore an existing text/numeric query from the current database

1.	Click Query (if not highlighted).

2.	Choose Search > Restore Query.

3.	Click the name of an existing query in the Select Object list box.

4.	Click OK (Mac=Open). The selected query is restored.

5.	(Optional) You can edit the existing query.


Editing an Existing Text and/or Numeric Query on the Form

Click one of the following items:

*	To delete characters from the query

*	To edit the characters of an existing query

*	To add an additional query component to an empty box or table cell


Editing an Existing Text and/or Numeric Query on the Form

Click one of the following items:

*	To delete characters from the query

*	To edit the characters of an existing query

*	To add an additional query component to an empty box or table cell


To delete characters from the query

1.	Select the text that you want to delete.

2.	Press the Back Space key.


To edit the characters of an existing query

Use this procedure to edit text or numeric characters in a box or a table cell.

1.	Select the box or table cell that contains the existing query that you want to edit.

2.	(Optional) You cannot add a second search operator to the same box or table cell, but you can replace the existing one. To replace a search operator, select it, and then type in the search operator that you want.

3.	(Optional) To edit text or numeric characters, select them and type in the characters that you want.

4.	(Optional) To add additional text or numeric characters, place the cursor in the position of your choice and type in the characters that you want.

Note: You can also enter partial text and/or numeric values and at least one wildcard.


To add an additional query component to an empty box or table cell

Use this procedure to add an additional query component to other boxes and/or table cells in an existing query. (Each query component is an individual query that you combine into a single search.) Examples

1.	Select an empty box or table cell.

2.	Enter a search operator.

3.	Enter a space.

4.	Enter the ID number of your choice.

Note: You can also enter partial text and/or numeric values and at least one wildcard.


To edit the characters of an existing query

Use this procedure to edit text or numeric characters in a box or a table cell.

1.	Select the box or table cell that contains the existing query that you want to edit.

2.	(Optional) You cannot add a second search operator to the same box or table cell, but you can replace the existing one. To replace a search operator, select it, and then type in the search operator that you want.

3.	(Optional) To edit text or numeric characters, select them and type in the characters that you want.

4.	(Optional) To add additional text or numeric characters, place the cursor in the position of your choice and type in the characters that you want.

Note: You can also enter partial text and/or numeric values and at least one wildcard.


To add an additional query component to an empty box or table cell

Use this procedure to add an additional query component to other boxes and/or table cells in an existing query. (Each query component is an individual query that you combine into a single search.) Examples

1.	Select an empty box or table cell.

2.	Enter a search operator.

3.	Enter a space.

4.	Enter the ID number of your choice.

Note: You can also enter partial text and/or numeric values and at least one wildcard.


To obtain an FMLA query and execute the search

Formula queries contain your choice of exact formulas or subformulas. You can include hydrogens in either exact formula or subformula queries but you cannot include wildcards. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Click the Structure box or table cell on the form (if not highlighted).

4.	Choose Search > Formula.

5.	Do one of the following:

*	Enter a new exact formula into the Query text box, and then choose [image] Exact Match.

*	Enter a new subformula into the Query text box, and then choose [image] Subformula.

6.	Click OK.

See also:

To abandon the search


Examples

Examples of Exact Formula Queries:

*	To find phenol, enter:

C6 H6 O.

*	To find phenolphthalein sodium, enter:

C20 H12 Na2 O4.

Examples of Subformula Queries:

*	To find molecules that are sodium salts, enter: Na.

*	To find molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms, enter:

C12 Br(1-2) S2.

*	To find molecules that contain six carbons, six hydrogens, and any number of other atom types, enter: C6 H6.


To enter a new query

1.	Choose Search > Formula.

2.	Do one of the following:

*	Enter a new exact formula, and then choose [image] Exact Match.

*	Enter a new subformula, and then choose [image] Subformula.


To obtain an FMLA query and execute the search

Formula queries contain your choice of exact formulas or subformulas. You can include hydrogens in either exact formula or subformula queries but you cannot include wildcards. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Click the Structure box or table cell on the form (if not highlighted).

4.	Choose Search > Formula.

5.	Do one of the following:

*	Enter a new exact formula into the Query text box, and then choose [image] Exact Match.

*	Enter a new subformula into the Query text box, and then choose [image] Subformula.

6.	Click OK.

See also:

To abandon the search


Examples

Examples of Exact Formula Queries:

*	To find phenol, enter:

C6 H6 O.

*	To find phenolphthalein sodium, enter:

C20 H12 Na2 O4.

Examples of Subformula Queries:

*	To find molecules that are sodium salts, enter: Na.

*	To find molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms, enter:

C12 Br(1-2) S2.

*	To find molecules that contain six carbons, six hydrogens, and any number of other atom types, enter: C6 H6.


To enter a new query

1.	Choose Search > Formula.

2.	Do one of the following

*	Enter a new exact formula, and then choose [image] Exact Match.

*	Enter a new subformula, and then choose [image] Subformula.


To obtain an FMLA query and execute the search

Formula queries contain your choice of exact formulas or subformulas. You can include hydrogens in either exact formula or subformula queries but you cannot include wildcards. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Click the Structure box or table cell on the form for the specific reaction component whose formula you want to find (if not highlighted).

4.	Choose Search > Formula.

5.	Do one of the following:

*	Enter a new exact formula into the Query text box, and then choose [image] Exact Match.

*	Enter a new subformula into the Query text box, and then choose [image] Subformula.

6.	Click OK.

See also:

To abandon the search


Examples

Examples of Exact Formula Queries:

*	To find the reactant phenol, enter:

C6 H6 O.

*	To find the reactant phenolphthalein sodium, enter:

C20 H12 Na2 O4.

Examples of Subformula Queries:

*	To find reactants that are sodium salts, enter: Na.

*	To find reactants that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms, enter:

C12 Br(1-2) S2.

*	To find reactants that contain six carbons, six hydrogens, and any number of other atom types, enter: C6 H6.


To enter a new query

1.	Choose Search > Formula.

2.	Do one of the following

*	Enter a new exact formula, and then choose [image] Exact Match.

*	Enter a new subformula, and then choose [image] Subformula.


To obtain an FMLA query and execute the search

Formula queries contain your choice of exact formulas or subformulas. You can include hydrogens in either exact formula or subformula queries but you cannot include wildcards. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Click the Structure box or table cell on the form for the specific reaction component whose formula you want to find (if not highlighted).

4.	Choose Search > Formula.

5.	Do one of the following:

*	Enter a new exact formula into the Query text box, and then choose [image] Exact Match.

*	Enter a new subformula into the Query text box, and then choose [image] Subformula.

6.	Click OK.

See also:

To abandon the search


Examples

Examples of Exact Formula Queries:

*	To find the reactant phenol, enter:

C6 H6 O.

*	To find the reactant phenolphthalein sodium, enter:

C20 H12 Na2 O4.

Examples of Subformula Queries:

*	To find reactants that are sodium salts, enter: Na.

*	To find reactants that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms, enter:

C12 Br(1-2) S2.

*	To find reactants that contain six carbons, six hydrogens, and any number of other atom types, enter: C6 H6.


To enter a new query

1.	Choose Search > Formula.

2.	Do one of the following

*	Enter a new exact formula, and then choose [image] Exact Match.

*	Enter a new subformula, and then choose [image] Subformula.


To obtain an ID query

ID queries contain either one text/numeric string in a box or one or more text/numeric strings in a table on the form. (Enter solely one text/numeric string per table cell to a maximum of 25). Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the box or table cell on the form that will hold the query.

4.	Either enter a new query

      or obtain an existing query.

See also:

Viewing More Than Twenty-Five ID Numbers in a Single Search


Examples

To find all records with the ID number 81157, enter:

= 81157

To find all records with ID numbers greater than 11250, enter:

> 11250

To find all records between and including 11250 and 81157, enter:

BETWEEN 11250 81157


Entering a New Query

You can enter a query that contains a single ID number, a set of ID numbers, or a range of ID numbers.

Click one of the following:

*	Single ID number or

*	Any set of ID numbers or

*	A specific range of ID numbers.


Obtaining an Existing Text/Numeric Query

You can either paste a text/numeric query from the Clipboard or you can restore a text/numeric query from the database that is open currently.

Click one of the following:

*	Paste a query from the Clipboard

*	Restore a query from the current database


To paste an existing text/numeric query from the Clipboard

This procedure assumes that you have a text/numeric query from any ASCII text editor on the Clipboard.

Caution: You can only enter a single text/numeric query into a single box or table cell on your form.

1.	Select the box or table cell on the form in ISIS/Base that will hold your ID query (if not selected).

2.	Choose Edit > Paste.

3.	Repeat Steps 1 and 2 as needed. You can enter a maximum of 25 ID numbers into individual table cells on the form. Examples

4.	(Optional) You can edit the existing query.


To restore an existing text/numeric query from the current database

1.	Click Query (if not highlighted).

2.	Choose Search > Restore Query.

3.	Click the name of an existing query in the Select Object list box.

4.	Click OK (Mac=Open). The selected query is restored.

5.	(Optional) You can edit the existing query.


To obtain an ID query

ID queries contain either one text/numeric string in a box or one or more text/numeric strings in a table on the form. (Enter solely one text/numeric string per table cell to a maximum of 25). Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the box or table cell on the form that will hold the query.

4.	Either enter a new query

      or obtain an existing query.

See also:

Viewing More Than Twenty-Five ID Numbers in a Single Search


Examples

To find all records with the ID number 81157, enter:

= 81157

To find all records with ID numbers greater than 11250, enter:

> 11250

To find all records between and including 11250 and 81157, enter:

BETWEEN 11250 81157


Entering a New Query

You can enter a query that contains a single ID number, a set of ID numbers, or a range of ID numbers.

Click one of the following:

*	Single ID number or

*	Any set of ID numbers or

*	A specific range of ID numbers.


Obtaining an Existing Text/Numeric Query

You can either paste a text/numeric query from the Clipboard or you can restore a text/numeric query from the database that is open currently.

Click one of the following:

*	Paste a query from the Clipboard

*	Restore a query from the current database


To paste an existing text/numeric query from the Clipboard

This procedure assumes that you have a text/numeric query from any ASCII text editor on the Clipboard.

Caution: You can only enter a single text/numeric query into a single box or table cell on your form.

1.	Select the box or table cell on the form in ISIS/Base that will hold your ID query (if not selected).

2.	Choose Edit > Paste.

3.	Repeat Steps 1 and 2 as needed. You can enter a maximum of 25 ID numbers into individual table cells on the form. Examples

4.	(Optional) You can edit the existing query.


To paste an existing text/numeric query from the Clipboard

This procedure assumes that you have a text/numeric query from any ASCII text editor on the Clipboard.

Caution: You can only enter a single text/numeric query into a single box or table cell on your form.

1.	Select the box or table cell on the form in ISIS/Base that will hold your ID query (if not selected).

2.	Choose Edit > Paste.

3.	Repeat Steps 1 and 2 as needed. You can enter a maximum of 25 ID numbers into individual table cells on the form. Examples

4.	(Optional) You can edit the existing query.


To restore an existing text/numeric query from the current database

1.	Click Query (if not highlighted).

2.	Choose Search > Restore Query.

3.	Click the name of an existing query in the Select Object list box.

4.	Click OK (Mac=Open). The selected query is restored.

5.	(Optional) You can edit the existing query.


To obtain an ID query

ID queries contain either one text/numeric string in a box or one or more text/numeric strings in a table on the form. (Enter solely one text/numeric string per table cell to a maximum of 25). Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the box or table cell on the form that will hold the query.

4.	Either enter a new query

      or obtain an existing query.

See also:

Viewing More Than Twenty-Five ID Numbers in a Single Search


Examples

To find all records with the ID number 81157, enter:

= 81157

To find all records with ID numbers greater than 11250, enter:

> 11250

To find all records between and including 11250 and 81157, enter:

BETWEEN 11250 81157


Entering a New Query

You can enter a query that contains a single ID number, a set of ID numbers, or a range of ID numbers.

Click one of the following:

*	Single ID number or

*	Any set of ID numbers or

*	A specific range of ID numbers.


Obtaining an Existing Text/Numeric Query

You can either paste a text/numeric query from the Clipboard or you can restore a text/numeric query from the database that is open currently.

Click one of the following:

*	Paste a query from the Clipboard

*	Restore a query from the current database


To paste an existing text/numeric query from the Clipboard

This procedure assumes that you have a text/numeric query from any ASCII text editor on the Clipboard.

Caution: You can only enter a single text/numeric query into a single box or table cell on your form.

1.	Select the box or table cell on the form in ISIS/Base that will hold your ID query (if not selected).

2.	Choose Edit > Paste.

3.	Repeat Steps 1 and 2 as needed. You can enter a maximum of 25 ID numbers into individual table cells on the form. Examples

4.	(Optional) You can edit the existing query.


To restore an existing text/numeric query from the current database

1.	Click Query (if not highlighted).

2.	Choose Search > Restore Query.

3.	Click the name of an existing query in the Select Object list box.

4.	Click OK (Mac=Open). The selected query is restored.

5.	(Optional) You can edit the existing query.


To obtain an ID query

ID queries contain either one text/numeric string in a box or one or more text/numeric strings in a table on the form. (Enter solely one text/numeric string per table cell to a maximum of 25). Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the box or table cell on the form that will hold the query.

4.	Either enter a new query

      or obtain an existing query.

See also:

Viewing More Than Twenty-Five ID Numbers in a Single Search


Examples

To find all records with the ID number 81157, enter:

= 81157

To find all records with ID numbers greater than 11250, enter:

> 11250

To find all records between and including 11250 and 81157, enter:

BETWEEN 11250 81157


Entering a New Query

You can enter a query that contains a single ID number, a set of ID numbers, or a range of ID numbers.

Click one of the following:

*	Single ID number or

*	Any set of ID numbers or

*	A specific range of ID numbers.


Obtaining an Existing Text/Numeric Query

You can either paste a text/numeric query from the Clipboard or you can restore a text/numeric query from the database that is open currently.

Click one of the following:

*	Paste a query from the Clipboard

*	Restore a query from the current database


To paste an existing text/numeric query from the Clipboard

This procedure assumes that you have a text/numeric query from any ASCII text editor on the Clipboard.

Caution: You can only enter a single text/numeric query into a single box or table cell on your form.

1.	Select the box or table cell on the form in ISIS/Base that will hold your ID query (if not selected).

2.	Choose Edit > Paste.

3.	Repeat Steps 1 and 2 as needed. You can enter a maximum of 25 ID numbers into individual table cells on the form. Examples

4.	(Optional) You can edit the existing query.


To restore an existing text/numeric query from the current database

1.	Click Query (if not highlighted).

2.	Choose Search > Restore Query.

3.	Click the name of an existing query in the Select Object list box.

4.	Click OK (Mac=Open). The selected query is restored.

5.	(Optional) You can edit the existing query.


To obtain an ID query

ID queries contain either one text/numeric string in a box or one or more text/numeric strings in a table on the form. (Enter solely one text/numeric string per table cell to a maximum of 25). Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the box or table cell on the form that will hold the query.

4.	Either enter a new query

      or obtain an existing query.

See also:

Viewing More Than Twenty-Five ID Numbers in a Single Search


Examples

To find all records with the ID number 81157, enter:

= 81157

To find all records with ID numbers greater than 11250, enter:

> 11250

To find all records between and including 11250 and 81157, enter:

BETWEEN 11250 81157


Entering a New Query

You can enter a query that contains a single ID number, a set of ID numbers, or a range of ID numbers.

Click one of the following:

*	Single ID number or

*	Any set of ID numbers or

*	A specific range of ID numbers.


Obtaining an Existing Text/Numeric Query

You can either paste a text/numeric query from the Clipboard or you can restore a text/numeric query from the database that is open currently.

Click one of the following:

*	Paste a query from the Clipboard

*	Restore a query from the current database


To paste an existing text/numeric query from the Clipboard

This procedure assumes that you have a text/numeric query from any ASCII text editor on the Clipboard.

Caution: You can only enter a single text/numeric query into a single box or table cell on your form.

1.	Select the box or table cell on the form in ISIS/Base that will hold your ID query (if not selected).

2.	Choose Edit > Paste.

3.	Repeat Steps 1 and 2 as needed. You can enter a maximum of 25 ID numbers into individual table cells on the form. Examples

4.	(Optional) You can edit the existing query.


To paste an existing text/numeric query from the Clipboard

This procedure assumes that you have a text/numeric query from any ASCII text editor on the Clipboard.

Caution: You can only enter a single text/numeric query into a single box or table cell on your form.

1.	Select the box or table cell on the form in ISIS/Base that will hold your ID query (if not selected).

2.	Choose Edit > Paste.

3.	Repeat Steps 1 and 2 as needed. You can enter a maximum of 25 ID numbers into individual table cells on the form. Examples

4.	(Optional) You can edit the existing query.


To restore an existing text/numeric query from the current database

1.	Click Query (if not highlighted).

2.	Choose Search > Restore Query.

3.	Click the name of an existing query in the Select Object list box.

4.	Click OK (Mac=Open). The selected query is restored.

5.	(Optional) You can edit the existing query.


To restore an existing text/numeric query from the current database

1.	Click Query (if not highlighted).

2.	Choose Search > Restore Query.

3.	Click the name of an existing query in the Select Object list box.

4.	Click OK (Mac=Open). The selected query is restored.

5.	(Optional) You can edit the existing query.


To edit the existing query

Use this procedure to edit an existing text/numeric query in the Query Builder in ISIS/Base.

1.	(Optional) To delete unwanted text, select the text, and then press the Back Space key.

2.	(Optional) To add an additional ID query, enter one of the boolean algebraic operators AND, OR, or NOT, enter a search operator, and then enter the additional ID number.

3.	(Optional) Repeat Step 2 as needed.

4.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To use a different graphical query in the Query Builder

1.	Click Read Structure. (If necessary, change directories.)

2.	Select the file name of the query of your choice.

3.	Click OK. You see the file name in the Structures list box.

4.	Select the unwanted query, and then press the Back Space key. (Leave the cursor at the position of the deleted file name.)

5.	Double click the file name of your choice in the Structures list box.

6.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


Transfer to ISIS/Draw


Transfer the Query Back to ISIS/Base

Note: If you are in ISIS/Draw and do not see the icon pictured above, do the following: Select the query and choose Edit > Copy. Then, switch to ISIS/Base and click the Query button. Click the appropriate structure box or column on the form, then choose Edit > Paste.


To enter a single ID number

1.	Select the box or table cell on the form in ISIS/Base that will hold your ID query (if not selected).

2.	Do one of the following:

*	If your ID number contains numbers without text, enter the search operator = (an equal sign), enter a space, and then enter the ID number.

*	If your ID number contains both numbers and text, enter the search operator LIKE, enter a space, and then enter the ID number in double quotes.

Note: Your ID number can contain wildcards. (ID numbers that contain text or wildcards require the search operator LIKE and the double quotes.)


To enter any set of ID numbers

Use this procedure to enter a set of ID numbers in any order into the individual table cells on the form in ISIS/Base. This set of ID numbers is a single ID query.

1.	Click a table cell on the form in ISIS/Base that will hold one of the ID numbers (if not selected).

2.	Do one of the following:

*	If your ID number contains numbers without text, enter a search operator, enter a space, and then enter the ID number.

*	If your ID number contains both numbers and text, enter the search operator LIKE, enter a space, and then enter the ID number in double quotes. You can enter a partial ID number with at least one wildcard.

3.	(Optional) Click another table cell that will hold an ID number and repeat Step 2. You can enter a maximum of 25 ID numbers into individual table cells on the form.


To enter a set of ID numbers from the Clipboard

This procedure assumes that you have a set of ID numbers from any ASCII text editor. You enter a set of ID numbers into the individual table cells on the form in ISIS/Base. The set of ID numbers is a single ID query. Examples

1.	Select the box or table cell on the form in ISIS/Base that will hold your ID query (if not selected).

2.	Do one of the following:

*	If your ID number contains numbers without text, enter a search operator (but do not enter the search operator LIKE), enter a space, copy an ID number from the ASCII text editor, and then choose Edit > Paste.

*	If your ID number contains both numbers and text, enter the search operator LIKE, enter a space, copy an ID number from the ASCII text editor, choose Edit > Paste, and then place double quotes around the ID number.

3.	(Optional) Click another table cell that will hold an ID number and repeat Step 2. You can enter a maximum of 25 ID numbers into individual table cells on the form.

4.	(Optional) To delete unwanted text from a box or table cell, select the text, and then press the Back Space key as necessary.


To enter a specific range of ID numbers

Use this procedure to retrieve records that fall between two ID numbers. The results include the two ID numbers in your query.

1.	Select the box or table cell on the form in ISIS/Base that will hold your ID query (if not selected).

2.	Enter the search operator BETWEEN, and then enter a space.

3.	Enter the ID number of lower value. If the ID number contains text or a wildcard, place double quotes around the ID number.

4.	Enter a space.

5.	Enter the ID number of higher value. If the ID number contains text or a wildcard, place double quotes around the ID number.


To enter any set of ID numbers

Use this procedure to enter a set of ID numbers in any order into the individual table cells on the form in ISIS/Base. This set of ID numbers is a single ID query.

1.	Click a table cell on the form in ISIS/Base that will hold one of the ID numbers (if not selected).

2.	Do one of the following:

*	If your ID number contains numbers without text, enter a search operator, enter a space, and then enter the ID number.

*	If your ID number contains both numbers and text, enter the search operator LIKE, enter a space, and then enter the ID number in double quotes. You can enter a partial ID number with at least one wildcard.

3.	(Optional) Click another table cell that will hold an ID number and repeat Step 2. You can enter a maximum of 25 ID numbers into individual table cells on the form.


To enter a set of ID numbers from the Clipboard

This procedure assumes that you have a set of ID numbers from any ASCII text editor. You enter a set of ID numbers into the individual table cells on the form in ISIS/Base. The set of ID numbers is a single ID query. Examples

1.	Select the box or table cell on the form in ISIS/Base that will hold your ID query (if not selected).

2.	Do one of the following:

*	If your ID number contains numbers without text, enter a search operator (but do not enter the search operator LIKE), enter a space, copy an ID number from the ASCII text editor, and then choose Edit > Paste.

*	If your ID number contains both numbers and text, enter the search operator LIKE, enter a space, copy an ID number from the ASCII text editor, choose Edit > Paste, and then place double quotes around the ID number.

3.	(Optional) Click another table cell that will hold an ID number and repeat Step 2. You can enter a maximum of 25 ID numbers into individual table cells on the form.

4.	(Optional) To delete unwanted text from a box or table cell, select the text, and then press the Back Space key as necessary.


Examples

You can either type in a single query per table cell or paste a single query per table cell from the Clipboard (from any ASCII text editor):

Note: You cannot paste several queries into different table cells at the same time.


Examples

Paste a single query per table cell from the Clipboard (from any ASCII text editor):

Note: You cannot paste several queries into different table cells at the same time.


Examples

You can either type in a single query per table cell or paste a single query per table cell from the Clipboard (from any ASCII text editor).

Note: You cannot paste several queries into different table cells at the same time.


Examples

Paste a single query per table cell from the Clipboard (from any ASCII text editor):

Note: You cannot paste several queries into different table cells at the same time.


To obtain an SSS/Biopoly query

SSS/Biopoly queries contain a fragment. You search for biopolymers that contain your query wholly within a larger, stored biopolymer. The matching residues might be anywhere within the stored biopolymer. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the MOLSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.

*	Paste a query that you have on the Clipboard.


To paste a query from the Clipboard

Use this procedure to paste a biopolymer query that is on the Clipboard into ISIS/Base.

1.	Click the box or table cell on the form that will hold your biopolymer query.

2.	Choose Edit > Paste.


Examples

The biopolymer Somatostatin with contracted residues:

Examples of fragments of Somatostatin with contracted residues:


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a Biopolymer Fragment or

Specifying Query Features on Atoms/Bonds or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


To import an existing query from a molfile

Use this procedure to import a single biopolymer query from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected biopolymer query is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a biopolymer query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected biopolymer query is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the biopolymer that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Biopolymer Fragment or

Specifying Query Features on Atoms/Bonds or

Specifying Stereochemistry.

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain an SSS/Biopoly query

SSS/Biopoly queries contain a fragment. You search for biopolymers that contain your query wholly within a larger, stored biopolymer. The matching residues might be anywhere within the stored biopolymer. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the MOLSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.

*	Paste a query that you have on the Clipboard.


Examples

The biopolymer Somatostatin with contracted residues:

Examples of fragments of Somatostatin with contracted residues:


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a Biopolymer Fragment or

Specifying Query Features on Atoms/Bonds or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


To import an existing query from a molfile

Use this procedure to import a single biopolymer query from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected biopolymer query is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a biopolymer query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected biopolymer query is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the biopolymer that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Biopolymer Fragment or

Specifying Query Features on Atoms/Bonds or

Specifying Stereochemistry.

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


To obtain a CFS/Biopoly query

CFS/Biopoly queries contain a fragment or unattached atoms and/or bonds with specific spatial restrictions (3D constraints). You search for biopolymers with functional groups that are torsionally fit to match your query. Examples

Caution: A CFS/Biopoly query must contain at least one of the following: distance, angle, dihedral angle, linearity constraint, planarity constraint, or submodel. If you use a CFS/Biopoly query that does not meet these requirements, you see an error message when you perform the search.

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the MODELSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Create a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.

*	Paste a query that you have on the Clipboard.


Examples

Endothelin is retrieved from the ISISPDB demo database with a query that specifies the retrieval of all biopolymers with reduced sulfur groups that are between 1 and 4 Angstroms apart:


To create a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a Biopolymer Fragment or

Drawing Unattached Atoms/Bonds and Functional Groups or

Specifying 2D Query Features on Atoms/Bonds or

Specifying Chemical Environments or

Specifying 3D Query Features or

Specifying Rgroup Query Features or

3.	Transfer the query back to ISIS/Base.


Drawing Unattached Atoms/Bonds and Functional Groups

You can add structural constraints to biopolymer fragments or to unattached atoms, bonds or functional groups to create your query.

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To restore an existing query from the database

You can restore a biopolymer query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MODELSTRUCTURE box (if not highlighted).

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected biopolymer is restored into your form.


To import an existing query from a molfile

Use this procedure to import a biopolymer query from a molfile that was created in ISIS or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MODELSTRUCTURE box (if not highlighted).

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). The name of the file appears in the Open File Name text box.

5.	Click OK (Mac=Open). The selected biopolymer is imported into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MODELSTRUCTURE box that contains the biopolymer that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Biopolymer Fragment or

Drawing Unattached Atoms/Bonds and Functional Groups or

Specifying 2D Query Features on Atoms/Bonds or

Specifying Chemical Environments or

Specifying 3D Query Features or

Specifying Rgroup Query Features or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


Specifying Query Features on Atoms/Bonds

A query feature is a restriction on an atom and/or a bond in residues of a biopolymer that specifies the retrieval of certain biopolymer records from an ISIS/Base database.

Click one of the following:

*	Specifying atom query features

*	Specifying bond query features


To enter a text/numeric SBF query

Use this procedure to enter a new text/numeric string (a query) to the boxes and table cells on the form. If you enter more than one query into a single form, ISIS joins your query strings automatically with the boolean algebraic operator AND.

1.	Select the box or table cell of your choice (if not highlighted).

2.	Enter the search operator.

3.	Enter a space.

4.	Enter the text and/or numeric values that you want to find. You can enter a maximum of 25 queries into the same table. Examples

Notes: (1) You can also enter a partial query with at least one wildcard. (Do not use wildcards with a partial formula query.) (2) Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

5.	(Optional) Repeat Steps 1 through 4 as needed.

See also:

To delete characters from the query

To edit the characters of an existing query


To enter a text/numeric SBF query

Use this procedure to enter a new text/numeric string (a query) to the boxes and table cells on the form. If you enter more than one query into a single form, ISIS joins your query strings automatically with the boolean algebraic operator AND.

1.	Select the box or table cell of your choice (if not highlighted).

2.	Enter the search operator.

3.	Enter a space.

4.	Enter the text and/or numeric values that you want to find. You can enter a maximum of 25 queries into the same table. Examples

Notes: (1) You can also enter a partial query with at least one wildcard. (Do not use wildcards with a partial formula query.) (2) Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

5.	(Optional) Repeat Steps 1 through 4 as needed.

See also:

To delete characters from the query

To edit the characters of an existing query


To edit a text/numeric SBF query

1.	(Optional) To delete unwanted text from a box or table cell, select the text, and then press the Back Space key.

2.	(Optional) To add text to the current query, click the box or table cell that contains a query string, and then enter the characters of your choice in the correct format for text/numeric strings.

3.	(Optional) To add another query string to a different box or a different table cell, click the box or table cell of your choice (if not highlighted), enter a search operator, enter a space, and then enter the target text and/or numeric values of your choice. (You can also enter partial text and/or numeric values and at least one wildcard.) Examples


To enter a text/numeric QB query

The following procedure allows you to enter a typical text/numeric query string into the Query Builder text box. However, this procedure is very general. To obtain the correct syntax for the specific search that you want to do in the Query Builder, click The ISIS/Base Chemical Searches -- and How to do Them, click the specific QB search that you need, click Searching Concepts /Examples, and read the section Specifying a QB Query.

1.	Double-click a database field name in the Database Fields box.

2.	Double-click a search operator in the Operator box.

3.	Type the text or numeric data criteria in the Query String text box.


To enter a text/numeric QB query

The following procedure allows you to enter a typical text/numeric query string into the Query Builder text box. However, this procedure is very general. To obtain the correct syntax for the specific search that you want to do in the Query Builder, click The ISIS/Base Chemical Searches -- and How to do Them, click the specific QB search that you need, click Searching Concepts /Examples, and read the section Specifying a QB Query.

1.	Double-click a database field name in the Database Fields box.

2.	Double-click a search operator in the Operator box.

3.	Type the text or numeric data criteria in the Query String text box.


To edit a text/numeric QB query

Use this procedure to edit an existing query in the Query Builder in ISIS/Base.

1.	(Optional) To delete unwanted text, select the text, and then press the Back Space key.

2.	(Optional) To add another query to your existing query string, enter a boolean algebraic operator, and then enter a query string that specifies either

text and/or numeric data or

a 2D structure.

3.	(Optional) Repeat Step 2 as needed.

4.	(Optional) Use a different graphical query than the one in the current query string.

5.	(Optional) Edit the current graphical query.


Viewing Search Results

The following procedure allows you to view the search results. However, it does not provide you with all the functionality that is available in ISIS for viewing search results. To obtain all the functionality, click The ISIS/Base Chemical Searches -- and How to do Them, and then click the specific search that you did. You see a help screen that contains all of the information that you need.

1.	Click the Browse mode (if not highlighted). You see the first record displayed on the boxes and tables in your form.

2.	To see how many records you retrieved, check the status bar.

3.	(Optional) Edit the chemical display of structures.

4.	Use [image], [image], [image], [image], and [image] to display the record that you want to view.

Keyboard Equivalents

See also:

To view stored search results

Viewing truncated data


Specifying Search Operators

The way that you specify a search operator depends entirely on the ISIS search that you do and the database that you use.

To obtain specific help, click here: The ISIS/Base Chemical Searches - and How to do Them, and click the specific search that you need. You see a help screen that contains all of the information that you need to specify a search operator.

Note: There are, for example, six types of substructure searches (SSS) on the ISIS/Base Chemical Searches - and How to do Them screen. Whether you search a remote OR local database for molecule, 3D structure, OR reaction records is significant when you decide on a search. Thus, your choice must be accurate.


Specifying Query Features on a Reaction

A query feature on a reaction is a restriction on the reacting centers or on the spatial arrangement of stereo bonds that specifies the retrieval of certain types of reaction records from the database.

For example, you can use the reacting center query feature MAKE/BREAK to specify that a bond is formed in the product of the records retrieved.

You can use the stereo bond query feature RET to specify that an Up bond is retained in the product of the records retrieved.

Note: These query features are solely for searching a remote database and cannot be used to search a local database.

Click one of the following:

*	To specify reacting center query features

*	To specify stereo bond query features


Searching for Records That Contain No Structures

No-structure records contain data only rather than both structures and data. To retrieve a no-structure record in a local or a remote database, you must search for it with data as your query. For example, enter a query that contains a specific REGNO or a compound name.

Note: You might see a no-structure label in a local database record. This label is solely for display purposes and is not searchable.


To restore a graphical query

You can restore a structure query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

Note: You can also import a graphical query into another remote-access file or into another program.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the query (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Do one of the following:

*	If your query is a molecule or substructure or a reaction component without a reaction arrow, choose Database > Restore Molecule.

*	If your query is a reaction or a reaction substructure or a reaction component with a reaction arrow, choose Database > Restore Reaction.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open).


To import a graphical query

You can import a molecule or substructure query as a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II. Or, you can import a reaction or a reaction substructure query as a rxnfile that was created in CPSS, ISIS, or REACCS.

Note: You can also restore a graphical query that you previously saved as an object in the remote-access file of your database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the table cell or box that will hold the query (if not highlighted). In an MDL database for example, the field for a reactant without a reaction arrow is RXN>reactant_link>MOL>MOLSTRUCTURE.

3.	Do one of the following:

*	If your query is a molecule or substructure or a reaction component without a reaction arrow, choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

*	If your query is a reaction or a reaction substructure or a reaction component with a reaction arrow, choose File > Import > Rxnfile. (To retrieve a PC-rxnfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open).


To edit a graphical query

The way that you edit a graphical query depends entirely on the ISIS search that you want to do with the edited query.

To obtain specific help, click here: The ISIS/Base Chemical Searches - and How to do Them, and click the specific search that you need. You see a help screen that contains all of the information that you need to edit your graphical query.

Note: There are, for example, six types of substructure searches (SSS) on the ISIS/Base Chemical Searches - and How to do Them screen. Whether you search a remote OR local database for molecule, 3D structure, OR reaction records is significant when you decide on a search. Thus, your choice must be accurate.


To restore a form

You can restore a form that you previously saved as an object in the remote-access file of your database.

Note: You can also import a form from another remote-access file or another program.

This procedure assumes that a database is already open.

1.	Choose File > Open Form.

2.	Click the name of the form that you want to restore.

3.	(Optional) To see this form each time you open the database, you require this setting: Set Default

4.	Click OK.


To import a form

You can import a form from another remote-access file or another program.

Note: You can also restore a form that you previously saved as an object in the remote-access file of your database.

This procedure assumes that a database is already open.

1.	Choose File > Import > Form. (To retrieve a PC-form file on the Macintosh, press and hold the Option key while you complete this step.)

2.	Navigate to where the form is located on your disk, and then click the form name in the Files list box.

3.	Click OK. The form appears in the ISIS/Base window. (Macintosh = if a PC-form does not appear, it probably was not translated correctly using the Apple File Exchange.)

Note: If you import a form from a database that contains different database fields, you need to edit the existing form to connect the boxes and table columns new database fields.

4.	To save the form in the current database, choose File > Save Form. Enter a name for the form, and then click OK.


Searching With Salts

You can use a salt as a query or find salts in your database:

*	A remote FLEX search allows you to either find all salt forms of a specific structure with your salt query or find all structures that contain a specific counterion with your counterion query.

*	A remote PARENT search allows you to find the parent structure of your salt query.

Click one of the following:

*	A FLEX Search in a Remote Molecule Database

*	A FLEX Search in a Remote Reaction Database

*	A PARENT Search in a Remote Molecule Database

*	A PARENT Search in a Remote Reaction Database


Searching Examples for Exact Match Searches

Click one of the following items:

MEXACT search (local molecule records)

MEXACT search (local reaction records)

MEXACT search (remote molecule records)

MEXACT search (remote reaction records)

REXACT/Comp search (remote reaction records)

REXACT/Rxn search (local reaction records)

REXACT/Rxn search (remote reaction records)

3DEXACT search (local 3D structure records)

3DEXACT search (remote 3D structure records)


Searching Examples for Flexmatch Searches

Click one of the following items:

FLEX search (remote molecule records)

FLEX search (remote reaction records)


Searching Examples for Isomer Searches

Click one of the following items:

ISOMER search (remote molecule records)

ISOMER search (remote reaction records)


Searching Examples for Parent Searches

Click one of the following items:

PARENT search (remote molecule records)

PARENT search (remote reaction records)


Searching Examples for Tautomer Searches

Click one of the following items:

TAUT search (remote molecule records)

TAUT search (remote reaction records)


To allow a specific number of attachments

This procedure is for these remote searches only. Use this procedure to specify the number of allowed non-hydrogen attachments (substituents) on an atom.

Examples:	s0 	s1 	s2 	s3 	s4 	s5 	s6 	s*

1.	Select the atoms that you want to specify as having non-hydrogen attachments.

2.	Double-click the selected atoms.

3.	Click the Query Atom tab.

4.	Click the Substitution count box.

5.	Do one of the following:

*	To specify no non-hydrogen attachments, choose 0.

*	To specify exactly 1, 2, 3, 4, or 5 non-hydrogen attachments, choose 1, 2, 3, 4, or 5.

*	To specify at least 6 non-hydrogen attachments, choose 6.

*	To specify solely those existing non-hydrogen attachments that you see, choose * (asterisk).

*	To remove the existing attachment notation, choose Off.

Note: Count double or triple bonds as one attachment.

6.	Click OK.

See also:

To transfer the query back to ISIS/Base


To specify reacting center query features

This procedure is for these remote searches only. Use this procedure to mark the reacting centers on bonds.

1.	Click

ISIS/Draw checks if the reaction is valid for mapping, and that there is only one reaction present in the sketch. If the reaction is not valid for mapping, or if there are more than one reaction, you see a message that tells you to use Chem Inspector.

2.	Click the bond on which to mark a reacting center. Each time you click the bond, you see a different reacting center mark. Keep clicking the bond until you see the desired reacting center mark:

*	X: The bond must not change

*	#: The bond changes unspecifically (can form, break, or change its bond type)

*	|: The bond changes its bond type

*	||: The bond is either formed or broken

*	|||: The bond s either formed or broken and changes its bond type

See also:

Specifying an Atom-Atom Map on a Reaction

To transfer the query back to ISIS/Base


Specifying Stereochemistry

Click one of the following items:

Stereoconfiguration of Bonds: Up or Down or Either  Cis or Trans

Stereoconfiguration of Molecules: Relative or Absolute


Editing Stereochemistry

Click one of the following items:

Stereoconfiguration of Bonds: Up or Down or Either  Cis or Trans

Stereoconfiguration of Molecules: Relative or Absolute


Editing Up, Down, or Either Bonds

Click one of the following items:

*	To change an unspecified bond to an Up or a Down bond

*	To change an Up or a Down bond to an unspecified bond

*	To change an Up or a Down bond to a single, a double, or a triple bond

*	To change the direction of an Up or a Down bond


Specifying AND, OR, and NOT in the Query Builder

In the Query Builder, you can connect queries with the boolean algebraic operators AND, OR, and NOT. For example, to find all molecules that contain indole and all molecules with a melting point below 190 degrees, enter:

MOL>MOLSTRUCTURE SSS indole AND MOL>MELTING.POINT < 190

To use the boolean operator NOT, you must also enclose the query string in parentheses. For example, to find all records that contain no data on melting points, enter:

NOT (MOL>MELTING.POINT EXISTS)

To combine a query that contains NOT with other queries, you must use AND NOT. For example, to find all molecules that contain indole but not molecules with a melting point below 190, enter:

MOL>MOLSTRUCTURE SSS indole AND NOT (MOL>MELTING.POINT < 190)


Specifying AND in a Search By Form Search

If you enter more than one query into a single form, ISIS joins your query strings automatically with the boolean algebraic operator AND. You can then conduct a Search By Form (SBF) search. Examples


Maximum Number of Queries in a Single Search

For a single ID search or a single Search By Form (SBF) search, the maximum number of query strings and/or structure queries that you can enter into a form is 25.

For a single Query Builder (QB) search, the maximum number of characters that you can enter into the Query Builder (separated by boolean operators AND, OR, or NOT) is 1000.

Note: If you enter more than the maximum number of query strings and/or structure queries allowed, ISIS ignores them during a search.


Obtaining a Suitable Form

Every search needs a suitable form. Check the contents of your current form to see if it is suitable.

When you open a search domain that you want to search, you should see a default form. If you do not see a default form, or if the default form is not suitable, you have four options.

Click one of these 4 items:

*	Restoring a form

*	Creating a form

*	Editing an existing form

*	Importing a form


Checking the Contents of the Current Form

Check that the current form contains the database fields that you want to search and the database fields that you want to view after the search.

To check the contents of the current form:

1.	Click Forms. You see all the database fields that are connected to each box or table column in the form.

2.	Check that you have the database field to hold your query and/or to hold the information that you want to view after you conduct a search.

3.	(Optional) Display the reaction conditions within the reactions retrieved. After you view the procedure, click Back to return to this screen.

Note: If your current form does not contain the database fields that you want to search and view, either edit the form, create a new form, or see your ISIS Administrator.


Obtaining Different Search Results with Multiple Queries in Tables

When you conduct a single search in a hierarchical database with multiple queries that are on different lines of a table, you retrieve different results from multiple queries that are on the same line of a table (or in boxes).

For more information, see:

Molecule records: SBF in a remote database or SBF in a local database

Reaction records: SBF in a remote database or SBF in a local database

3D Structure records: SBF in a remote database or SBF or in a local database


Example

You might want to find literature references in a reaction database by an author named R. L. Smith. To do this, you can conduct a Search By Form (SBF) with the query LIKE "%R. L. SMITH%" in a box or table that is connected to the field RXN>VARIATION>LITTEXT>littext_ref.

Each reaction record can have several variation subrecords, and each variation subrecord can contain multiple literature-reference (LITTEXT) subrecords. ISIS retrieves all reactions that contain at least one literature reference that matches your query. However, the reactions that you retrieve might also contain subrecords that do not match your query.

To display only the variations and literature references that match your query, you must filter the search results.


Obtaining Different Search Results with Multiple Queries in Tables

When you conduct a single search in a hierarchical database with multiple queries that are on different lines of a table, you retrieve different results from multiple queries that are on the same line of a table (or in boxes).

For more information, see Section 37.1.3 in Searching Concepts/Examples.


Obtaining Different Search Results with Multiple Queries in Tables

When you conduct a single search in a hierarchical database with multiple queries that are on different lines of a table, you retrieve different results from multiple queries that are on the same line of a table (or in boxes).

For more information, see Section 38.1.3 in Searching Concepts/Examples.


Obtaining Different Search Results with Multiple Queries in Tables

When you conduct a single search in a hierarchical database with multiple queries that are on different lines of a table, you retrieve different results from multiple queries that are on the same line of a table (or in boxes).

For more information, see Section 39.1.3 in Searching Concepts/Examples.


Obtaining Different Search Results with Multiple Queries in Tables

When you conduct a single search in a hierarchical database with multiple queries that are on different lines of a table, you retrieve different results from multiple queries that are on the same line of a table (or in boxes).

For more information, see Section 40.1.3 in Searching Concepts/Examples.


Obtaining Different Search Results with Multiple Queries in Tables

When you conduct a single search in a hierarchical database with multiple queries that are on different lines of a table, you retrieve different results from multiple queries that are on the same line of a table (or in boxes).

For more information, see Section 41.1.4 in Searching Concepts/Examples.


Obtaining Different Search Results with Multiple Queries in Tables

When you conduct a single search in a hierarchical database with multiple queries that are on different lines of a table, you retrieve different results from multiple queries that are on the same line of a table (or in boxes).

For more information, see Searching Concepts/Examples.


Registering, Deleting or Updating Records

For information on registering information in a database, updating records, or deleting records in ISIS, see The ISIS/Base Database Maintenance manual.


Viewing 2D and 3D Records

In REACCS or MACCS-II, to view both the 2D and 3D structures, you need to use the Xfm (transform) command. ISIS does not contain this command because the form allows you to view both structures at the same time if you connect a box to the database field that contains a 2D structure and a box to the database field that contains a 3D structure. (In ISIS, you can view the search results only if the boxes or tables on your form are connected to the database fields that you want to view.)


To delete a database object

In ISIS, you can delete the following objects from your database: A search query, a list of search results, a form, sorting instructions, and a PL program (Procedural Language).

Caution: When you delete an object, you cannot retrieve it again. We strongly recommend that you backup your database or export the object to a file on your hard disk before you delete the object.

This procedure assumes that the database with the objects that you want to delete is open:

1.	Choose Database > Object Manager.

2.	Click the type of object in the Object Type box that you want to delete. For example, click PL programs.

3.	Click the file name of the object that you want to delete. If you do not see a name in the list box, then no database object exists for your selection. (If you selected the PL program, you can see whether the program is executed on startup.)

4.	Click Delete. The object is deleted from the database immediately.(You cannot delete an object that has read-only status.)

5.	Click Close.


To modify a database object

In ISIS, you can modify the following objects that are stored in your database: A search query, a list of search results, a form, sorting instructions, and a PL program (Procedural Language).

Modify the name or description of an object or change the status of the object to either read-write or read only. In addition, a list, structure, or query can be either temporary or permanent.

This procedure assumes that the database with the objects that you want to modify is open:

1.	Choose Database > Object Manager.

2.	Click the type of object in the Object Type box that you want to modify. For example, click PL programs.

3.	Click the file name of the object that you want to modify. If you do not see a name in the list box, then no database object exists for your selection. (If you selected the PL program, you can see whether the program is executed on startup.)

4.	Click Modify.

5.	Do one of the following:

*	Click in the Name box and edit the name. (You cannot modify the name of an object that has a read-only status.)

*	Click in the Description box and edit or enter the description. (You cannot modify the description of an object that has a read-only status.)

*	To specify that the object cannot be modified, set [image] Read-Only.

*	To specify that the object can be modified, set [image] Read-Only.

*	For lists, structures, and queries only:

-	To specify that the object is stored in the database after you close ISIS/Base, set [image] Permanent.

-	To specify that the object is not stored in the database after you close ISIS/Base (temporary), set [image] Permanent.

Note: You cannot modify a list that was created in a remote database.

6.	Click OK.

7.	Click Close.


To view a database object

In ISIS, you can view the following objects that are stored in your database: A search query, a list of search results, a form, sorting instructions, and a PL program (Procedural Language).

View any of the following: The description of the object (if previously saved), the time and date that the object was last saved, whether the object is read-only or read-write, permanent or temporary (lists, structures, or queries only),

This procedure assumes that the database with the objects that you want to view is open:

1.	Choose Database > Object Manager.

2.	Click the type of object in the Object Type box that you want to view. For example, click PL programs.

3.	To view the objects, click the file name of the object that you want to view. (Click one name at a time.) If you do not see a name in the list box, then no database object exists for your selection.

4.	Click Close.


To obtain an SSS3D/Biopoly query

SSS3D/Biopoly queries contain your query as a 3D biopolymer structure. You search for 3D biopolymers that contain your query wholly within another structure. Examples

1.	Click the Query mode (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

2.	Click the MODELSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Create a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples

A 3D biopolymer query can contain Rgroups, 2D query features, 3D query features, and submodels:


To create a new SSS3D query

Searching Concepts/Examples

1.	(Optional) Obtain a 3D structure to use in a submodel.

2.	Transfer to ISIS/Draw.

3.	(Optional) Create the submodel portion of the query.

4.	Draw the remaining features of the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing a Biopolymer Fragment or

Specifying Query Features on Atoms/Bonds (2D Query Features) or

Specifying 3D Query Features

Specifying Chemical Environments or

5.	Transfer the query back to ISIS/Base.


To import an existing query from a molfile

Use this procedure to import a single biopolymer query from a molfile that was created in CPSS, ISIS, REACCS, or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected biopolymer query is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a biopolymer query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected biopolymer query is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the biopolymer that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing a Biopolymer Fragment or

Specifying Query Features on Atoms/Bonds (2D Query Features) or

Specifying 3D Query Features

Specifying Chemical Environments or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


Searching by SEMA Name

The SEMA name is an encoded identifier that uniquely defines a molecule with respect to its atoms, their connectivity, stereochemistry, charge, and isotopic properties. The following SEMA searches allow you to search for unique structures (including stereoisomers as distinct structures):

Molecule records: = and ISOMER search operators in a QB search of a remote database

Reaction records: = and ISOMER search operators in a QB search of a remote database

Note: The SEMA name does not contain information on attached data, polymers, ordered mixtures, or unordered mixtures. Consequently, these features are ignored when you search by SEMA name.


To obtain a QB query and execute the search

QB queries can contain any combination of text/numeric strings and/or the file names of 2D structures or 2D substructures in the Query Builder dialog box. You can also connect queries with the boolean algebraic operators AND, OR, and NOT. Example

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Choose Search > Query Builder.

4.	(Optional) To delete any existing text, click Clear.

5.	Do one of the following:

*	Enter a new query

*	Obtain an existing query.

6.	(Optional) To create a new graphical component that you can add to your query, draw a new query.

7.	Click OK.

See also:

To abandon the search


To enter a new query

Searching Concepts/Examples

1.	Do one of the following:

*	Enter a query string that specifies text and/or numeric data

*	Enter a query string that specifies a 2D structure

2.	(Optional) To delete unwanted text, select the text, and then press the Back Space key.

3.	(Optional) To add another query string, enter one of the boolean algebraic operators AND, OR, or NOT, and then repeat Step 1.

4.	(Optional) Repeat Step 3 as needed.

5.	Click OK.


To obtain an existing query

Use this procedure to restore a text/numeric query from a file in the database that is open currently in ISIS/Base.

1.	Choose Search > Restore Query.

2.	Click the name of an existing file in the Select Object list box.

3.	Click OK (Mac=Open). The selected file is restored.

4.	Click OK.

5.	Choose Search > Query Builder. You see the existing query.

6.	(Optional) You can edit the existing query.


To enter a query string that specifies a 2D structure

Searching Concepts/Examples

1.	Double-click MOLSTRUCTURE in the Database Fields box.

2.	Double-click a search operator in the Operator box.

3.	Do one of the following:

*	To enter a structure that is on the form in ISIS/Base, double-click query in the Structures box.

*	To enter a structure that was saved in the database, double-click the name of the structure in the Structures box.

*	To enter a molfile, click Read Structure, enter the name of the structure in the Files text box, click OK, and then double-click the name of the structure in the Structures box.

You see the structure in the Structure Picture box.

4.	(Optional) Specify options for MSIMILAR or FLEXMATCH.

5.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To enter a query string that specifies a 2D structure

Searching Concepts/Examples

1.	Double-click MOLSTRUCTURE in the Database Fields box.

2.	Double-click a search operator in the Operator box.

3.	Do one of the following:

*	To enter a structure that is on the form in ISIS/Base, double-click query in the Structures box.

*	To enter a structure that was saved in the database, double-click the name of the structure in the Structures box.

*	To enter a molfile, click Read Structure, enter the name of the structure in the Files text box, click OK, and then double-click the name of the structure in the Structures box.

You see the structure in the Structure Picture box.

4.	(Optional) Specify options for MSIMILAR or FLEXMATCH.

5.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


Specifying Options for MSIMILAR or FLEXMATCH Operators

If you specified the MSIMILAR or FLEXMATCH operator, you must specify the options for that operator.

Click one of the following:

*	To specify options for the MSIMILAR operator

*	To specify options for the FLEXMATCH operator


To specify options for the MSIMILAR operator

Searching Concepts/Examples

This procedure assumes that the Query Builder dialog box is open, and that you have already specified the MOLSTRUCTURE database field, MSIMILAR operator, and 2D structure.

1.	Type a double quote (").

2.	Do one of the following:

*	To retrieve molecules with the same structural complexity as your query, enter no additional characters.

*	To retrieve molecules with greater structural complexity than your query, type super.

*	To retrieve molecules with less structural complexity than your query, type sub.

3.	Type a number between 0 and 100. The higher the number, the more the records that you retrieve resemble your query.

4.	Type a double quote (").

5.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


Example

Dead topic?

The following query specifies a search that retrieves molecules with the same structural complexity as your query, with a structural similarity value of 60:

The following query specifies a search that retrieves molecules with greater structural complexity than your query, with a structural similarity value of 80:


To specify options for the FLEXMATCH operator

Searching Concepts/Examples

This procedure assumes that the Query Builder dialog box is open, and that you have already specified the MOLSTRUCTURE database field, the FLEXMATCH operator, and the 2D structure that you want.

1.	Type a double quote (").

2.	Type a three-letter code that specifies a flexmatch parameter.

3.	(Optional) To specify another flexmatch parameter, type a slash (/) and then type the three-letter code.

4.	(Optional) To enter more flexmatch parameters, repeat Step 3.

5.	Type a double quote (").

6.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To enter a query string that specifies a 2D structure

Searching Concepts/Examples

1.	Double-click MOLSTRUCTURE in the Database Fields box.

2.	Double-click a search operator in the Operator box.

3.	Do one of the following:

*	To enter a structure that is on the form in ISIS/Base, double-click query in the Structures box.

*	To enter a structure that was saved in the database, double-click the name of the structure in the Structures box.

*	To enter a molfile, click Read Structure, enter the name of the structure in the Files text box, click OK, and then double-click the name of the structure in the Structures box.

You see the structure in the Structure Picture box.


To enter a query string that specifies text or numeric data

Searching Concepts/Examples

1.	Double-click a database field name in the Database Fields box. You see the field in the Query string text box.

2.	Double-click a search operator in the Operator box. You see the operator in the Query string text box.

3.	Type the text or numeric data criteria in the Query string text box. You can use wildcards. You can enter a maximum of 1000 characters. (Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.)

4.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


Examples

To find all molecules that contain benzaldehyde AND all molecules with a melting point greater than 220 degrees, enter:

To find all molecules that contain both indole and a molecular weight greater than 200 but NOT those molecules with a melting point below 190, enter:


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. If you need help, click:

Drawing a 2D Substructure or

Drawing a 2D Structure or

Specifying Query Features or

Specifying Stereochemistry

Drawing Mixtures: MDL Requirements for Database Searching and Registration

3.	Transfer the query back to ISIS/Base.


Drawing a 2D Substructure

A 2D substructure is a fragment of a molecule that is drawn without regard to its 3D spatial arrangement. You retrieve molecules that contain your 2D substructure query embedded wholly within them. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Drawing Mixtures: MDL Requirements for Database Searching and Registration

*	Verifying the Chemistry of Sketches


Drawing a 2D Structure

A 2D structure is a molecule that is drawn without regard to its 3D spatial arrangement. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Drawing Mixtures: MDL Requirements for Database Searching and Registration

*	Verifying the Chemistry of Sketches


To edit an existing query in the Query Builder

Searching Concepts/Examples

Use this procedure to edit an existing query in the Query Builder in ISIS/Base.

1.	(Optional) To delete unwanted text, select the text, and then press the Back Space key.

2.	(Optional) To add another query to your existing query string, enter a boolean algebraic operator, and then enter a query string that specifies either

text and/or numeric data or

a 2D structure.

3.	(Optional) Repeat Step 2 as needed.

4.	(Optional) Use a different graphical query than the one in the current query string.

5.	(Optional) Edit the current graphical query.

6.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


Boolean Algebraic Operators

The boolean algebraic operators AND, OR, and NOT allow you to join queries together so that you can conduct one single search.


To edit the current graphical query

Searching Concepts/Examples

1.	Click Cancel.

2.	Click Search > Restore Query, and then select the query of your choice in the Select Object list box.

3.	Click OK.

4.	Click the structure. You see the structure in ISIS/Draw.

5.	Edit the query. If you need help, click:

Drawing a 2D Substructure or

Drawing a 2D Structure or

Specifying Query Features or

Specifying Stereochemistry or

Guidelines for Revising the Query.

6.	Transfer the query back to ISIS/Base.

7.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To obtain a QB query and execute the search

QB queries can contain any combination of text/numeric strings and/or the file names of 2D structures or 2D substructures in the Query Builder dialog box. You can also connect queries with the boolean algebraic operators AND, OR, and NOT. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Choose Search > Query Builder.

4.	(Optional) To delete any existing text, click Clear.

5.	Do one of the following:

*	Enter a new query

*	Obtain an existing query.

6.	(Optional) To create a new graphical component that you can add to your query, draw a new query.

7.	Click OK.

See also:

To abandon the search


To enter a new query

Searching Concepts/Examples

1.	Do one of the following:

*	Enter a query string that specifies text and/or numeric data

*	Enter a query string that specifies a 2D structure

2.	(Optional) To delete unwanted text, select the text, and then press the Back Space key.

3.	(Optional) To add another query string, enter one of the boolean algebraic operators AND, OR, or NOT, and then repeat Step 1.

4.	(Optional) Repeat Step 3 as needed.

5.	Click OK.


To enter a query string that specifies text or numeric data

Searching Concepts/Examples

1.	Double-click a database field name in the Database Fields box. You see the field in the Query string text box.

2.	Double-click a search operator in the Operator box. You see the operator in the Query string text box.

3.	Type the text or numeric data criteria in the Query string text box. You can use wildcards. You can enter a maximum of 1000 characters. (Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.)

4.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To obtain an existing query

Use this procedure to restore a text/numeric query from a file in the database that is open currently in ISIS/Base.

1.	Choose Search > Restore Query.

2.	Click the name of an existing file in the Select Object list box.

3.	Click OK (Mac=Open). The selected file is restored.

4.	Click OK.

5.	Choose Search > Query Builder. You see the existing query.

6.	(Optional) You can edit the existing query.


To enter a query string that specifies a 2D structure

Searching Concepts/Examples

1.	Double-click MOLSTRUCTURE in the Database Fields box.

2.	Double-click a search operator in the Operator box.

3.	Do one of the following:

*	To enter a structure that is on the form in ISIS/Base, double-click query in the Structures box.

*	To enter a structure that was saved in the database, double-click the name of the structure in the Structures box.

*	To enter a molfile, click Read Structure, enter the name of the structure in the Files text box, click OK, and then double-click the name of the structure in the Structures box.

You see the structure in the Structure Picture box.

4.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To enter a query string that specifies a 2D structure

Searching Concepts/Examples

1.	Double-click MOLSTRUCTURE in the Database Fields box.

2.	Double-click a search operator in the Operator box.

3.	Do one of the following:

*	To enter a structure that is on the form in ISIS/Base, double-click query in the Structures box.

*	To enter a structure that was saved in the database, double-click the name of the structure in the Structures box.

*	To enter a molfile, click Read Structure, enter the name of the structure in the Files text box, click OK, and then double-click the name of the structure in the Structures box.

You see the structure in the Structure Picture box.

4.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


Examples

To find all molecules that contain benzaldehyde AND all molecules with a melting point greater than 220 degrees, enter:

To find all molecules that contain both indole and a molecular weight greater than 200 but NOT those molecules with a melting point below 190, enter:


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. If you need help, click:

Drawing a 2D Substructure or

Drawing a 2D Structure or

Specifying Query Features or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a 2D Substructure

A 2D substructure is a portion of a molecule that is drawn without regard to its 3D spatial arrangement. You retrieve molecules that contain your 2D substructure query embedded wholly within them. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


Drawing a 2D Structure

A 2D structure is a molecule that is drawn without regard to its 3D spatial arrangement. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To edit an existing query in the Query Builder

Searching Concepts/Examples

Use this procedure to edit an existing query in the Query Builder in ISIS/Base.

1.	(Optional) To delete unwanted text, select the text, and then press the Back Space key.

2.	(Optional) To add another query to your existing query string, enter a boolean algebraic operator, and then enter a query string that specifies either

text and/or numeric data or

a 2D structure.

3.	(Optional) Repeat Step 2 as needed.

4.	(Optional) Use a different graphical query than the one in the current query string.

5.	(Optional) Edit the current graphical query.

6.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To edit the current graphical query

Searching Concepts/Examples

1.	Click Cancel.

2.	Click Search > Restore Query, and then select the query of your choice in the Select Object list box.

3.	Click OK.

4.	Click the structure. You see the structure in ISIS/Draw.

5.	Edit the query. If you need help, click:

Drawing a 2D Substructure or

Drawing a 2D Structure or

Specifying Query Features or

Specifying Stereochemistry or

Guidelines for Revising the Query.

6.	Transfer the query back to ISIS/Base.

7.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To obtain a QB query and execute the search

QB queries can contain any combination of text/numeric strings and/or the file names of graphical structures in the Query Builder dialog box. You can also connect queries with the boolean algebraic operators AND, OR, and NOT. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Choose Search > Query Builder.

4.	(Optional) To delete any existing text, click Clear.

5.	Do one of the following:

*	Enter a new query

*	Obtain an existing query.

6.	(Optional) To create a new graphical component that you can add to your query, draw a new query.

7.	Click OK.

See also:

To abandon the search


To enter a new query

Searching Concepts/Examples

1.	Do one of the following:

*	Enter a query string that specifies text or numeric data

*	Enter a query string that specifies a reaction

*	Enter a query string that specifies a reactant or product structure

2.	(Optional) To delete unwanted text, select the text, and then press the Back Space key.

3.	(Optional) To add another query string, enter one of the boolean algebraic operators AND, OR, or NOT, and then repeat Step 1.

4.	(Optional) Repeat Step 3 as needed.

5.	Click OK.


To enter a query string that specifies text or numeric data

Searching Concepts/Examples

1.	Double-click a database field name in the Database Fields box. You see the field in the Query string text box.

2.	Double-click a search operator in the Operator box. You see the operator in the Query string text box.

3.	Type the text or numeric data criteria in the Query string text box. You can use wildcards. You can enter a maximum of 1000 characters. (Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.)

4.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To obtain an existing query

Use this procedure to restore a text/numeric query from a file in the database that is open currently in ISIS/Base.

1.	Choose Search > Restore Query.

2.	Click the name of an existing file in the Select Object list box.

3.	Click OK (Mac=Open). The selected file is restored.

4.	Click OK.

5.	Choose Search > Query Builder. You see the existing query.

6.	(Optional) You can edit the existing query.


To enter a query string that specifies a reaction

Searching Concepts/Examples

1.	Double-click RXNSTRUCTURE in the Database Fields box.

2.	Double-click a search operator in the Operator box.

3.	Do one of the following:

*	To enter a reaction that is on the form in ISIS/Base, double-click rquery in the Structures box.

*	To enter a reaction that was saved in the database, double-click the name of the reaction in the Structures box.

*	To enter a rxnfile, click Read Structure, enter the name of the reaction in the Files text box, click OK, and then double-click the name of the reaction in the Structures box.

You see the reaction in the Structure Picture box.

4.	(Optional) Specify options for the RSIMILAR operator.

5.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To enter a query string that specifies a reaction

Searching Concepts/Examples

1.	Double-click RXNSTRUCTURE in the Database Fields box.

2.	Double-click a search operator in the Operator box.

3.	Do one of the following:

*	To enter a reaction that is on the form in ISIS/Base, double-click rquery in the Structures box.

*	To enter a reaction that was saved in the database, double-click the name of the reaction in the Structures box.

*	To enter a rxnfile, click Read Structure, enter the name of the reaction in the Files text box, click OK, and then double-click the name of the reaction in the Structures box.

You see the reaction in the Structure Picture box.

4.	(Optional) Specify options for the RSIMILAR operator.


To enter a query string that specifies a reactant or product structure

Searching Concepts/Examples

1.	Double-click a MOLSTRUCTURE field in the Database Fields box.

2.	Double-click a search operator in the Operator box.

3.	Do one of the following:

*	To enter a reaction component that is on the form in ISIS/Base, double-click query in the Structures box.

*	To enter a reaction component that was saved in the database, double-click the name of the reaction component in the Structures box.

*	To enter a molfile, click Read Structure, enter the name of the reaction component in the Files text box, click OK, and then double-click the name of the reaction component in the Structures box.

You see the reaction component in the Structure Picture box.

4.	(Optional) Specify options for the MSIMILAR or FLEXMATCH operator.

5.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To enter a query string that specifies a reactant or product structure

Searching Concepts/Examples

1.	Double-click a MOLSTRUCTURE field in the Database Fields box.

2.	Double-click a search operator in the Operator box.

3.	Do one of the following:

*	To enter a reaction component that is on the form in ISIS/Base, double-click query in the Structures box.

*	To enter a reaction component that was saved in the database, double-click the name of the reaction component in the Structures box.

*	To enter a molfile, click Read Structure, enter the name of the reaction component in the Files text box, click OK, and then double-click the name of the reaction component in the Structures box.

You see the reaction component in the Structure Picture box.

4.	(Optional) Specify options for the MSIMILAR or FLEXMATCH operator.


To enter a query string that specifies a reactant or product structure

Searching Concepts/Examples

1.	Double-click a MOLSTRUCTURE field in the Database Fields box.

2.	Double-click a search operator in the Operator box.

3.	Do one of the following:

*	To enter a reaction component that is on the form in ISIS/Base, double-click query in the Structures box.

*	To enter a reaction component that was saved in the database, double-click the name of the reaction component in the Structures box.

*	To enter a molfile, click Read Structure, enter the name of the reaction component in the Files text box, click OK, and then double-click the name of the reaction component in the Structures box.

You see the reaction component in the Structure Picture box.

4.	(Optional) Specify options for the MSIMILAR or FLEXMATCH operator.


Examples

To find all reactants that contain benzaldehyde AND all reactants with a melting point greater than 220 degrees, enter:

To find all reactants that contain both indole and a molecular weight greater than 200 but NOT those reactants with a melting point below 190, enter:


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. If you need help, click:

Drawing a Reaction Component Substructure or

Drawing a Reaction Component Structure or

Drawing a Reaction Substructure or

Drawing a Reaction Structure or

Specifying Query Features on a Reaction Component or

Specifying Query Features on a Reaction or

Specifying Rgroup Query Features or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Component Substructure

A reaction component substructure is a two-dimensional representation of a portion of a molecule that participates in a reaction. You retrieve reactions that contain your 2D substructure query embedded wholly within the reaction components. For example:

Note: This example displays the reacting centers.

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


Drawing a Reaction Component Structure

A reaction component structure is a 2D structure (molecule) from a reaction. For example, a product:

Note: This example displays the reacting centers.

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


Drawing a Reaction Substructure

A reaction substructure is a portion of a reaction. You retrieve reactions that contain your reaction substructure query embedded wholly within them. For example:

Note: When you search a remote reaction database, always atom-atom map your query. This example displays the mapped atoms and reacting centers.

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


Drawing a Reaction Structure

A reaction structure specifies the molecules (2D structures) that participate in a reaction. For example:

Note: This example displays the reacting centers.

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To edit an existing query in the Query Builder

Searching Concepts/Examples

Use this procedure to edit an existing query in the Query Builder in ISIS/Base.

1.	(Optional) To delete unwanted text, select the text, and then press the Back Space key.

2.	(Optional) To add another query to your existing query string, enter a boolean algebraic operator, and then enter a query string that specifies either

text and/or numeric data or

a reaction or

a reactant or product structure.

3.	(Optional) Repeat Step 2 as needed.

4.	(Optional) Use a different graphical query than the one in the current query string.

5.	(Optional) Edit the current graphical query.

6.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To edit the current graphical query

Searching Concepts/Examples

1.	Click Cancel.

2.	Click Search > Restore Query, and then select the query of your choice in the Select Object list box.

3.	Click OK.

4.	Click the structure. You see the structure in ISIS/Draw.

5.	Edit the query. If you need help, click:

Drawing a Reaction Component Substructure or

Drawing a Reaction Component Structure or

Drawing a Reaction Substructure or

Drawing a Reaction Structure or

Specifying Query Features on a Reaction Component or

Specifying Query Features on a Reaction or

Specifying Rgroup Query Features or

Specifying Stereochemistry or

Guidelines for Revising the Query.

6.	Transfer the query back to ISIS/Base.

7.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To obtain a QB query and execute the search

QB queries can contain any combination of text/numeric strings and/or the file names of graphical structures in the Query Builder dialog box. You can also connect queries with the boolean algebraic operators AND, OR, and NOT. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Choose Search > Query Builder.

4.	(Optional) To delete any existing text, click Clear.

5.	Do one of the following:

*	Enter a new query

*	Obtain an existing query.

6.	(Optional) To create a new graphical component that you can add to your query, draw a new query.

7.	Click OK.

See also:

To abandon the search


To enter a new query

Searching Concepts/Examples

1.	Do one of the following:

*	Enter a query string that specifies text or numeric data

*	Enter a query string that specifies a reaction

*	Enter a query string that specifies a reactant or product structure

2.	(Optional) To delete unwanted text, select the text, and then press the Back Space key.

3.	(Optional) To add another query string, enter one of the boolean algebraic operators AND, OR, or NOT, and then repeat Step 1.

4.	(Optional) Repeat Step 3 as needed.

5.	Click OK.


To enter a query string that specifies text or numeric data

Searching Concepts/Examples

1.	Double-click a database field name in the Database Fields box. You see the field in the Query string text box.

2.	Double-click a search operator in the Operator box. You see the operator in the Query string text box.

3.	Type the text or numeric data criteria in the Query string text box. You can use wildcards. You can enter a maximum of 1000 characters. (Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.)

4.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To obtain an existing query

Use this procedure to restore a text/numeric query from a file in the database that is open currently in ISIS/Base.

1.	Choose Search > Restore Query.

2.	Click the name of an existing file in the Select Object list box.

3.	Click OK (Mac=Open). The selected file is restored.

4.	Click OK.

5.	Choose Search > Query Builder. You see the existing query.

6.	(Optional) You can edit the existing query.


To enter a query string that specifies a reaction

Searching Concepts/Examples

1.	Double-click RXNSTRUCTURE in the Database Fields box.

2.	Double-click a search operator in the Operator box.

3.	Do one of the following:

*	To enter a reaction that is on the form in ISIS/Base, double-click rquery in the Structures box.

*	To enter a reaction that was saved in the database, double-click the name of the reaction in the Structures box.

*	To enter a rxnfile, click Read Structure, enter the name of the reaction in the Files text box, click OK, and then double-click the name of the reaction in the Structures box.

You see the reaction in the Structure Picture box.

4.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To enter a query string that specifies a reactant or product structure

Searching Concepts/Examples

1.	Double-click a MOLSTRUCTURE field in the Database Fields box.

2.	Double-click a search operator in the Operator box.

3.	Do one of the following:

*	To enter a reaction component that is on the form in ISIS/Base, double-click query in the Structures box.

*	To enter a reaction component that was saved in the database, double-click the name of the reaction component in the Structures box.

*	To enter a molfile, click Read Structure, enter the name of the reaction component in the Files text box, click OK, and then double-click the name of the reaction component in the Structures box.

You see the reaction component in the Structure Picture box.

4.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


Specifying Options for the RSIMILAR Operator

Click here for step-by-step instructions

If you specified the RSIMILAR operator, you must also specify the options for that operator.


To specify options for the RSIMILAR operator

Searching Concepts/Examples

This procedure assumes that the Query Builder dialog box is open, and that you have already specified the RXNSTRUCTURE database field, RSIMILAR operator, and the reaction query.

1.	Type a double quote (").

2.	Do one of the following:

*	To retrieve reaction components with the same structural complexity as your query, do nothing at this step.

*	To retrieve reaction components with greater structural complexity than your query, type super.

*	To retrieve reaction components with less structural complexity than your query, type sub.

3.	Type a number between 0 and 100. The higher the number, the higher the transformational similarity to your query.

4.	Type a number between 0 and 100. The higher the number, the higher the structural similarity to your query.

5.	Type a double quote (").

6.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


Specifying Options for MSIMILAR or FLEXMATCH Operators

If you specified the MSIMILAR or FLEXMATCH operator, you must specify the options for that operator.

Click one of the following:

*	To specify options for the MSIMILAR operator

*	To specify options for the FLEXMATCH operator


To specify options for the MSIMILAR operator

Searching Concepts/Examples

This procedure assumes that the Query Builder dialog box is open, and that you have already specified a MOLSTRUCTURE database field, MSIMILAR operator, and the structure of the reaction component.

1.	Type a double quote (").

2.	Do one of the following:

*	To retrieve molecules with the same structural complexity as your query, enter no additional characters.

*	To retrieve molecules with greater structural complexity than your query, type super.

*	To retrieve molecules with less structural complexity than your query, type sub.

3.	Type a number between 0 and 100. The higher the number, the more the structures that you retrieve resemble your query.

4.	Type a double quote (").

5.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To specify options for the FLEXMATCH operator

Searching Concepts/Examples

This procedure assumes that the Query Builder dialog box is open, and that you have already specified a MOLSTRUCTURE database field, the FLEXMATCH operator, and the structure of the reaction component.

1.	Type a double quote (").

2.	Type a three-letter code that specifies a flexmatch parameter.

3.	(Optional) To specify another flexmatch parameter, type a slash (/) and then type the three-letter code.

4.	(Optional) To enter more flexmatch parameters, repeat Step 3.

5.	Type a double quote (").

6.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


Examples

To find all reactants that contain benzaldehyde AND all reactants with a melting point greater than 220 degrees, enter:

To find all reactants that contain both indole and a molecular weight greater than 200 but NOT those reactants with a melting point below 190, enter:


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. If you need help, click:

Drawing a Reaction Component Substructure or

Drawing a Reaction Component Structure or

Drawing a Reaction Substructure or

Drawing a Reaction Structure or

Specifying Query Features on a Reaction Component or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a Reaction Component Substructure

A reaction component substructure is a two-dimensional representation of a portion of a molecule that participates in a reaction. You retrieve reactions that contain your 2D substructure query embedded wholly within the reaction components. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


Drawing a Reaction Component Structure

A reaction component structure is a two-dimensional representation of a molecule that participates in a reaction. For example, a product:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


Drawing a Reaction Substructure

A reaction substructure is a portion of a reaction. You retrieve reactions that contain your reaction substructure query embedded wholly within them. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


Drawing a Reaction Structure

A reaction structure specifies the molecules (2D structures) that participate in a reaction. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To edit an existing query in the Query Builder

Searching Concepts/Examples

Use this procedure to edit an existing query in the Query Builder in ISIS/Base.

1.	(Optional) To delete unwanted text, select the text, and then press the Back Space key.

2.	(Optional) To add another query to your existing query string, enter a boolean algebraic operator, and then enter a query string that specifies either

text and/or numeric data or

a reaction or

a reactant or product structure.

3.	(Optional) Repeat Step 2 as needed.

4.	(Optional) Use a different graphical query than the one in the current query string.

5.	(Optional) Edit the current graphical query.

6.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To edit the current graphical query

Searching Concepts/Examples

1.	Click Cancel.

2.	Click Search > Restore Query, and then select the query of your choice in the Select Object list box.

3.	Click OK.

4.	Click the structure. You see the structure in ISIS/Draw.

5.	Edit the query. If you need help, click:

Drawing a Reaction Component Substructure or

Drawing a Reaction Component Structure or

Drawing a Reaction Substructure or

Drawing a Reaction Structure or

Specifying Query Features on a Reaction Component or

Specifying Stereochemistry or

Guidelines for Revising the Query.

6.	Transfer the query back to ISIS/Base.

7.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To obtain a QB query and execute the search

QB queries can contain any combination of text/numeric strings and/or the file names of graphical structures in the Query Builder dialog box. You can also connect queries with the boolean algebraic operators AND, OR, and NOT. Example

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Choose Search > Query Builder.

4.	(Optional) To delete any existing text, click Clear.

5.	Do one of the following:

*	Enter a new query

*	Obtain an existing query.

6.	(Optional) To create a new graphical component that you can add to your query, create a new query

7.	Click OK.

See also:

To abandon the search


Specifying Hydrogen Sprouting on 3D Structures

Click here for step-by-step instructions

3D structures in remote databases generally do not contain explicit representations of hydrogen atoms and lone-pair electrons. To conduct a search with a 3D graphical query, you need to specify how you want to sprout hydrogen atoms on the 3D structures that you retrieve from the database.

By default, ISIS sprouts hydrogens and lone pairs solely at sites where hydrogens and lone pairs appear on the query.


To specify hydrogen sprouting on 3D structures

1.	Choose Options > Settings > Session. You see a dialog box.

2.	Click the Search tab (if not selected).

3.	Do one of the following:

*	To sprout no hydrogens on 3D structures, click the Sprout hydrogens and lone pairs box and choose Off.

*	To sprout hydrogens and lone pairs solely at sites where hydrogens and lone pairs also appear on the query, click the Sprout hydrogens and lone pairs box and choose Query Atoms Only.

*	To sprout hydrogens at all sites, and lone pairs at sites where lone pairs also appear on the query, click the Sprout hydrogens and lone pairs box and choose All.

4.	Click OK.


To enter a new query

Searching Concepts/Examples

1.	Do one of the following:

*	Enter a query string that specifies text or numeric data

*	Enter a query string that specifies a 3D structure

*	Enter a query string that specifies a 2D structure

2.	(Optional) To delete unwanted text, select the text, and then press the Back Space key.

3.	(Optional) To add another query string, enter one of the boolean algebraic operators AND, OR, or NOT, and then repeat Step 1.

4.	(Optional) Repeat Step 3 as needed.

5.	Click OK.


To enter a query string that specifies a 2D structure

Searching Concepts/Examples

1.	Double-click MOLSTRUCTURE in the Database Fields box.

2.	Double-click a search operator in the Operator box.

3.	Do one of the following:

*	To enter a structure that is on the form in ISIS/Base, double-click query in the Structures box.

*	To enter a structure that was saved in the database, double-click the name of the structure in the Structures box.

*	To enter a molfile, click Read Structure, enter the name of the structure in the Files text box, click OK, and then double-click the name of the structure in the Structures box.

You see the structure in the Structure Picture box.

4.	(Optional) Specify options for MSIMILAR or FLEXMATCH operator.

5.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To enter a query string that specifies text or numeric data

Searching Concepts/Examples

1.	Double-click a database field name in the Database Fields box. You see the field in the Query string text box.

2.	Double-click a search operator in the Operator box. You see the operator in the Query string text box.

3.	Type the text or numeric data criteria in the Query string text box. You can use wildcards. You can enter a maximum of 1000 characters. (Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.)

4.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


Specifying Options for MSIMILAR or FLEXMATCH Operators

If you specified the MSIMILAR or FLEXMATCH operator, you must specify the options for that operator.

Click one of the following:

*	To specify options for the MSIMILAR operator

*	To specify options for the FLEXMATCH operator


To specify options for the MSIMILAR operator

Searching Concepts/Examples

This procedure assumes that the Query Builder dialog box is open, and that you have already specified a MOLSTRUCTURE database field, the MSIMILAR operator, and the structure.

1.	Type a double quote (").

2.	Do one of the following:

*	To retrieve molecules with the same structural complexity as your query, enter no additional characters.

*	To retrieve molecules with greater structural complexity than your query, type super.

*	To retrieve molecules with less structural complexity than your query, type sub.

3.	Type a number between 0 and 100. The higher the number, the more the records that you retrieve resemble your query.

4.	Type a double quote (").

5.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To specify options for the FLEXMATCH operator

Searching Concepts/Examples

This procedure assumes that the Query Builder dialog box is open, and that you have already specified the MOLSTRUCTURE database field, the FLEXMATCH operator, and the 2D structure that you want.

1.	Type a double quote (").

2.	Type a three-letter code that specifies a flexmatch parameter.

3.	(Optional) To specify another flexmatch parameter, type a slash (/) and then type the three-letter code.

4.	(Optional) To enter more flexmatch parameters, repeat Step 3.

5.	Type a double quote (").

6.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To obtain an existing query

Use this procedure to restore a text/numeric query from a file in the database that is open currently in ISIS/Base.

1.	Choose Search > Restore Query.

2.	Click the name of an existing file in the Select Object list box.

3.	Click OK (Mac=Open). The selected file is restored.

4.	Click OK.

5.	Choose Search > Query Builder. You see the existing query.

6.	(Optional) You can edit the existing query.


To enter a query string that specifies a 3D structure

Searching Concepts/Examples

1.	Double-click MODELSTRUCTURE in the Database Fields box.

2.	Double-click a search operator in the Operator box.

3.	Do one of the following:

*	To enter a 3D structure that is on the form in ISIS/Base, double-click query in the Structures box.

*	To enter a 3D structure that was saved in the database, double-click the name of the 3D structure in the Structures box.

*	To enter a molfile, click Read Structure, enter the name of the 3D structure in the Files text box, click OK, and then double-click the name of the 3D structure in the Structures box.

You see the 3D structure in the Structure Picture box.

4.	(Optional) Specify options for the SAMEAS or SSS3D operator.

5.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


Specifying Options for SAMEAS3D or SSS3D Operators

If you specified the SAMEAS3D or SSS3D operator, you must specify the options for that operator.

Click one of the following:

*	To specify options for the SAMEAS3D operator

*	To specify options for the SSS3D operator


To specify options for the SAMEAS3D operator

Searching Concepts/Examples

This procedure assumes that the Query Builder dialog box is open, and that you have already specified the MODELSTRUCTURE database field, SAMEAS3D operator, and 3D structure.

1.	Type a double quote (").

2.	Type a value (in Angstroms) for the maximum atomic displacement.

3.	Type a space.

4.	Type a value (in Angstroms) for the maximum RMS deviation.

5.	Type a double quote (").

6.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To specify options for the SSS3D operator

Searching Concepts/Examples

To conduct a search with the SSS3D operator, you need to specify whether you want to conduct a rigid 3D substructure search or a Conformationally Flexible Substructure (CFS) search. This procedure assumes that the Query Builder dialog box is open, and that you have already specified the MODELSTRUCTURE field, the SSS3D operator, and the 3D substructure query that you want.

1.	Type a double quote (").

2.	If your query contains fixed-atoms, do the following:

a.	Type a value (in Angstroms) for the maximum atomic displacement.

b.	Type a space.

c.	Type a value (in Angstroms) for the maximum RMS deviation.

3.	Do one of the following:

*	To conduct a rigid 3D substructure search, enter no additional characters. Example

*	To conduct a CFS search with the default CFS options, type /CFS Example

*	To conduct a CFS search with nondefault CFS options, type /CFS=<option-list>, where <option-list> is the set of CFS options and values that you want to use, delimited by commas. Example

4.	Type a double quote (").

5.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


Example

The following query specifies a static 3D substructure search with a maximum atomic displacement of 0.5 Angstroms and a maximum RMS deviation of 0.5 Angstroms:


Example

The following query specifies a CFS search with a maximum atomic displacement of 0.5 Angstroms, a maximum RMS deviation of 0.5 Angstroms, and default values for all CFS options:


Example

The following query specifies a CFS search with a maximum atomic displacement of 0.5 Angstroms, with a maximum RMS deviation of 0.5 Angstroms, with ring flexing (bonds in rings of 6 to 24 atoms are considered flexible), with the maximum number of attempted fittings set to 25, and with default values for all other CFS options:


CFS Options and Values

The following are the CFS options that you can use with the Query Builder. Default values are in boldface.


Example

To find all 3D structures that contain a substructure of spirapril (within 0.5 Angstroms deviation of individual and overall atoms) AND that have a molecular weight less than 500, enter:


Creating a New Graphical Query

Click one of the following:

*	To create a new 2D query

*	To create a new 3D query


To create a new 2D query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. If you need help, click:

Drawing a 2D Substructure or

Drawing a 2D Structure or

Specifying 2D Query Features or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


To create a new 3D query

Searching Concepts/Examples

1.	(Optional) Obtain a 3D structure.

Note: You can not draw a 3D structure in ISIS/Draw, because atoms that you draw do not have the necessary 3D spatial arrangement.

2.	Transfer to ISIS/Draw.

3.	(Optional) Create the submodel portion of the query.

4.	(Optional) Draw additional features on the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing 2D Substructures or

Specifying 2D Query Features or

Specifying Chemical Environments or

Specifying 3D Query Features

5.	Transfer the query back to ISIS/Base.


Obtaining a 3D Structure

To create a complete 3D structure, or to create a 3D substructure that contains submodel components, you must obtain a 3D structure that contains atoms in the spatial arrangement that you want. You can not draw a 3D structure or a submodel in ISIS/Draw, because structures that you draw in ISIS/Draw do not have atoms in the correct spatial arrangement.

Click one of the following:

*	Retrieve a 3D structure from the database.

*	Import a 3D structure from a molfile.

*	Restore a 3D structure that you previously saved as an object in the database.


Drawing a 2D Substructure

A 2D substructure is a portion of a molecule that is drawn without regard to its 3D spatial arrangement. You retrieve molecules that contain your 2D substructure query embedded wholly within them. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


Drawing a 2D Structure

A 2D structure is a molecule that is drawn without regard to its 3D spatial arrangement. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To edit an existing query in the Query Builder

Searching Concepts/Examples

Use this procedure to edit an existing query in the Query Builder in ISIS/Base.

1.	(Optional) To delete unwanted text, select the text, and then press the Back Space key.

2.	(Optional) To add another query to your existing query string, enter a boolean algebraic operator, and then enter a query string that specifies either

text and/or numeric data or

a 2D structure or

a 3D structure.

3.	(Optional) Repeat Step 2 as needed.

4.	(Optional) Use a different graphical query than the one in the current query string.

5.	(Optional) Edit the current graphical query.

6.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


Editing the Current Graphical Query

Click one of the following:

*	To edit a 2D graphical query

*	To edit a 3D graphical query


To edit a 2D graphical query

Searching Concepts/Examples

1.	Click Cancel.

2.	Click Search > Restore Query, and then select the query of your choice in the Select Object list box.

3.	Click OK.

4.	Click the structure. You see the structure in ISIS/Draw.

5.	Edit the query. If you need help, click:

Drawing a 2D Substructure or

Drawing a 2D Structure or

Specifying 2D Query Features or

Specifying Stereochemistry or

Guidelines for Revising the Query.

6.	Transfer the query back to ISIS/Base.

7.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To edit a 3D graphical query

Searching Concepts/Examples

1.	Click Cancel.

2.	Click Search > Restore Query, and then select the query of your choice in the Select Object list box.

3.	Click OK.

4.	Click the structure. You see the structure in ISIS/Draw.

5.	Edit the query. If you need help, click:

Drawing a 2D Substructure or

Specifying Chemical Environments or

Specifying 3D Query Features or

Specifying 2D Query Features or

Guidelines for Revising the Query.

6.	Transfer the query back to ISIS/Base.

7.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To obtain a QB query and execute the search

QB queries can contain any combination of text/numeric strings and/or the file names of graphical structures in the Query Builder dialog box. You can also connect queries with the boolean algebraic operators AND, OR, and NOT. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Choose Search > Query Builder.

4.	(Optional) To delete any existing text, click Clear.

5.	Do one of the following:

*	Enter a new query

*	Obtain an existing query.

6.	(Optional) To create a new graphical component that you can add to your query, create a new query.

7.	Click OK.

See also:

To abandon the search


To enter a new query

Searching Concepts/Examples

1.	Do one of the following:

*	Enter a query string that specifies text or numeric data

*	Enter a query string that specifies a 3D structure

*	Enter a query string that specifies a 2D structure

2.	(Optional) To delete unwanted text, select the text, and then press the Back Space key.

3.	(Optional) To add another query string, enter one of the boolean algebraic operators AND, OR, or NOT, and then repeat Step 1.

4.	(Optional) Repeat Step 3 as needed.

5.	Click OK.


To enter a query string that specifies a 2D structure

Searching Concepts/Examples

1.	Double-click MOLSTRUCTURE in the Database Fields box.

2.	Double-click a search operator in the Operator box.

3.	Do one of the following:

*	To enter a structure that is on the form in ISIS/Base, double-click query in the Structures box.

*	To enter a structure that was saved in the database, double-click the name of the structure in the Structures box.

*	To enter a molfile, click Read Structure, enter the name of the structure in the Files text box, click OK, and then double-click the name of the structure in the Structures box.

You see the structure in the Structure Picture box.

4.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To enter a query string that specifies text or numeric data

Searching Concepts/Examples

1.	Double-click a database field name in the Database Fields box. You see the field in the Query string text box.

2.	Double-click a search operator in the Operator box. You see the operator in the Query string text box.

3.	Type the text or numeric data criteria in the Query string text box. You can use wildcards. You can enter a maximum of 1000 characters. (Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.)

4.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To obtain an existing query

Use this procedure to restore a text/numeric query from a file in the database that is open currently in ISIS/Base.

1.	Choose Search > Restore Query.

2.	Click the name of an existing file in the Select Object list box.

3.	Click OK (Mac=Open). The selected file is restored.

4.	Click OK.

5.	Choose Search > Query Builder. You see the existing query.

6.	(Optional) You can edit the existing query.


To enter a query string that specifies a 3D structure

Searching Concepts/Examples

1.	Double-click MODELSTRUCTURE in the Database Fields box.

2.	Double-click a search operator in the Operator box.

3.	Do one of the following:

*	To enter a 3D structure that is on the form in ISIS/Base, double-click query in the Structures box.

*	To enter a 3D structure that was saved in the database, double-click the name of the 3D structure in the Structures box.

*	To enter a molfile, click Read Structure, enter the name of the 3D structure in the Files text box, click OK, and then double-click the name of the 3D structure in the Structures box.

You see the 3D structure in the Structure Picture box.

4.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


Creating a New Graphical Query

Click one of the following:

*	To create a new 2D query

*	To create a new 3D query


To create a new 2D query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. If you need help, click:

Drawing a 2D Substructure or

Drawing a 2D Structure or

Specifying 2D Query Features or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


To create a new 3D query

Searching Concepts/Examples

1.	Obtain a 3D structure.

Note: You can not draw a 3D structure in ISIS/Draw, because atoms that you draw do not have the necessary 3D spatial arrangement.

2.	Transfer to ISIS/Draw.

3.	(Optional) Edit the 3D structure.

Notes: If you want to create a 3D substructure, you need to edit the structure that you obtained in Step 1. If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.

4.	Transfer the query back to ISIS/Base.


Obtaining a 3D Structure

To create a query that contains a 3D structure or substructure, you need to obtain a 3D structure.

Click one of the following:

*	Retrieve a 3D structure from the database.

*	Import a 3D structure from a molfile.

*	Restore a 3D structure that you previously saved as an object in the database.


Examples

To find all 3D structures that contain a substructure of spirapril, enter:

To find all 3D structures that have a molecular weight less than 500, enter:


To create a new 2D query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. If you need help, click:

Drawing a 2D Substructure or

Drawing a 2D Structure or

Specifying 2D Query Features or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


Drawing a 2D Substructure

A 2D substructure is a portion of a molecule that is drawn without regard to its 3D spatial arrangement. You retrieve molecules that contain your 2D substructure query embedded wholly within them. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


Drawing a 2D Structure

A 2D structure is a molecule that is drawn without regard to its 3D spatial arrangement. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


Editing a 3D Structure

To edit a 3D structure to use as a query in a local database, you remove the parts of the structure that you do not want to include in your query. For example:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Verifying the Chemistry of Sketches


To edit an existing query in the Query Builder

Searching Concepts/Examples

Use this procedure to edit an existing query in the Query Builder in ISIS/Base.

1.	(Optional) To delete unwanted text, select the text, and then press the Back Space key.

2.	(Optional) To add another query to your existing query string, enter a boolean algebraic operator, and then enter a query string that specifies either

text and/or numeric data or

a 2D structure or

a 3D structure.

3.	(Optional) Repeat Step 2 as needed.

4.	(Optional) Use a different graphical query than the one in the current query string.

5.	(Optional) Edit the current graphical query.

6.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


Editing the Current Graphical Query

Click one of the following:

*	To edit a 2D graphical query

*	To edit a 3D graphical query


To edit a 2D graphical query

Searching Concepts/Examples

1.	Click Cancel.

2.	Click Search > Restore Query, and then select the query of your choice in the Select Object list box.

3.	Click OK.

4.	Click the structure. You see the structure in ISIS/Draw.

5.	Edit the query. If you need help, click:

Drawing a 2D Substructure or

Drawing a 2D Structure or

Specifying 2D Query Features or

Specifying Stereochemistry or

Guidelines for Revising the Query.

6.	Transfer the query back to ISIS/Base.

7.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To edit a 3D graphical query

Searching Concepts/Examples

1.	Click Cancel.

2.	Click Search > Restore Query, and then select the query of your choice in the Select Object list box.

3.	Click OK.

4.	Click the structure. You see the structure in ISIS/Draw.

5.	Edit the query. If you need help, click:

Editing a 3D structure or

Guidelines for Revising the Query.

6.	Transfer the query back to ISIS/Base.

7.	Click Back (at top of help screen) to return to the previous screen and continue the instructions on that screen.


To obtain a 3DEXACT query

3DEXACT queries contain the 3D structure of a molecule. The 3D structure of a molecule defines the spatial arrangement of atoms in the molecule. You search for 3D structures that match the 3D spatial arrangement of the atoms in your query exactly. Example

Note: You can not draw a 3D structure in ISIS/Draw, because atoms that you draw do not have the necessary 3D spatial arrangement.

1.	Click the Query mode (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Click the MODELSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Retrieve a 3D structure from the database.

*	Import a 3D structure from a molfile.

*	Restore a 3D structure that you previously saved as an object in the database.


Example

A 3D structure defines the spatial arrangement of all atoms in a molecule. In contrast, a 2D structure of a molecule contains information on number, type, and connectivity of atoms in a molecule, and on the configuration of atoms around chiral centers:


Retrieving a 3D Structure From the Database

You can retrieve an existing 3D structure from the database to use as a query. For example, you can use any of the following searches to retrieve a 3D structure:

*	ID search

*	Formula search

*	MEXACT search for the corresponding 2D structure

*	Search By Form (SBF) for the structure name (MOLNAME or MODELNAME) or for model number (MODELREGNO)

Note: You can not draw a 3D structure in ISIS/Draw, because atoms that you draw do not have the necessary 3D spatial arrangement.


Retrieving a 3D Structure From the Database

You can retrieve an existing 3D structure from the database to use as a query. For example, you can use any of the following searches to retrieve a 3D structure:

*	ID search

*	Formula search

*	MEXACT search for the corresponding 2D structure

*	Search By Form (SBF) for the structure name (MOLNAME or MODELNAME) or for model number (MODELREGNO)

Note: You can not draw a 3D structure in ISIS/Draw, because atoms that you draw do not have the necessary 3D spatial arrangement.


Retrieving a 3D Structure From the Database

You can retrieve an existing 3D structure from the database to use in a submodel. For example, you can use any of the following searches to retrieve a 3D structure:

*	ID search

*	Formula search

*	MEXACT search for the corresponding 2D structure

*	Search By Form (SBF) for the structure name (MOLNAME or MODELNAME) or for model number (MODELREGNO)

Note: You can not draw a 3D structure in ISIS/Draw, because atoms that you draw do not have the necessary 3D spatial arrangement.


To restore a 3D structure from the database

Use this procedure to restore a 3D structure query from a database that is open currently in ISIS/Base.

1.	Click the Query mode (if not highlighted).

2.	Click the MODELSTRUCTURE box (if not highlighted).

3.	Choose Database > Restore Molecule. You see the Select Object dialog box.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected 3D structure is restored into your form.


To import a 3D structure from a molfile

Use this procedure to import a 3D structure query into ISIS/Base from a molfile that was created in ISIS, MACCS-II, or a modeling software program.

1.	Click the Query mode (if not highlighted).

2.	Click the MODELSTRUCTURE box (if not highlighted).

3.	Choose File > Import > Molfile. You see the File Open dialog box. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected 3D structure is imported into your form.


To import a 3D structure from a molfile

Use this procedure to import a 3D structure query into ISIS/Base from a molfile that was created in ISIS, MACCS-II, or a modeling software program.

1.	Click the Query mode (if not highlighted).

2.	Click the MODELSTRUCTURE box (if not highlighted).

3.	Choose File > Import > Molfile. You see the File Open dialog box. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected 3D structure is imported into your form.


To restore a 3D structure from the database

Use this procedure to restore a 3D structure from a database that is open currently in ISIS/Base.

1.	Click the Query mode (if not highlighted).

2.	Click the MODELSTRUCTURE box (if not highlighted).

3.	Choose Database > Restore Molecule. You see the Select Object dialog box.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected 3D substructure is restored into your form.


To restore a 3D structure from the database

Use this procedure to restore a 3D structure from a database that is open currently in ISIS/Base.

1.	Click the Query mode (if not highlighted).

2.	Select the MODELSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule. You see the Select Object dialog box.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected 3D substructure is restored into your form.


To edit an existing query

Use this procedure to edit an existing 3D structure query that you see in a box or table column in ISIS/Base.

1.	Click the MODELSTRUCTURE box that contains the 3D structure that you want to edit. An ISIS/Draw window opens that contains the 3D structure.

2.	Edit the query. If you need help, click:

Revising the Query.

3.	Transfer the query back to ISIS/Base.


To obtain a 3DEXACT query

3DEXACT queries contain the 3D structure of a molecule. The 3D structure of a molecule defines the spatial arrangement of atoms in the molecule. You search for 3D structures that match the 3D spatial arrangement of the atoms in your query exactly. Example

1.	Click the Query mode (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Click the MODELSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Retrieve a 3D structure from the database.

*	Import a 3D structure from a molfile.

*	Restore a 3D structure that you previously saved as an object in the database.


Example

A 3D structure defines the spatial arrangement of all atoms in a molecule. In contrast, a 2D structure of a molecule contains information on number, type, and connectivity of atoms in a molecule, and on the configuration of atoms around chiral centers:


To restore a 3D structure from the database

Use this procedure to restore a 3D structure that is stored as an object in a database that is open currently in ISIS/Base.

1.	Click the Query mode (if not highlighted).

2.	Click the MODELSTRUCTURE box (if not highlighted).

3.	Choose Database > Restore Molecule. You see the Select Object dialog box.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected 3D structure is restored into your form.


To import a 3D structure from a molfile

Use this procedure to import a 3D structure query into ISIS/Base from a molfile that was created in ISIS, MACCS-II, or a modeling software program.

1.	Click the Query mode (if not highlighted).

2.	Click the MODELSTRUCTURE box (if not highlighted).

3.	Choose File > Import > Molfile. You see the File Open dialog box. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected 3D structure is imported into your form.


To edit an existing query

Use this procedure to edit an existing 3D structure query that you see in a box or table column in ISIS/Base.

1.	Click the MODELSTRUCTURE box that contains the 3D structure that you want to edit. An ISIS/Draw window opens that contains the 3D structure.

2.	Edit the query. If you need help, click:

Revising the Query

3.	Transfer the query back to ISIS/Base.


Examples

A 3D substructure query can contain Rgroups, 2D query features, 3D query features, and submodels:


Obtaining a 3D Structure To Use in a Submodel

To create a submodel, you must delete parts of an existing 3D structure and specify the atoms that you want to maintain in a fixed spatial arrangement (F):

Click one of the following:

*	Retrieve a 3D structure from the database.

*	Import a 3D structure from a molfile.

*	Restore a 3D structure that you previously saved as an object in the database.


Creating the Submodel Portion of the Query

Click here for step-by-step instructions

If you obtained a 3D structure in Step 1, you need to create the submodel now. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.)


To create the submodel components of the query

Use this procedure to create the submodel components of your query. This procedure assumes that you have a 3D structure that you retrieved from a 3D database or imported from a molfile.

1.	Delete the parts of the structure that are not part of the submodel. If you make a mistake, use Edit > Undo to correct your mistake.

Caution

2.	Select the atoms that you want to spatially maintain in a fixed position.

Note: You must specify two or more fixed atoms. A single fixed atom is not meaningful in a query.

3.	Choose Chemistry > 3D > Fix Position. You see an (F) at each atom that you selected.

4.	Click Back (at top of help screen) to return to the previous screen and continue with Step 4 on that screen.

See also:

To add fixed atoms to the submodel query

To delete fixed atoms from the submodel query


To create the submodel components of the query

Use this procedure to create the submodel components of a query for a CFS, CFS/Biopoly, SSS3D, or SSS3D/Biopoly search. This procedure assumes that you are in ISIS/Draw, and have a 3D database open in ISIS/Base.

Note: You can not draw a submodel in ISIS/Draw, because atoms that you draw do not have the necessary 3D spatial arrangement.

1.	Transfer to ISIS/Base.

2.	Do one of the following:

*	Retrieve a 3D structure from the database.

*	Import a 3D structure from a molfile.

*	Restore a 3D structure that you previously saved as an object in the database.

3.	Transfer the 3D structure to ISIS/Draw.

4.	Delete the parts of the structure that are not part of the submodel. If you accidentally delete atoms that you want, use Edit > Undo to correct your mistake.

Caution

5.	Select the atoms that you want to spatially maintain in a fixed position.

Note: You must specify two or more fixed atoms in a submodel query. A single fixed atom is not meaningful in a query.

6.	Choose Chemistry > 3D > Fix Position. You see an (F) at each atom that you selected.

See also:

To add fixed atoms to the submodel query

To delete fixed atoms from the submodel query


Caution

If you accidentally delete an atom that you want to be part of a submodel, you must use Edit > Undo to correct your mistake. You can not redraw a deleted atom, because atoms that you draw lack the desired 3D spatial relationships. If you cannot use Edit > Undo to correct the error, you must transfer to ISIS/Base and obtain the 3D structure again.


To obtain an SSS3D query

SSS3D queries contain your query as a 3D substructure. You search for 3D structures that contain your query wholly within another structure. Examples

1.	Click the Query mode (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

2.	Click the MODELSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Create a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples

A 3D substructure query can contain Rgroups, 2D query features, 3D query features, and submodels:


To create a new SSS3D query

Searching Concepts/Examples

1.	(Optional) Obtain a 3D structure to use in a submodel.

Note: You can not draw a submodel in ISIS/Draw, because atoms that you draw do not have the necessary 3D spatial arrangement.

2.	Transfer to ISIS/Draw.

3.	(Optional) Create the submodel portion of the query.

4.	Draw the remaining features of the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing 2D Substructures or

Specifying 2D Query Features or

Specifying Chemical Environments or

Specifying 3D Query Features

5.	Transfer the query back to ISIS/Base.


Drawing a 2D Substructure

A 2D substructure is a fragment of a molecule that is drawn without regard to its 3D spatial arrangement, such as the aldehyde fragment of the molecule benzaldehyde:

A 2D substructure query retrieves larger structures that contain the 2D substructure wholly within them.

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Checking the Chemistry of Sketches


To restore an existing query from the database

You can restore a 3D substructure query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click the Query mode (if not highlighted).

2.	Click the MODELSTRUCTURE box (if not highlighted).

3.	Choose Database > Restore Molecule. You see the Select Object dialog box.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected 3D substructure is restored into your form.

6.	(Optional) You can edit the existing query.


To import an existing query from a molfile

Use this procedure to import a 3D substructure query from a molfile that was created in ISIS or MACCS-II.

1.	Click the Query mode (if not highlighted).

2.	Click the MODELSTRUCTURE box (if not highlighted).

3.	Choose File > Import > Molfile. You see the File Open dialog box. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected 3D substructure is imported into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing 3D substructure query that you see in a box or table column in ISIS/Base.

1.	Click the MODELSTRUCTURE box that contains the 3D substructure that you want to edit. An ISIS/Draw window opens that contains the 3D substructure .

2.	Edit the query. If you need help, click:

Drawing a 2D Substructure or

Specifying Chemical Environments or

Specifying 3D Query Features or

Specifying 2D Query Features or

Revising the Query

3.	Transfer the query back to ISIS/Base.


To obtain a CFS query

CFS queries contain your query as a 3D substructure. You search for 3D structures that contain your query wholly within another structure. Examples

Caution: A CFS query must contain at least one of the following: distance, angle, dihedral angle, linearity constraint, planarity constraint, or submodel. If you use a CFS query that does not meet these requirements, you obtain an error message when you perform the search.

1.	Click the Query mode (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Click the MODELSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Create a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Examples

A 3D substructure query can contain Rgroups, 2D query features, 3D query features, and submodels:

Note: Some options for CFS searching restrict the types of 3D query features that you can use. For more information on CFS options, see CFS Searching Concepts/Examples.


To create a new CFS query

Searching Concepts/Examples

1.	(Optional) Obtain a 3D structure to use in a submodel.

Note: You can not draw a submodel in ISIS/Draw, because atoms that you draw do not have the necessary 3D spatial arrangement.

2.	Transfer to ISIS/Draw.

3.	(Optional) Create the submodel portion of the query.

4.	Draw the remaining features of the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing 2D Substructures or

Specifying 2D Query Features or

Specifying Chemical Environments or

Specifying 3D Query Features or

5.	Transfer the query back to ISIS/Base.


Drawing a 2D Substructure

A 2D substructure is a fragment of a molecule that is drawn without regard to its 3D spatial arrangement, such as the aldehyde fragment of the molecule benzaldehyde:

A 2D substructure query retrieves larger structures that contain the 2D substructure wholly within them.

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Checking the Chemistry of Sketches


To restore an existing query from the database

You can restore a 3D substructure query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click the Query mode (if not highlighted).

2.	Click the MODELSTRUCTURE box (if not highlighted).

3.	Choose Database > Restore Molecule. You see the Select Object dialog box.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected 3D substructure is restored into your form.

6.	(Optional) You can edit the existing query.


To import an existing query from a molfile

Use this procedure to import a 3D substructure query from a molfile that was created in ISIS or MACCS-II.

1.	Click the Query mode (if not highlighted).

2.	Click the MODELSTRUCTURE box (if not highlighted).

3.	Choose File > Import > Molfile. You see the File Open dialog box. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected 3D substructure is imported into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing CFS query that you see in a box or table column in ISIS/Base.

1.	Click the MODELSTRUCTURE box that contains the 3D substructure that you want to edit. An ISIS/Draw window opens that contains the 3D substructure .

2.	Edit the query. If you need help, click:

Drawing a 2D Substructure or

Specifying Chemical Environments or

Specifying 3D Query Features or

Specifying 2D Query Features or

Revising the Query.

3.	Transfer the query back to ISIS/Base.


To obtain an SBF query

SBF queries can contain any combination of text/numeric strings and/or structures in different boxes and tables on the form. Examples

1.	Click the Query mode (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	(Optional) To enter text or numeric data, do one of the following:

*	Enter a new text/numeric query

*	Obtain an existing text/numeric query.

4.	(Optional) Click a box or column on the form that will hold a 3D structure or substructure, and then do one of the following:

*	Create a new graphical query.

*	Import a graphical query from a molfile.

*	Restore a graphical query that you previously saved as an object in the database.

5.	(Optional) Repeat Steps 3 and 4 as needed. You can conduct a single search with a maximum of 25 queries.

Note: The placement of multiple queries within a table in an SBF search might produce different search results. For more information, see Obtaining Different Search Results with Multiple Queries in Tables.


Structures in SBF Queries

A structure in an SBF query is a graphical image in a box or column on the form that specifies the retrieval of graphical data. A structure can be any one of the following:


Examples

In this example, you want to find all molecules with a specific 3D substructure wholly within them and that have a molecular weight that is less than 400:


To create a new graphical query

Searching Concepts/Examples

1.	(Optional) Obtain a 3D structure to use in a submodel.

Note: You can not draw a 3D structure in ISIS/Draw, because atoms that you draw do not have the necessary 3D spatial arrangement.

2.	Transfer to ISIS/Draw.

3.	(Optional) Create the submodel portion of the query.. (If you obtained a 3D structure in Step 1, you need to create the submodel now.)

4.	Draw the remaining features of the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing 2D Substructures or

Specifying Chemical Environments or

Specifying 2D Query Features or

Specifying 3D Query Features

5.	Transfer the query back to ISIS/Base.


Drawing a 2D Substructure

A 2D substructure is a fragment of a molecule that is drawn without regard to its 3D spatial arrangement, such as the aldehyde fragment of the molecule benzaldehyde:

A 2D substructure query retrieves larger structures that contain the 2D substructure wholly within them.

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Checking the Chemistry of Sketches


Drawing A 2D Substructure
Drawing a 2D Structure

A 2D structure is a molecule that is drawn without regard to its 3D spatial arrangement, such as benzaldehyde:

Click one of the following:

*	ISIS/Draw “Quick Start”

*	Using Template Tools and Pages

*	Drawing With the Keyboard

*	Manipulating Objects

*	Checking the Chemistry of Sketches


Obtaining an Existing SBF Query

You can save a graphical query as an object in the remote-access file of your database. To access a graphical query that you saved as a database object, you must restore it into a box or table column on the form in ISIS/Base.

You can also export a graphical query to a molfile on your workstation. To access a query that is stored anywhere on your hard disk or on a floppy, you must import it into a box or table column on the form in ISIS/Base. You can import a graphical query but not a text query.

Click one of these 2 items:

*	Restore an existing graphical query

*	Import an existing graphical query


To restore an existing graphical query

Use this procedure to restore a 2D or 3D graphical query from a database that is open currently in ISIS/Base.

1.	Click the Query mode (if not highlighted).

2.	Do one of the following:

*	To import a 2D structure or substructure, select the MOLSTRUCTURE box.

*	To import a 3D structure or substructure, select the MODELSTRUCTURE box.

3.	Choose Database > Restore Molecule. You see the Select Object dialog box.

4.	Click the name of an existing molecule in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing graphical query


To import an existing graphical query

Use this procedure to import a 2D or 3D graphical query from a molfile that was created in ISIS or MACCS-II.

1.	Click the Query mode (if not highlighted).

2.	Do one of the following:

*	To import a 2D structure or 2D substructure, select the MOLSTRUCTURE box.

*	To import a 3D structure or 3D substructure, select the MODELSTRUCTURE box.

3.	Choose File > Import > Molfile. You see the File Open dialog box. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected substructure is imported into your form.

6.	(Optional) You can edit the existing graphical query.


Editing a Graphical Query

Click one of the following:

*	Edit an existing 2D query structure

*	Edit an existing 3D query structure


To edit an existing 2D query structure

Use this procedure to edit an existing 2D graphical query (2D structure or 2D substructure,) that you see in a box or table column in ISIS/Base.

1.	Click the box that contains the 2D structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Edit the structure. If you need help, click:

Drawing a 2D Substructure or

Specifying 2D Query Features or

Revising the Query.

3.	Transfer the query back to ISIS/Base.


To edit an existing 3D query structure

Use this procedure to edit an existing 3D graphical query (3D structure or 3D substructure,) that you see in a box or table column in ISIS/Base.

1.	Click the box that contains the 3D structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Edit the structure. If you need help, click:

Drawing a 2D Substructure or

Specifying Chemical Environments or

Specifying 2D Query Features or

Specifying 3D Query Features or

Revising the Query.

3.	Transfer the query back to ISIS/Base.


To enter a new text/numeric query

Use this procedure to enter a new text/numeric string (a query) to the boxes and table cells on the form. If you enter more than one query into a single form, ISIS joins your query strings automatically with the boolean algebraic operator AND. Examples

1.	Click the box or table cell of your choice (if not highlighted).

2.	Enter the search operator.

3.	Enter a space.

4.	Enter the text and/or numeric values that you want to find. You can enter as many as 25 queries into the same table. Examples

Notes: (1) You can also enter a partial query with at least one wildcard. (Do not use wildcards with a partial formula query.) (2) Your text/numeric string is case-sensitive solely when you use a relational database or a Unix platform.

5.	(Optional) Repeat Steps 1 through 4 as needed.

See also:

To delete characters from the query

To add characters to the query


Examples

To find compounds with antibiotic activity and a molecular weight that is less than 500:

Note: The percent sign (%) is a wildcard. (Do not use wildcards with a partial formula query.)


Exact Formulas

An exact formula is the complete formula of a molecule. Conduct an exact formula search to find molecules that contain the exact formula in your query.

Your query must include all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required. For example: To find phenol, enter C6 H6 O. To find phenolphthalein sodium, enter C20 H12 Na2 O4.


Subformulas

A subformula is the partial formula of a molecule. Conduct a subformula search to find molecules that contain specific atoms.

Your query can include a range of atom counts and typically excludes the hydrogens. You can use a single space to separate atoms, and capital letters are not required. For example, to find molecules that are sodium salts, enter Na. To find molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms, enter: C12 Br(1-2) S2. To find molecules that contain six carbons, six hydrogens, and any number of other atom types, enter: C6 H6.


Structures in SBF Queries

A structure in an SBF query is a graphical image in a box or cell on the form that specifies the retrieval of graphical data. A structure can be any one of the following:

*	2D structure, a two-dimensional representation of a molecule, such as the molecule Benzaldehyde:

*	2D substructure, any portion of a 2D structure. For example:


Structures in SBF Queries

A structure in an SBF query is a graphical image in a box or cell on the form that specifies the retrieval of graphical data. A structure can be any one of the following:

*	2D structure, a two-dimensional representation of a reaction component, such as the reaction component Benzaldehyde:

*	2D substructure, any portion of a 2D structure. For example:

*	Transformation (reaction), reactants and products with a reaction arrow. For example:


Text/Numeric Strings in SBF Queries

A text/numeric string in an SBF query is a phrase in a box or cell on the form that specifies the retrieval of data.

Each phrase contains:

*	A search operator that specifies the type of search (such as an equal sign, =, to specify a search that finds solely the exact target text in the query).

*	The text or numeric target value (specific data) that you want to find.

For example, to find structures with a molecular weight greater than 350, enter > 350 in the Molecular Weight box (where > is the search operator and 350 is the target value).


Text/Numeric Strings in SBF Queries

A text/numeric string in an SBF query is a phrase in a box or cell on the form that specifies the retrieval of data.

Each phrase contains:

*	A search operator that specifies the type of search (such as an equal sign, =, to specify a search that finds solely the exact target text in the query).

*	The text or numeric target value (specific data) that you want to find.

For example, to find products with a yield greater than 95%, enter > 95 in the Product Yield box (where > is the search operator and 95 is the target value).


Flexmatch Parameters

With Flexmatch parameters, you define features of retrieved structures that must match your query. If you change the default values of these parameters, you loosen the definition of an exact match. This allows you to find structures that:

*	Have different counterions than the salt in your query.

*	Match your query, but have different isotopic labels.

*	Match your query, but might be represented differently in the database. For example, the pi-metal bonds in ferrocene can be represented in different ways.

For example, you can specify that all bond types in the records do not have to match your query or that the radical value on each atom does not have to match.


Text/Numeric Strings in ID Queries

A text/numeric string is a phrase in a box or cell on the form that specifies the retrieval of specific records. This phrase is the ID query. Each phrase contains:

*	A search operator that specifies the type of search.

*	The ID number of the record that you want to find.


Exact Formulas

An exact formula is the complete formula of a molecule. Conduct an exact formula search to find molecules that contain the exact formula in your query. The exact formula includes all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required.


Subformulas

A subformula is the partial formula of a molecule. Conduct a subformula search to find molecules that contain certain atoms. The subformula formula can include a range of atom counts and typically excludes the hydrogens. You can use a single space to separate atoms, and capital letters are not required.


Exact Formulas

An exact formula is the complete formula of a reaction component, such as a reactant or a product. Conduct an exact formula search to find records that contain the exact formula in your query. The exact formula includes all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required.


Subformulas

A subformula is the partial formula of a reaction component, such as a reactant or a product. Conduct a subformula search to find records that contain certain atoms. The subformula formula can include a range of atom counts and typically excludes the hydrogens. You can use a single space to separate atoms, and capital letters are not required.


Wildcards

A wildcard is a place holder within a string of text or numeric values that represents unspecified characters. Wildcards are not allowed with a partial formula query.

Wildcard        Definition

     %               A place holder for at least

                       one unspecified character

     _                A place holder for solely one

                       unspecified character

For example:


Wildcards

A wildcard is a place holder within a string of text or numeric values that represents unspecified characters.

Note

Wildcard        Definition

     %               A place holder for at least

                       one unspecified character

     _                A place holder for solely one

                       unspecified character


Note

Without a wildcard in your query, you retrieve solely the word or phrase that you specified. You might not retrieve records that contain additional words or phrases. Thus, we recommend that you always use a wildcard!

Exceptions: (1) Wildcards are not allowed with a partial formula query. (2) In a reaction database, you cannot use the query LIKE "_", the wildcard % may only appear at the beginning or end of the search query string, and you cannot include the letters "to" in your query because ISIS interprets them as a range.


Wildcards

A wildcard is a place holder within a string of text or numeric values that represents unspecified characters.

Note

Wildcard        Definition

     %               A place holder for at least

                       one unspecified character

     _                A place holder for solely one

                       unspecified character


Wildcards

A wildcard is a place holder within a string of text or numeric values that represents unspecified characters.

Note

Wildcard        Definition

     %               A place holder for at least

                       one unspecified character

     _                A place holder for solely one

                       unspecified character


Note

Without a wildcard in your query, you retrieve solely the word or phrase that you specified. You might not retrieve records that contain additional words or phrases. Thus, we recommend that you always use a wildcard!

Exception: Wildcards are not allowed with a partial formula query.


Wildcards

A wildcard is a place holder within a string of text or numeric values that represents unspecified characters.

Note

Wildcard        Definition

     %               A place holder for at least

                       one unspecified character

     _                A place holder for solely one

                       unspecified character

For example:


Note

Without a wildcard in your query, you retrieve solely the word or phrase that you specified. You might not retrieve records that contain additional words or phrases. Thus, we recommend that you always use a wildcard!

Exceptions: In a reaction database, you cannot use the query LIKE "_", the wildcard % may only appear at the beginning or end of the search query string, and you cannot include the letters "to" in your query because ISIS interprets them as a range.


Wildcards

A wildcard is a place holder within a string of text or numeric values that represents unspecified characters.

Note

Wildcard        Definition

     %               A place holder for at least

                       one unspecified character

     _                A place holder for solely one

                       unspecified character

For example:


Note

Without a wildcard in your query, you retrieve solely the word or phrase that you specified. You might not retrieve records that contain additional words or phrases. Thus, we recommend that you always use a wildcard!

Exception: Wildcards are not allowed with a partial formula query.


Wildcards

A wildcard is a place holder within a string of text or numeric values that represents unspecified characters.

Note

Wildcard        Definition

     %               A place holder for at least

                       one unspecified character

     _                A place holder for solely one

                       unspecified character


Note

Without a wildcard in your query, you retrieve solely the word or phrase that you specified. You might not retrieve records that contain additional words or phrases. Thus, we recommend that you always use a wildcard!

Exceptions: In a reaction database, you cannot use the query LIKE "_", the wildcard % may only appear at the beginning or end of the search query string, and you cannot include the letters "to" in your query because ISIS interprets them as a range.


Wildcards

A wildcard is a place holder within a string of text or numeric values that represents unspecified characters.

Note

Wildcard        Definition

     %               A place holder for at least

                       one unspecified character

     _                A place holder for solely one

                       unspecified character

For example, to retrieve all records that contain TG092 somewhere within the ID number for the record, enter:

LIKE "%TG092%"


Note

Without a wildcard in your query, you retrieve solely the word or phrase that you specified. You might not retrieve records that contain additional words or phrases. Thus, we recommend that you always use a wildcard!


Wildcards

A wildcard is a place holder within a string of text or numeric values that represents unspecified characters.

Note

Wildcard        Definition

     %               A place holder for at least

                       one unspecified character

     _                A place holder for solely one

                       unspecified character

For example, to retrieve all records that contain TG092 somewhere within the ID number for the record, enter:

LIKE "%TG092%"


Wildcards

A wildcard is a place holder within a string of text or numeric values that represents unspecified characters.

Note

Wildcard        Definition

     %               A place holder for at least

                       one unspecified character

     _                A place holder for solely one

                       unspecified character

For example, to retrieve all records between LODE00000001 or MUSE00000001 and MUSE00000009, enter:

BETWEEN "%E%01%" "MUSE00000009"


2D Structure

A 2D structure is a two-dimensional representation of a molecule. For example, the 2D structure of Benzaldehyde can be represented as follows:


2D Structure

A 2D structure is a two-dimensional representation of a reaction component. For example, the 2D structure of the reactant Benzaldehyde can be represented as follows:


2D Substructure

A 2D substructure is any portion of a 2D structure. (A 2D structure is a two-dimensional representation of a molecule.)

Examples of 2D substructures of Benzaldehyde:

The 2D structure Benzaldehyde:


2D Substructure

A 2D substructure is any portion of a 2D structure. (A 2D structure is a two-dimensional representation of a reaction component.)

Examples of 2D substructures of Benzaldehyde:

The 2D structure Benzaldehyde:


Search Operator

A search operator specifies the type of search to be conducted. For example, to conduct a search that retrieves the exact match of the ID number in your search query:

*	Use the search operator = (equal sign) if your ID number contains no text.

*	Use the search operator LIKE (with double quotes around the ID number) if your ID number contains text (or text and numeric values).


Search Operator

A search operator specifies the type of search to be conducted. For example, to conduct a search that retrieves the exact match of the CAS number in your search query:

*	Use the search operator = (equal sign) if your CAS number contains no text.

*	Use the search operator LIKE (with double quotes around the CAS number) if your CAS number contains text (or text and numeric values).


Search Operator

A search operator specifies the type of search to be conducted. For example, to conduct a search that retrieves the exact match of the company name in your search query, use the search operator LIKE (with double quotes around the company name).


Search Operator

A search operator specifies the type of search to be conducted. For example, to conduct a search that retrieves the exact match of the molecular weight in your search query, use the search operator = (equal sign).


Search Operator

A search operator specifies the type of search to be conducted. For example, to conduct a search that retrieves the exact match of the compound name in your search query, use the search operator LIKE (with double quotes around the compound name).


Search Operator

A search operator specifies the type of search to be conducted. For example, to conduct a search that retrieves the exact match of the type of activity in your search query, use the search operator LIKE (with double quotes around the activity).


Search Operator

A search operator specifies the type of search to be conducted. For example, to conduct a search that retrieves the exact match of the melting point in your search query, use the search operator = (equal sign).


Search Operator

A search operator specifies the type of search to be conducted. For example, to conduct a search that retrieves the exact match of the name of the author in your search query, use the search operator LIKE (with double quotes around the author).


Search Operator

A search operator specifies the type of search to be conducted. For example, to conduct a search that retrieves the exact match of the yield in your search query, use the search operator = (equal sign).


Search Operator

A search operator specifies the type of search to be conducted. For example, to conduct a search that retrieves the exact match of the reaction temperature in your search query, use the search operator = (equal sign).


Search Operator

A search operator specifies the type of search to be conducted. For example, use the search operator = (equal sign) to conduct a search that finds records that match your numeric target value exactly. A target value can contain wildcards. (Target values that contain text or wildcards require double quotes.)


Search Operator

A search operator specifies the type of search to be conducted. For example, use the search operator = (equal sign) to conduct a search that finds records that match a numeric value exactly, such as = 95.


Search Operator

A search operator specifies the type of search to be conducted. For example, use the search operator = (equal sign) to conduct a search that finds records that match your numeric target value exactly. (Target values that contain text require double quotes.)


Search Operator

A search operator specifies the type of search to be conducted. For example, use the search operator => (greater than or equal to) to conduct a search that finds records that are greater than or equal to your numeric target value. A target value can contain wildcards. (Target values that contain text or wildcards require double quotes.)


Search Operator

A search operator specifies the type of search to be conducted. Use the search operator BETWEEN to conduct a search that finds records that are between (and including) your upper and lower target values. A target value can contain wildcards. (Target values that contain text or wildcards require double quotes.)


Search Operator

A search operator specifies the type of search to be conducted. For example, use the search operator = (equal sign) to conduct a search that finds records that match your numeric target value exactly. A target value can contain wildcards. (Target values that contain text or wildcards require double quotes.)


File Names of 2D Structures or 2D Substructures

To include a graphical structure in the QB query, you must enter its file name (not the structure). For example, you might enter the file name BENZALD for the 2D structure (the two-dimensional representation of a molecule) of Benzaldehyde:

Or, you might enter the file name BENZFRAG for any of these 2D substructures (any portion of a 2D structure) of Benzaldehyde:


File Names of 2D Structures or 2D Substructures

To include a graphical structure in the QB query, you must enter its file name (not the structure). For example, you might enter the file name BENZALD for the 2D structure (the two-dimensional representation of a molecule) of Benzaldehyde:

Or, you might enter the file name BENZFRAG for any of these 2D substructures (any portion of a 2D structure) of Benzaldehyde:


Graphical Data

To include a graphical structure in the QB query, you must enter its file name (not the structure). For example, you might enter the file name BENZALD for the 2D structure (the two-dimensional representation of a molecule) of Benzaldehyde:

Or, you might enter the file name BENZFRAG for any of these 2D substructures (any portion of a 2D structure) of Benzaldehyde:


File Names of Graphical Structures

To include a graphical structure in the QB query, you must enter its file name (not the structure). For example, you might enter the file name BENZALD for the 2D structure (the two-dimensional representation of a molecule) of the reactant Benzaldehyde:

Or, you might enter the file name RXN1 for a reaction structure or a reaction substructure:


File Names of Graphical Structures

To include a graphical structure in the QB query, you must enter its file name (not the structure). For example, you might enter the file name BENZALD for the 2D structure of benzaldehyde:

Or, you might enter the file name Q3D for a 3D structure or 3D substructure:


File Names of Graphical Structures

To include a graphical structure in the QB query, you must enter its file name (not the structure). For example, you might enter the file name BENZALD for the 2D structure of benzaldehyde:

Or, you might enter the file name Q3D for a 3D substructure:


Text/Numeric Strings in QB Queries

A text/numeric string is a phrase in a box or cell on the form that specifies the retrieval of specific records. This phrase is the QB query. Each phrase contains:

*	The database field that you want to search (such as the melting point field MOL>MELTING.POINT).

*	A search operator that specifies the type of search (such as a greater than sign, =, to specify a search that finds solely the target text in the query).

*	The text or numeric target value (specific data) that you want to find.

For example, to find records that contain structures with a melting point that is greater than 220, enter: MOL>MELTING.POINT > 220

Note: You can combine statements in a single text/numeric string with one of the logical operators AND, OR, and NOT.


Text or Numeric Data

A text/numeric string is a phrase in a box or cell on the form that specifies the retrieval of specific records. This phrase is the QB query. Each phrase contains:

*	The database field that you want to search (such as the melting point field MOL>MELTING.POINT).

*	A search operator that specifies the type of search (such as a greater than sign, =, to specify a search that finds solely the target text in the query).

*	The text or numeric target value (specific data) that you want to find.

For example, to find records that contain structures with a melting point that is greater than 220, enter: MOL>MELTING.POINT > 220

Note: You can combine statements in a single text/numeric string with one of the logical operators AND, OR, and NOT.


Text/Numeric Strings in QB Queries

A text/numeric string is a phrase in a box or cell on the form that specifies the retrieval of specific records. This phrase is the QB query. Each phrase contains:

*	The database field that you want to search (such as the melting point field MOL>MELTING.POINT).

*	A search operator that specifies the type of search (such as a greater than sign, =, to specify a search that finds solely the target text in the query).

*	The text or numeric target value (specific data) that you want to find.

For example, to find records that contain reactants with a melting point that is greater than 220, enter:

RXN>reactant_link>MOL>MELTING.POINT > 220

Note: You can combine statements in a single text/numeric string with one of the logical operators AND, OR, and NOT.


Text/Numeric Strings in QB Queries

A text/numeric string is a phrase in a box or cell on the form that specifies the retrieval of specific records. This phrase is the QB query. Each phrase contains:

*	The database field that you want to search (such as the molecular weight field MODEL>MOL>MOL.WEIGHT).

*	A search operator that specifies the type of search (such as a greater than sign, =, to specify a search that finds solely the target text in the query).

*	The text or numeric target value (specific data) that you want to find.

For example, to find records that contain structures with a melting point that is greater than 500, enter: MODEL>MOL>MOL.WEIGHT > 500

Note: You can combine statements in a single text/numeric string with one of the logical operators AND, OR, and NOT.


Search Operators

Use the following search operators with structural data (2D structures, 3D structures, or reactions):

Operator	Search Type

=	exact match

SSS	2D substructure

ISOMER	isomer (remote databases)

TAUTOMER	tautomer (remote databases)

PARENT	parent (remote databases)

FLEXMATCH <v1>	Flexmatch (remote databases)

MSIMILAR <type><v1>	molecule similarity (remote databases)

SAMEAS3D <v1> <v2>	3D exact match

SSS3D <v1> <v2> <cfs>	CFS (remote databases)

SSS3D <v1> <v2>	3D substructure searches where the query contains submodel components (remote databases)

SSS	3D substructure where the query does not contain submodel components (remote databases)

RSS	reaction substructure

SUBSET	reaction subset (remote databases)

RSIMILAR <v1><v2>	reaction similarity (remote)

For FLEXMATCH, <v1> is a three-letter code that tells ISIS which flexmatch parameters are switched off and on.

For MSIMILAR, <type> is a text string that specifies the amount of similarity to your query (normal, SUB, or SUPER), and <v1> is the similarity value.

For RSIMILAR, <v1> is the transformational similarity value and <v2> is the structural similarity value.

For SAMEAS3D and SSS3D, <v1> is the value of the maximum atomic displacement and <v2> is the value of the maximum RMS deviation. Both <v1> and <v2> are required.

For SSS3D, <cfs> specifies a CFS search and CFS options. The <cfs> value is optional.

For RSIMILAR, <v1> is the transformational similarity value and <v2> is the structural similarity value.


Search Operators

Use the following search operators with 2D structures in remote databases:

Operator	Search Type

=	exact match

SSS	substructure

ISOMER	isomer

TAUTOMER	tautomer

PARENT	parent

FLEXMATCH <v1>	Flexmatch

MSIMILAR <type><v1>	molecule similarity

For FLEXMATCH, <v1> is a three-letter code that tells ISIS which flexmatch parameters are switched off and on.

For MSIMILAR, <type> is a text string that specifies the amount of similarity to your query (normal, SUB, or SUPER), and <v1> is the similarity value.

For more information, see Searching Concepts/Examples.


Search Operators

Use the following search operators with 2D structures in local databases:

Operator	Search Type

=	exact match

SSS	substructure

For more information, see Searching Concepts/Examples.


Search Operators

Use the following search operators with 2D structures in remote databases:

Operator	Search Type

=	exact match

SSS	substructure

ISOMER	isomer

TAUTOMER	tautomer

PARENT	parent

FLEXMATCH <v1>	Flexmatch

MSIMILAR <type><v1>	molecule similarity

For FLEXMATCH, <v1> is a three-letter code that tells ISIS which flexmatch parameters are switched off and on.

For MSIMILAR, <type> is a text string that specifies the amount of similarity to your query (normal, SUB, or SUPER), and <v1> is the similarity value.

For more information, see Searching Concepts/Examples.


Search Operators

Use the following search operators with 2D structures in local databases:

Operator	Search Type

=	exact match

SSS	substructure

For more information, see Searching Concepts/Examples.


Search Operators

Use the following search operators with structures in remote databases:

Operator	Search Type

=	exact match

SSS	substructure

ISOMER	isomer

TAUTOMER	tautomer

PARENT	parent

FLEXMATCH <v1>	Flexmatch

MSIMILAR <type><v1>	molecule similarity

For FLEXMATCH, <v1> is a three-letter code that tells ISIS which flexmatch parameters are switched off and on.

For MSIMILAR, <type> is a text string that specifies the amount of similarity to your query (normal, SUB, or SUPER), and <v1> is the similarity value.

For more information, see Searching Concepts/Examples.


Search Operators

Use the following search operators with structures in local databases:

Operator	Search Type

=	exact match

SSS	substructure

For more information, see Searching Concepts/Examples.


Search Operators

Use the following search operators with reactions in remote databases:

Operator	Search Type

=	exact match

RSS	reaction substructure

SUBSET	reaction subset

RSIMILAR <v1><v2>	reaction similarity

For RSIMILAR, <v1> is the transformational similarity value and <v2> is the structural similarity value.

For more information, see Searching Concepts/Examples.


Search Operators

Use the following search operators with reactions in local databases:

Operator	Search Type

=	exact match

RSS	reaction substructure

For more information, see Searching Concepts/Examples.


Search Operators

Use the following search operators with 3D structures in remote databases:

Operator	Search Type

SAMEAS3D <v1> <v2>	3D exact match

SSS3D <v1> <v2> <cfs>	CFS

SSS3D <v1> <v2>	3D substructure searches where the query contains submodel components

SSS	3D substructure where the query does not contain submodel components

For SAMEAS3D and SSS3D, <v1> is the value of the maximum atomic displacement and <v2> is the value of the maximum RMS deviation. Both <v1> and <v2> are required.

For SSS3D, <cfs> specifies a CFS search and CFS options. The <cfs> value is optional.

For more information, see Searching Concepts/Examples.


Search Operators

Use the following search operator with 3D structures in local databases:

Operator	Search Type

=	exact match

SSS	substructure

For more information, see Searching Concepts/Examples.


Search Operators

Use the following search operators with text or numeric data:

Operator	Definition

<	less than

<=	less than or equal to

>	greater than

>=	greater than or equal to

<>	not equal

=	equal

LIKE	text substring

BETWEEN	numeric or text range

EXISTS	numeric or text values for a field that accepts this search operator (or you see an error message)


The Complete List of Searches

There are over sixty different searches in ISIS/Base. Whether you search a remote OR local database for molecule OR reaction records is significant when you decide on a search.

Note: Some searches are for remote databases only! For example, you cannot conduct isomer, tautomer, flexmatch, or similarity searches in a local database.

To obtain specific help, click The ISIS/Base Chemical Searches -- and How to do Them, click the specific search that you need, and then click Step-by-Step Instructions. You will find a help screen that contains all the information that you need to conduct your search.


Revising a Query

If you do not obtain the correct search results, you might want to revise your query, and then conduct the same search again.

To obtain specific help, click The ISIS/Base Chemical Searches -- and How to do Them, click the specific search that you need, and then click Searching Concepts/Examples. Scroll to the section Guidelines for Revising the Query. You will find a help screen that contains all the information that you need to revise your query.


Searching Examples

There is a unique set of searching examples for each type of search. These examples are with the step-by-step instructions for each search.

In order to find the correct examples, it is important to choose exactly the correct search. For example, whether you search a remote OR local database for molecule OR reaction records is significant.

To obtain a specific set of searching examples, click The ISIS/Base Chemical Searches -- and How to do Them, click the specific search that you need, and then click Searching Concepts /Examples.

Each set of searching examples is in a format that you can easily print. The examples also include a full search definition, concepts and guidelines, and ways that you can define or revise your query.


To obtain a POLY/Sub query

Searching Concepts/Examples

POLY/Sub queries contain a combination of a polymer structure and/or text/numeric strings in different boxes and tables on the form. Example

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the MOLSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new graphical query.

*	Import a graphical query from a molfile.

*	Restore a graphical query that you previously saved as an object in the database.

5.	(Optional) To enter text or numeric data, do one of the following:

*	Enter a new text/numeric query

*	Obtain an existing text/numeric query.

6.	(Optional) Repeat Step 5 as needed. You can conduct a single search with a maximum of 25 queries.


Structures in POLY/Sub Queries

A polymer structure in a POLY/Sub query is the graphical image in a box or cell on the form that specifies the retrieval of polymer structures. A polymer structure can be either of the following:

*	Polymer structure, a two-dimensional representation of a polymer, such as:

*	Polymer substructure, any portion of a polymer structure. The substructure can also contain query features. For example:


Text/Numeric Strings in POLY/Sub Queries

A text/numeric string in a POLY/Sub query is a phrase in a box or cell on the form that specifies the retrieval of data.

Each phrase contains:

*	A search operator that specifies the type of search (such as an equal sign, =, to specify a search that finds solely the exact target text in the query).

*	The text or numeric target value (specific data) that you want to find.

For example, to find structures with a number-average molecular weight greater than 20,000, enter > 20000 in the Number-Average Molecular Weight box (where > is the search operator and 20000 is the target value).


Examples
Example


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing Polymers: MDL Requirements for Database Searching and Registration or

Drawing a 2D Structure or

Specifying Query Features or

Specifying Stereochemistry or

Guidelines for Revising the Query.

3.	Transfer the query back to ISIS/Base.


To import an existing query from a molfile

Searching Concepts/Examples

Use this procedure to import a structure query from a molfile that was created in ISIS or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

Searching Concepts/Examples

You can restore a structure query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Searching Concepts/Examples

Use this procedure to edit an existing polymer structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing Polymers: MDL Requirements for Database Searching and Registration or

Drawing a 2D Structure or

Specifying Query Features or

Specifying Stereochemistry.

4.	Transfer the query back to ISIS/Base.


To enter a new text/numeric query

Searching Concepts/Examples

Use this procedure to enter a new text/numeric string (a query) to the boxes and table cells on the form. If you enter more than one query into a single form, ISIS joins your query strings automatically with the boolean algebraic operator AND. Example

1.	Select the box or table cell of your choice (if not highlighted).

2.	Enter the search operator.

3.	Enter a space.

4.	Enter the text and/or numeric values that you want to find. You can enter a maximum of 25 queries into the same table. Examples

Notes: (1) You can also enter a partial query with at least one wildcard. (Do not use wildcards with a partial formula query.) (2) Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

5.	(Optional) Repeat Steps 1 through 4 as needed.

See also:

To delete characters from the query

To edit the characters of an existing query


To obtain a POLY/Co query

POLY/Co queries contain a combination of a polymer structure and/or text/numeric strings in different boxes and tables on the form. Example

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the MOLSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.

5.	(Optional) To enter text or numeric data, do one of the following:

*	Enter a new text/numeric query

*	Obtain an existing text/numeric query.

6.	(Optional) Repeat Step 5 as needed. You can conduct a single search with a maximum of 25 queries.


Structures in POLY/Co Queries

A polymer structure in a POLY/Co query is the graphical image in a box or cell on the form that specifies the retrieval of copolymers that contain the query. For example:


Text/Numeric Strings in POLY/Sub Queries
Text/Numeric Strings in POLY/Co Queries

A text/numeric string in a POLY/Co query is a phrase in a box or cell on the form that specifies the retrieval of data.

Each phrase contains:

*	A search operator that specifies the type of search (such as an equal sign, =, to specify a search that finds solely the exact target text in the query).

*	The text or numeric target value (specific data) that you want to find.

For example, to find structures with a number-average molecular weight greater than 20,000, enter > 20000 in the Number-Average Molecular Weight box (where > is the search operator and 20000 is the target value).


Example


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing Polymers: MDL Requirements for Database Searching and Registration or

Drawing a 2D Structure or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


To import an existing query from a molfile

Use this procedure to import a structure query from a molfile that was created in ISIS or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a structure query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing Polymers: MDL Requirements for Database Searching and Registration or

Drawing a 2D Structure or

Specifying Query Features or

Specifying Stereochemistry.

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base


To enter a new text/numeric query

Searching Concepts/Examples

Use this procedure to enter a new text/numeric string (a query) to the boxes and table cells on the form. If you enter more than one query into a single form, ISIS joins your query strings automatically with the boolean algebraic operator AND. Example

1.	Select the box or table cell of your choice (if not highlighted).

2.	Enter the search operator.

3.	Enter a space.

4.	Enter the text and/or numeric values that you want to find. You can enter a maximum of 25 queries into the same table. Examples

Notes: (1) You can also enter a partial query with at least one wildcard. (Do not use wildcards with a partial formula query.) (2) Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

5.	(Optional) Repeat Steps 1 through 4 as needed.

See also:

To delete characters from the query

To edit the characters of an existing query


To obtain a POLY/Both query

POLY/Both queries contain a combination of a polymer structure and/or text/numeric strings in different boxes and tables on the form. Example

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the MOLSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.

5.	(Optional) To enter text or numeric data, do one of the following:

*	Enter a new text/numeric query

*	Obtain an existing text/numeric query.

6.	(Optional) Repeat Step 5 as needed. You can conduct a single search with a maximum of 25 queries.


Structures in POLY/Both Queries

A polymer structure in a POLY/Both query is the graphical image in a box or cell on the form that specifies the retrieval of polymer structures. For example:


Text/Numeric Strings in POLY/Both Queries

A text/numeric string in a POLY/Both query is a phrase in a box or cell on the form that specifies the retrieval of data.

Each phrase contains:

*	A search operator that specifies the type of search (such as an equal sign, =, to specify a search that finds solely the exact target text in the query).

*	The text or numeric target value (specific data) that you want to find.

For example, to find structures with a number-average molecular weight greater than 20,000, enter > 20000 in the Number-Average Molecular Weight box (where > is the search operator and 20000 is the target value).


Examples
Example


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing Polymers: MDL Requirements for Database Searching and Registration or

Drawing a 2D Structure or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


To import an existing query from a molfile

Use this procedure to import a structure query from a molfile that was created in ISIS or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a structure query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing Polymers: MDL Requirements for Database Searching and Registration or

Drawing a 2D Structure or

Specifying Stereochemistry.

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base


To enter a new text/numeric query

Searching Concepts/Examples

Use this procedure to enter a new text/numeric string (a query) to the boxes and table cells on the form. If you enter more than one query into a single form, ISIS joins your query strings automatically with the boolean algebraic operator AND. Example

1.	Select the box or table cell of your choice (if not highlighted).

2.	Enter the search operator.

3.	Enter a space.

4.	Enter the text and/or numeric values that you want to find. You can enter a maximum of 25 queries into the same table. Examples

Notes: (1) You can also enter a partial query with at least one wildcard. (Do not use wildcards with a partial formula query.) (2) Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

5.	(Optional) Repeat Steps 1 through 4 as needed.

See also:

To delete characters from the query

To edit the characters of an existing query


To obtain a POLY/Exact query

POLY/Exact queries contain a combination of a polymer structure and/or text/numeric strings in different boxes and tables on the form. Example

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the MOLSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.

5.	(Optional) To enter text or numeric data, do one of the following:

*	Enter a new text/numeric query

*	Obtain an existing text/numeric query.

6.	(Optional) Repeat Step 5 as needed. You can conduct a single search with a maximum of 25 queries.


Structures in POLY/Exact Queries

A polymer structure in a POLY/Exact query is the graphical image in a box or cell on the form that specifies the retrieval of polymer structures. For example:


Text/Numeric Strings in POLY/Exact Queries

A text/numeric string in a POLY/Exact query is a phrase in a box or cell on the form that specifies the retrieval of data.

Each phrase contains:

*	A search operator that specifies the type of search (such as an equal sign, =, to specify a search that finds solely the exact target text in the query).

*	The text or numeric target value (specific data) that you want to find.

For example, to find structures with a number-average molecular weight greater than 20,000, enter > 20000 in the Number-Average Molecular Weight box (where > is the search operator and 20000 is the target value).


Examples
Example


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing Polymers: MDL Requirements for Database Searching and Registration or

Drawing a 2D Structure or

Specifying Stereochemistry.

3.	Transfer the query back to ISIS/Base.


To import an existing query from a molfile

Use this procedure to import a polymer query from a molfile that was created in ISIS or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected structure is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a polymer query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected structure is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the structure that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing Polymers: MDL Requirements for Database Searching and Registration or

Drawing a 2D Structure or

Specifying Stereochemistry.

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base


To enter a new text/numeric query

Searching Concepts/Examples

Use this procedure to enter a new text/numeric string (a query) to the boxes and table cells on the form. If you enter more than one query into a single form, ISIS joins your query strings automatically with the boolean algebraic operator AND. Example

1.	Select the box or table cell of your choice (if not highlighted).

2.	Enter the search operator.

3.	Enter a space.

4.	Enter the text and/or numeric values that you want to find. You can enter a maximum of 25 queries into the same table. Examples

Notes: (1) You can also enter a partial query with at least one wildcard. (Do not use wildcards with a partial formula query.) (2) Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

5.	(Optional) Repeat Steps 1 through 4 as needed.

See also:

To delete characters from the query

To edit the characters of an existing query


To obtain an SSS/Poly query

Searching Concepts/Examples

SSS/Poly queries contain a polymer structure. You search for polymers that contain your query wholly within a larger, stored polymer. Examples

1.	Click Query (if not highlighted).

2.	(Optional) To remove all data from the form, choose Edit > Clear Data > Form.

3.	Select the MOLSTRUCTURE box (if not highlighted).

4.	Do one of the following:

*	Draw a new query.

*	Import a query from a molfile.

*	Restore a query that you previously saved as an object in the database.


Structures in SSS/Poly Queries

A polymer structure in an SSS/Poly query is the graphical image in a box or cell on the form that specifies the retrieval of polymer structures. A polymer structure can be either of the following:

*	Polymer structure, a two-dimensional representation of a polymer, such as:

*	Polymer substructure, any portion of a polymer structure. The substructure can also contain query features.  For example:


Examples
Example


To draw a new query

Searching Concepts/Examples

1.	Transfer to ISIS/Draw.

2.	Draw the query. (If you printed a specific query while in the SearchSelector, you need to create your adaptation of this query now.) If you need help, click:

Drawing Polymers: MDL Requirements for Database Searching and Registration or

Drawing a 2D Structure or

Specifying Query Features or

Specifying Stereochemistry or

3.	Transfer the query back to ISIS/Base.


To import an existing query from a molfile

Use this procedure to import a single polymer query from a molfile that was created in ISIS or MACCS-II.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose File > Import > Molfile. (To retrieve a PC-molfile on the Macintosh, press and hold the Option key while you complete this step.)

4.	Click the name of an existing file in the Files list box (change your directory or folder if necessary). You see the name of the file in the Open File Name text box.

5.	Click OK (Mac=Open). The selected polymer query is imported into your form.

6.	(Optional) You can edit the existing query.


To restore an existing query from a database

You can restore a polymer query that you previously saved as an object in the remote-access file of your database. Use this procedure to restore a query from a database that is open currently in ISIS/Base.

1.	Click Query (if not highlighted).

2.	Select the MOLSTRUCTURE box. It highlights.

3.	Choose Database > Restore Molecule.

4.	Click the name of an existing file in the Select Object list box.

5.	Click OK (Mac=Open). The selected polymer query is restored into your form.

6.	(Optional) You can edit the existing query.


To edit an existing query

Use this procedure to edit an existing structure that you see in a box or table cell in ISIS/Base.

1.	Select the MOLSTRUCTURE box that contains the polymer that you want to edit. An ISIS/Draw window opens that contains the structure.

2.	Click the structure. You see the structure in ISIS/Draw.

3.	Edit the query. If you need help, click:

Drawing Polymers: MDL Requirements for Database Searching and Registration or

Drawing a 2D Structure or

Specifying Query Features or

Specifying Stereochemistry or

Guidelines for Revising the Query.

4.	Transfer the query back to ISIS/Base.


A Temporary List, Structure, or Query

A temporary list, structure, or query is a database object that is not stored in the database when you close the database.


The ISIS/Base SearchSelector (TM)

How to Choose the Best Type of Search -- and How To Do It

There are approximately 100 different types of chemistry questions that you can ask in ISIS. How do you determine which is the best search for your particular question? The SearchSelector will help you find the best search:

1. We will soon show you a comprehensive list of sample chemistry questions. 2. You then choose the sample question that most closely resembles your question. 3. We will then show you how to convert your question into an ISIS search, complete with step-by-step instructions.

The SearchSelector will guide you to the most relevant search only if you choose your responses carefully!

Click here to continue:


The ISIS/Base SearchSelector [TM]
The ISIS/Base SearchSelector (TM)

I want to find information on (click one):

*	Reactions (including entire reactions, reactants, products, solvents, catalysts, and parent compounds)

*	Molecules (that are not part of any reaction)

*	3D Structures (3D representations of molecules)

*	Suppliers (Manufacturers of chemicals)

*	Specific ID Numbers in my database

*	All Records in my database

*	Biopolymers


Which database do you use?

Click one of the following:

Remote molecule database

Remote reaction database

Remote 3D database

Local molecule database

Local reaction database

Local 3D database


Remote Molecule Database

A remote molecule database is a database with information on molecules that typically exists on a mainframe computer. To do a remote search, you need to obtain network access information.

An ID search finds the records that contain the corporate identification numbers that you specify in your query. To do this type of search, you need:

*	An ID field in your database. This is a field in the database that contains corporate identification numbers for the records in your database.

*	A box or table in a form that is linked to the ID field. A form is the set of boxes and/or tables that you use to hold your query and to view the results of a search.

If you do not have these items, see your ISIS Administrator.

Click here for step-by-step instructions


Local Molecule Database

A local molecule database is a database with information on molecules that typically exists on your hard disk. To do a local search on your hard disk, you do not need to access network information.

Note: To do a local search that is accessed from a shared network, you need to access network information.

An ID search finds the records that contain the corporate identification numbers that you specify in your query. To do this type of search, you need:

*	An ID field in your database. This is a field in the database that contains corporate identification numbers for the records in your database.

*	A box or table in a form that is linked to the ID field. A form is the set of boxes and/or tables that you use to hold your query and to view the results of a search.

If you do not have these items, see your ISIS Administrator.

Click here for step-by-step instructions


Remote Reaction Database

A remote reaction database is a database with information on reactions and reaction components that typically exists on a mainframe computer. To do a remote search, you need to obtain network access information.

An ID search finds the records that contain the corporate identification numbers that you specify in your query. To do this type of search, you need:

*	An ID field in your database. This is a field in the database that contains corporate identification numbers for the records in your database.

*	A box or table in a form that is linked to the ID field. A form is the set of boxes and/or tables that you use to hold your query and to view the results of a search.

If you do not have these items, see your ISIS Administrator.

Click here for step-by-step instructions


Local Reaction Database

A local reaction database is a database with information on reactions and reaction components that typically exists on your hard disk. To do a local search on your hard disk, you do not need to access network information.

Note: To do a local search that is accessed from a shared network, you need to access network information.

An ID search finds the records that contain the corporate identification numbers that you specify in your query. To do this type of search, you need:

*	An ID field in your database. This is a field in the database that contains corporate identification numbers for the records in your database.

*	A box or table in a form that is linked to the ID field. A form is the set of boxes and/or tables that you use to hold your query and to view the results of a search.

If you do not have these items, see your ISIS Administrator.

Click here for step-by-step instructions


Remote 3D Database

A remote 3D database is a database with information on 3D structures that typically exists on a mainframe computer. To do a remote search, you need to obtain network access information.

An ID search finds the records that contain the corporate identification numbers that you specify in your query. To do this type of search, you need:

*	An ID field in your database. This is a field in the database that contains corporate identification numbers for the records in your database.

*	A box or table in a form that is linked to the ID field. A form is the set of boxes and/or tables that you use to hold your query and to view the results of a search.

If you do not have these items, see your ISIS Administrator.

Click here for step-by-step instructions


Local 3D Database

A local 3D database is a database with information on 3D that typically exists on your hard disk. To do a local search on your hard disk, you do not need to access network information.

Note: To do a local search that is accessed from a shared network, you need to access network information.

An ID search finds the records that contain the corporate identification numbers that you specify in your query. To do this type of search, you need:

*	An ID field in your database. This is a field in the database that contains corporate identification numbers for the records in your database.

*	A box or table in a form that is linked to the ID field. A form is the set of boxes and/or tables that you use to hold your query and to view the results of a search.

If you do not have these items, see your ISIS Administrator.

Click here for step-by-step instructions


Which database do you use?

Click one of the following:

Remote molecule database

Remote reaction database

Remote 3D database

Local molecule database

Local reaction database

Local 3D database


Remote Molecule Database

A remote molecule database is a database with information on molecules that typically exists on a mainframe computer. To do a remote search, you need to obtain network access information.

An ALL search finds every record in the database. You do not use a query for this search.

Click here for step-by-step instructions


Local Molecule Database

A local molecule database is a database with information on molecules that typically exists on your hard disk. To do a local search on your hard disk, you do not need to access network information.

Note: To do a local search that is accessed from a shared network, you need to access network information.

An ALL search finds every record in the database. You do not use a query for this search.

Click here for step-by-step instructions


Remote Reaction Database

A remote reaction database is a database with information on reactions and reaction components that typically exists on a mainframe computer. To do a remote search, you need to obtain network access information.

An ALL search finds every record in the database. You do not use a query for this search.

Click here for step-by-step instructions


Local Reaction Database

A local reaction database is a database with information on reactions and reaction components that typically exists on your hard disk. To do a local search on your hard disk, you do not need to access network information.

Note: To do a local search that is accessed from a shared network, you need to access network information.

An ALL search finds every record in the database. You do not use a query for this search.

Click here for step-by-step instructions


Remote 3D Database

A remote 3D database is a database with information on 3D structures that typically exists on a mainframe computer. To do a remote search, you need to obtain network access information.

An ALL search finds every record in the database. You do not use a query for this search.

Click here for step-by-step instructions


Local 3D Database

A local 3D database is a database with information on 3D that typically exists on your hard disk. To do a local search on your hard disk, you do not need to access network information.

Note: To do a local search that is accessed from a shared network, you need to access network information.

An ALL search finds every record in the database. You do not use a query for this search.

Click here for step-by-step instructions


  I Want to Find Information on Reactions

Click one of these items:

*	I need to transform one functional group to another. I want to find reagent/catalysts/conditions, other associated data, or related transformations.

*	I have specific reagent/catalysts or specific types of reagent/catalysts of interest. I want to include or exclude transformations that use these specific reagent/catalysts or types of reagent/catalysts.

*	I need to synthesize specific types of products. I want to find reagent/catalysts/conditions, other associated data, or related syntheses.

*	I have one specific product of interest. I want to find all routes of its synthesis, all the routes of synthesis for related products, or all associated data.

*	I want explore the chemistry of specific reactants. I want to find all transformations that use them, transformations that use related reactants, or specific data that is associated with them.

*	I have some specific data or a combination of structures and data. I want to find all related transformations.

*	I have a specific transformation of interest. I want to find reagent/catalysts, conditions, other associated data, or related transformations.

What to do if you could not find a suitable sample question


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

I need to transform one functional group to another.  For this transformation, I want to find:

1.	All reported reagent/catalysts and conditions. (Example: Transformation of cinnamaldehyde to cinnamyl alcohol)

2.	Reactants and/or products with the following structural constraint:

(a) Must be aromatic. (Example: Aromatic aldehydes, where an aromatic bond is attached to the aldehyde)

(b) Must convert stereospecifically. (Example: Stereospecific conversion to a Down bond for the functional group 2-methylcyclopentanone)

(c) Must not react. (Example: An acyclic ketone that must not react when a cyclic ketone is reduced)

(d) Must contain a specific atom. (Example: Reactants and products that contain a bromine 4 carbons from an aldehyde that is oxidized to a carboxylic acid)

(e) Must contain one of a list of alternative atoms. (Example: All heterocyclic unsaturated reactants and heterocyclic saturated products with one of 3 defined heteroatoms, N, S, or O, at a single position in the ring)

(f) Must exclude a specific atom or a specific list of alternative atoms. (Example: All 3-methylpyridine reactants and nicotinic acid products that exclude bromine and chlorine at Position 5 in the pyridine ring)

(g) Must contain a specific functional group. (Example: The transformation must form a primary alcohol as the product.)


Question 1: "I want to find..."
     Question 1: I want to find all reported reagent/catalysts and conditions for the transformation of one functional group to another.

Example: I want to find the all reported reagent/catalysts and conditions for the transformation of cinnamaldehyde to cinnamyl alcohol.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the functional group of the reactant (in this example, cinnamaldehyde) and the functional group of the product (in this example, cinnamyl alcohol).

You need to create a search query that is a transformation.

To create the query for this example, draw the functional groups in the transformation and add the atom-atom maps (You will later place the query into the RXNSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Rxn


Question 2a: "I want to find..."
     Question 2a: I want to find all reactants and/or products in the transformation of one aromatic functional group to another aromatic functional group.

Example: I want to find all reactants and/or products in the transformation of an aromatic ketone to an aromatic aldehyde.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the functional group of the reactant (in this example, an aromatic ketone) and the functional group of the product (in this example, an aromatic aldehyde).

You need to create a search query that is a transformation.

To create the query for this example, draw the functional groups in the transformation, add the ISIS bond-query feature AROMATIC (adjacent solid and dashed lines) to allow solely aromatic bonds at the specified positions, and add the ISIS atom-query feature A to allow any atom except hydrogen at the specified positions. Then add the atom-atom maps (You will later place the query into the RXNSTRUCTURE box on the form.):

Note: If you use the automap feature, the atom-atom maps are added automatically.

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Rxn


Question 2b: "I want to find..."
     Question 2b: I want to find all reactants and/or products in the transformation of one functional group to another where the reactant is stereospecifically converted.

Example: I want to find all reactants with a specific Up bond that is stereospecifically converted to a Down bond for the functional group 2-methylcyclopentanone.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the functional group of the reactant (in this example, 2-methylcyclopentanone with an Up stereo bond) and the functional group of the product (in this example, 2-methylcyclopentanone with a Down stereo bond).

You need to create a search query that is a transformation.

To create the query for this example, draw the functional groups in the transformation with the Up and Down stereo bonds. Add the ISIS bond-query feature .Inv. in both the reactant and the product functional groups to specify that you want the Up stereo bond to stereospecifically invert to a Down bond at the specified position. Add the atom-atom maps. Then add the stereochemical designation CHIRAL to specify the retrieval of solely the absolute stereoconfigurations (You will later place the query into the RXNSTRUCTURE box on the form.):

Note: If you use the automap feature, the inversion marks on the stereo bonds and the atom-atom maps are added automatically.

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Rxn


Question 2c: "I want to find..."
     Question 2c: I want to find all reactants and/or products in the transformation of one functional group to another that contain a specific functional group that must not react.

Example: I want to find all reactants and/or products for which an acyclic ketone must not react when a cyclic ketone is reduced.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the functional group that must not react (in this example, an acyclic ketone) and the functional group that does react (in this example, a cyclic ketone).

You need to create a search query that is a transformation.

To create the query for this example, draw the functional groups in the transformation and add the ISIS bond-query features Ch to allow solely chain bonds at the specified positions and Rn to allow solely a ring bond at the specified position. Then add the atom-atom maps (You will later place the query into the RXNSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Rxn


Question 2d: "I want to find..."
     Question 2d: I want to find all reactants and/or products in the transformation of one functional group to another that contain a specific atom.

Example: I want to find all reactants and/or products that contain a bromine that is 4 carbons from an aldehyde that is oxidized to a carboxylic acid.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the functional group of the reactant (in this example, an aldehyde), the functional group of the product (in this example, a carboxylic acid), and the specific atom (in this example, a bromine that is 4 carbons from the aldehyde of the reactant and the carboxylic acid of the product).

You need to create a search query that is a transformation.

To create the query for this example, draw the functional groups in the transformation and add the ISIS bond-query feature ANY (dashed lines) to allow any bond type at the specified positions. Then add the atom-atom maps (You will later place the query into the RXNSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Rxn


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Rxn


Question 2e: "I want to find..."
     Question 2e: I want to find all reactants and/or products in the transformation of one functional group to another that contain one of a list of alternative atoms at a specific position.

Example: I want to find all heterocyclic unsaturated reactants and heterocyclic saturated products with one of 3 defined heteroatoms, N, S, or O, at a single position in the ring.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the functional groups (in this example, the heterocyclic unsaturated reactant and the heterocyclic saturated product) and the list of alternative atoms allowed at a specific position in the ring (in this example, one of 3 defined heteroatoms, N, S, or O).

You need to create a search query that is a transformation.

To create the query for this example, draw the functional groups in the transformation and add the ISIS atom-query feature List to allow the heteroatoms N, S, or O at the specified positions. Then add the atom-atom maps (You will later place the query into the RXNSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Rxn


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Rxn


Question 2e: "I want to find..."
     Question 2f: I want to find all reactants and/or products in the transformation of one functional group to another that exclude one of a list of alternative atoms at a specific position.

Example: I want to find all 3-methylpyridine reactants and nicotinic acid products that exclude bromine and chlorine at Position 5 in the pyridine ring.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the functional groups (in this example, 3-methylpyridine reactants and nicotinic acid products) and the list of alternative atoms excluded at a specific position (in this example, the exclusion of Br and Cl at Position 5 in the pyridine ring).

You need to create a search query that is a transformation.

To create the query for this example, draw the functional groups in the transformation and add the ISIS atom-query feature NOT List to exclude the halogens Br and Cl at the specified positions. Then add the atom-atom maps (You will later place the query into the RXNSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Question 2f: "I want to find..."
     Question 2g: I want to find all reactants and/or products in the transformation of one functional group to another that contain a specific functional group.

Example: I want to find all reactants and products in the transformation of one functional group to another where the product is a primary alcohol.

You can do this example in ISIS/Base only or in ISIS/Base with Reaction Browser. Each method requires a unique strategy.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the functional group (in this example, the product is a primary alcohol).

You need to do the following (for which you will receive step-by-step instructions when you need them):

*	Create a search query with the structure as the reactant (Query 1). To create Query 1, draw the reactant without the reaction arrow, and then add explicit hydrogens to prevent substitutions at other specified positions:

*	Place Query 1 into the REACTANT_STRUCTURE box on the form, execute a search, and then save the search results.

*	Clear Query 1 from the REACTANT_STRUCTURE box on the form.

*	Create a search query with the same structure as the product (Query 2):

*	Place Query 2 into the PRODUCT_STRUCTURE box on the form, execute a search, and then save the search results.

*	Subtract the search results of Query 1 from the search results of Query 2. You want the search results that remain.

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Using ISIS/Base With IRDAS

The ISIS Reaction Database Access System 1.1 or 1.2 (IRDAS) is a specialized ISIS application that allows you to do the example in a single search instead of two searches. If IRDAS is available at your site, you need to install it, and then refer to the following manual for instructions on how to conduct a By Form search: "ISIS Reaction Database Access System" (Version 1.1 or 1.2).

To create the IRDAS search query in this example, draw the structure without the reaction arrow, and then add explicit hydrogens to prevent substitutions at other specified positions.  In the IRDAS form, click Struc, SSS, and Prod for the product and NOT, Struc, SSS, and Reac for the reactant:


Using ISIS/Base With the Reaction Browser

The Reaction Browser is a specialized ISIS application that is designed to replace the ISIS application IRDAS 1.2. The Reaction Browser allows you to do the example in a single search instead of two searches. If the Reaction Browser is available at your site, you need to install it. For information on installing the Reaction Browser, see your ISIS Administrator.

To conduct the search in this example, select the Query Assistant in Reaction Browser. Then, follow the instructions on the screen to choose [image] No information for the REACTANT and [image] Substructure search for the PRODUCT. Then, click OK. You see the Query Assistant Form with a form box for the product molecule. The type of molecule search is Substructure (SSS)¸ and the role of the molecule in the reaction is Product not Reactant.

Double-click the form box and draw the product structure (without the reaction arrow) in ISIS/Draw:

Click [image] to return to Reaction Browser, then click SEARCH to conduct the search.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SSS


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SSS


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

I need to include or exclude transformations that use specific reagent/catalysts or specific types of reagent/catalysts. For these specific reagent/catalysts or types of reagent/catalysts, I want to find all transformations that:

1.	Use a specific reagent/catalyst. (Example: All epoxidation reactions that use the reagent/catalyst peroxybenzoic acid)

2.	Are general replacement reactions that use a set of reagent/catalysts. (Example: Transformations in which a cyanide group replaces any atom that is attached to a single or a double bond at a specific position in the presence of variable ring-size crown ethers)

3.	Exclude a specific reagent/catalyst or set of reagent/catalysts. (Example: Reductions of nitros to amines that DO NOT use the reagent/catalyst sodium borohydride)


Question 1: "I want to find..."
     Question 1: I want to find all transformations that use a specific reagent/catalyst.

Example: I want to find all epoxidation transformations that use the specific reagent/catalyst peroxybenzoic acid.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the specific type of transformation (in this example, epoxidation transformations) and the specific reagent/catalyst (in this example, peroxybenzoic acid).

You need to create a search query that contains both a transformation and a reagent/catalyst.

To create the query for this example, draw the functional groups in the transformation with the atom-atom maps (You will later place the query into the RXNSTRUCTURE box on the form.):

To create the reagent/catalyst for this example, draw the structure of the reagent/catalyst (You will later place the query into the CATALYST_STRUCTURE box or table cell on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Question 2: "I want to find..."
     Question 2: I want to find all general replacement reactions that use a specific type of reagent/catalyst.

Example: I want to find all transformations in which a cyanide group replaces any atom that is attached to a single or a double bond at a specified position in the presence of variable ring-size crown ethers.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the type of transformation (in this example, the general replacement reaction in which a cyanide group replaces any atom that is attached to a single or a double bond at a specified position) and the type of reagent/catalyst (in this example, variable ring-size crown ethers).

You need to create a search query that contains both a specific type of transformation and a specific type of reagent/catalyst.

To create the transformation for this example query, draw the functional groups in the transformation. Add the ISIS atom-query feature A to allow any atom at the specified position. Add the ISIS bond-query feature SINGLE/DOUBLE (double dashed lines) to allow solely single or double bonds at the specified positions. Add the ISIS reaction-query feature Make/Break (bonds marked with //) to specify that the bonds at these specified positions (the reacting center bonds) are formed or broken. Then add the atom-atom maps (You will later place the query into the RXNSTRUCTURE box on the form.):

Note: If you use the automap feature, the reacting center bonds and the atom-atom maps are added automatically.

To create the reagent/catalyst for this example query, draw the minimum sized structure, and then add the ISIS bond-query feature Rn to specify that the bonds at the specified positions are attached solely to rings (You will later place the query into the CATALYST_STRUCTURE box or table cell on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Graphical Query 1 For a Remote Database
Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Question 3: "I want to find..."
     Question 3: I want to find all transformations that exclude a specific reagent/catalyst or a specific type of reagent/catalyst.

Example: I want to find all reductions of nitros to amines that do not use the reagent/catalyst sodium borohydride.

Note: This example is for remote searching only.

You can do this example in ISIS/Base only or in ISIS/Base with Reaction Browser. Each method requires a unique strategy.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the type of transformation (in this example, reductions of nitros to amines) and the specific reagent/catalyst or type of reagent/catalyst (in this example, the reagent/catalyst sodium borohydride).

You need to do the following (for which you will receive step-by-step instructions when you need them):

*	Create a search query with the reagent/catalyst. To create the reagent/catalyst query, enter the following formula for the catalyst sodium borohydride in the box or table cell on the form that will hold a catalyst:

Na BH 4

*	Execute a search with the reagent/catalyst query, and then save the search results.

*	Clear the query from the box or table cell on the form.

*	Create a search query with the transformation. To create the transformation query, draw the functional groups in the transformation and add the ISIS reaction-query feature Make/Break (bonds marked with //) to specify that the bonds at these specified positions (the reacting center bonds) are formed or broken. Then add the atom-atom maps:

Note: If you use the automap feature, the reacting center bonds and the atom-atom maps are added automatically.

*	Place the transformation query into the RXNSTRUCTURE box on the form, execute a search, and then save the search results.

*	Subtract the search results of the reagent/catalyst query from the search results of the transformation query. You want the search results that remain.

3.	Click here to identify the type of searches that you need to do and to see the step-by-step instructions.


Using ISIS/Base With IRDAS

The ISIS Reaction Database Access System 1.1 or 1.2 (IRDAS) is a specialized ISIS application that allows you to do the example in a single search instead of two searches. If IRDAS is available at your site, you need to install it, and then refer to the following manual for instructions on how to conduct a By Form search: "ISIS Reaction Database Access System" (Version 1.1 or 1.2).

To create the query in this example, draw the functional groups in the transformation and add the ISIS reaction-query feature Make/Break (bonds marked with //) to specify that the bonds at these specified positions (the reacting center bonds) are formed or broken. Then add the atom-atom maps.

Note: If you use the automap feature, the reacting center bonds and the atom-atom maps are added automatically.

In the IRDAS form, click NOT, FMLA, and CAT, and then enter the formula NaBH4 for the catalyst sodium borohydride:


Using ISIS/Base With the Reaction Browser

The Reaction Browser is a specialized ISIS application that is designed to replace the ISIS application IRDAS 1.2. The Reaction Browser allows you to do the example in a single search instead of two searches. If the Reaction Browser is available at your site, you need to install it. For information on installing the Reaction Browser, see your ISIS Administrator.

To conduct the search in this example, select the Query Assistant in Reaction Browser. Then, follow the instructions on the screen to [image] Substructure search for both REACTANT and PRODUCT. To specify the role of the reagent/catalyst, click the Down arrow on the box for molecules with other roles in the reaction. In the dialog, select Reagent as the role of the molecule in the reaction, and set [image] Exclude from the results (NOT logic). Click OK to return to the Query Assistant dialog. You see NOT Reagent as the role of the molecule. Set [image] Formula as the search type, and click OK. You see the Query Assistant Form with two boxes, one for the reaction query and one for the reagent/catalyst query.

Double-click the reaction query box and draw the following reaction query in ISIS/Draw:

Click [image] to return to Reaction Browser. You see that Reaction Browser has automatically applied the automap feature, so that the reaction query looks like this:

In the reagent/catalyst form box, you see that Formula is the type of molecule search, and that Reagent is the role of the molecule in the reaction. Click the box to display the Enter Molecular Formula dialog. Set [image] Full Formula search, and type the formula Na B H4 with spaces between the atom symbols. Click OK to return to the Query Assistant Form, then click SEARCH to conduct the search.


Graphical Query For a Remote Database

This is the correct search for both queries. Click it to see a definition and step-by-step instructions.

* SBF


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

I need to synthesize specific types of products. For these specific types of products, I want to find:

1.	All reported reagent/catalysts and conditions. (Example: Synthesis of all 2-nitrobenzoic acids in the database)

2.	Products with the following structural constraint:

(a) Must be aromatic. (Example: Synthesis of aromatic aldehydes, where an aromatic bond is attached to the aldehyde)

(b) Must contain a specific reacting center that makes or breaks a bond or that changes the bond type. (Example: Synthesis of benzamides in which the CO-NH amide bond is formed)

(c) Must contain a specific atom. (Example: Synthesis of 2-nitrobenzoic acids with a bromine that is para to the carboxylic acid)

(d) Must contain one of a set of alternative atoms. (Example: Synthesis of cyclopentanes with one of three defined heteroatoms, N, S, or O)

(e) Must exclude a specific atom or a specific list of alternative atoms. (Example: Synthesis of nicotinic acids that exclude bromine and chlorine at Position 5 in the ring)

(f) Must contain a specific functional group. (Example: Synthesis of primary amines)


Question 1: "I want to find..."
     Question 1: "I want to find all reported reagent/catalysts and conditions for the synthesis of specific types of products.

Example: I want to find all reported reagent/catalysts and conditions for the synthesis of all 2-nitrobenzoic acids in the database.

You can do this example in ISIS/Base only or in ISIS/Base with Reaction Browser. Each method requires a unique strategy.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the specific type of product (in this example, all 2-nitrobenzoic acids in the database).

You need to do the following (for which you will receive step-by-step instructions when you need them):

*	Create a search query with the structure as the reactant (Query 1). To create Query 1, draw the type of reactant with the reaction arrow:

*	Place Query 1 into the RXNSTRUCTURE box on the form, execute a search, and then save the search results.

*	Clear Query 1 from the RXNSTRUCTURE box on the form.

*	Create a search query with the structure as the product (Query 2). To create Query 2, draw the type of product with the reaction arrow:

*	Place Query 2 into the RXNSTRUCTURE box on the form, execute a search, and then save the search results.

*	Subtract the search results of Query 1 from the search results of Query 2. You want the search results that remain.

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Using ISIS/Base with IRDAS

The ISIS Reaction Database Access System 1.1 or 1.2 (IRDAS) is a specialized ISIS application that eliminates structurally similar reactants in the search results. With ISIS/Base only, you retrieve both structurally similar reactants and products. If IRDAS is available at your site, you need to install it, and then refer to the following manual for instructions on how to conduct a By Form search: "ISIS Reaction Database Access System" (Version 1.1 or 1.2).

To create the query for this example, draw the reaction component. In the IRDAS form, click Struc, SSS, and Prod for the product and NOT, Struc, SSS, and Reac for the reactant.

The IRDAS query:


Using ISIS/Base With the Reaction Browser

The Reaction Browser is a specialized ISIS application that is designed to replace the ISIS application IRDAS 1.2. The Reaction Browser allows you to do the example in a single search instead of two searches. If the Reaction Browser is available at your site, you need to install it. For information on installing the Reaction Browser, see your ISIS Administrator.

To conduct the search in this example, select the Query Assistant in Reaction Browser. Then, follow the instructions on the screen to choose [image] No information for the REACTANT and [image] Substructure search for the PRODUCT. Then, click OK. You see the Query Assistant Form with a form box for the product molecule. The type of molecule search is Substructure (SSS)¸ and the role of the molecule in the reaction is Product not Reactant.

Double-click the form box and draw the structure of 2-nitrobenzoic acid (without the reaction arrow) in ISIS/Draw:

Click [image] to return to Reaction Browser, then click SEARCH to conduct the search.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Question 2a: "I want to find..."
     Question 2a: I want to find all records for the synthesis of specific types of products that are aromatic.

Example: I want to find all records for the synthesis of aromatic aldehydes.

You can do this example in ISIS/Base only or in ISIS/Base with Reaction Browser. Each method requires a unique strategy.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the specific type of product (in this example, aldehydes) and that it is aromatic (in this example, an aromatic bond is attached to the aldehyde).

You need to do the following (for which you will receive step-by-step instructions when you need them):

*	Create a search query with the structure as the reactant (Query 1). To create Query 1, draw the type of reactant with the reaction arrow, add the explicit hydrogen to block substitution at the specified position, add the ISIS bond-query feature AROMATIC (adjacent solid and dashed lines) to allow solely aromatic bonds at the specified positions, and then add the ISIS atom-query feature A to allow any atom except hydrogen at that position:

*	Place Query 1 into the RXNSTRUCTURE box on the form, execute a search, and then save the search results.

*	Clear Query 1 from the RXNSTRUCTURE box on the form.

*	Create a search query with the structure as the product (Query 2). To create Query 2, draw the type of reactant with the reaction arrow, add the explicit hydrogen to block substitution at the specified position, and then add the ISIS bond-query feature AROMATIC (adjacent solid and dashed lines) to allow solely aromatic bonds at the specified positions:

*	Place Query 2 into the RXNSTRUCTURE box on the form, execute a search, and then save the search results.

*	Subtract the search results of Query 1 from the search results of Query 2. You want the search results that remain.

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Using ISIS/Base With IRDAS

The ISIS Reaction Database Access System 1.1 or 1.2 (IRDAS) is a specialized ISIS application that eliminates structurally similar reactants in the search results. With ISIS/Base only, you retrieve both structurally similar reactants and products. If IRDAS is available at your site, you need to install it, and then refer to the following manual for instructions on how to conduct a By Form search: "ISIS Reaction Database Access System" (Version 1.1 or 1.2).

To create the query for this example, draw the reaction component, add the ISIS bond-query feature AROMATIC (adjacent solid and dashed lines) to allow solely aromatic bonds at the specified positions, and then add the ISIS atom-query feature A to allow any atom except hydrogen at the specified positions. In the IRDAS form, click Struc, SSS, and Prod for the product and NOT, Struc, SSS, and Reac for the reactant:

The IRDAS query:


Using ISIS/Base With the Reaction Browser

The Reaction Browser is a specialized ISIS application that is designed to replace the ISIS application IRDAS 1.2. The Reaction Browser allows you to do the example in a single search instead of two searches. If the Reaction Browser is available at your site, you need to install it. For information on installing the Reaction Browser, see your ISIS Administrator.

To conduct the search in this example, select the Query Assistant in Reaction Browser. Then, follow the instructions on the screen to choose [image] No information for the REACTANT and [image] Substructure search for the PRODUCT. Then, click OK. You see the Query Assistant Form with a form box for the product molecule. The type of molecule search is Substructure (SSS)¸ and the role of the molecule in the reaction is Product not Reactant.

Double-click the form box and draw the molecule query for an aromatic alcohol (without the reaction arrow) in ISIS/Draw:

Click [image] to return to Reaction Browser, then click SEARCH to conduct the search.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Question 2b: "I want to find..."
     Question 2b: I want to find all records for the synthesis of specific types of products that contain a specific reacting center.

Example: I want to find all records for the synthesis of benzamides in which the CO-NH amide bond is formed.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the specific type of product (in this example, benzamides) and that it contains a specific reacting center (in this example, formation of a CO-NH amide bond).

You need to create a search query that is the product.

To create the query for this example, draw the type of product with the reaction arrow, and then add the ISIS reaction-query feature Make/Break (bonds marked with //) to specify that the bond at the specified position (the reacting center bond) is formed or broken (You will later place the query into the RXNSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Question 2c: "I want to find..."
     Question 2c: I want to find all records for the synthesis of specific types of products that contain a specific atom.

Example: I want to find all records for the synthesis of 2-nitrobenzoic acids with a bromine that is para to the carboxylic acid.

You can do this example in ISIS/Base only or in ISIS/Base with Reaction Browser. Each method requires a unique strategy.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the specific type of product (in this example, 2-nitrobenzoic acids) and that it contains a specific atom (in this example, a bromine that is para to the carboxylic acid).

You need to do the following (for which you will receive step-by-step instructions when you need them):

*	Create a search query with the structure as the reactant (Query 1). To create Query 1, draw the type of reactant with the reaction arrow:

*	Place Query 1 into the RXNSTRUCTURE box on the form, execute a search, and then save the search results.

*	Clear Query 1 from the RXNSTRUCTURE box on the form.

*	Create a search query with the structure as the product (Query 2). To create Query 2, draw the type of product with the reaction arrow:

*	Place Query 2 into the RXNSTRUCTURE box on the form, execute a search, and then save the search results.

*	Subtract the search results of Query 1 from the search results of Query 2. You want the search results that remain.

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


An Using ISIS/Base With IRDAS
Using ISIS/Base with IRDAS

The ISIS Reaction Database Access System 1.1 or 1.2 (IRDAS) is a specialized ISIS application that eliminates structurally similar reactants in the search results. With ISIS/Base only, you retrieve both structurally similar reactants and products. If IRDAS is available at your site, you need to install it, and then refer to the following manual for instructions on how to conduct a By Form search: "ISIS Reaction Database Access System" (Version 1.1 or 1.2).

To create the query for this example, draw the reaction component. In the IRDAS form, click Struc, SSS, and Prod for the product and NOT, Struc, SSS, and Reac for the reactant.

The IRDAS query:


Using ISIS/Base With the Reaction Browser

The Reaction Browser is a specialized ISIS application that is designed to replace the ISIS application IRDAS 1.2. The Reaction Browser allows you to do the example in a single search instead of two searches. If the Reaction Browser is available at your site, you need to install it. For information on installing the Reaction Browser, see your ISIS Administrator.

To conduct the search in this example, select the Query Assistant in Reaction Browser. Then, follow the instructions on the screen to choose [image] No information for the REACTANT and [image] Substructure search for the PRODUCT. Then, click OK. You see the Query Assistant Form with a form box for the product molecule. The type of molecule search is Substructure (SSS)¸ and the role of the molecule in the reaction is Product not Reactant.

Double-click the form box and draw the following molecule query (without the reaction arrow) in ISIS/Draw:

Click [image] to return to Reaction Browser, then click SEARCH to conduct the search.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Question 2d: "I want to find..."
     Question 2d: I want to find all records for the synthesis of specific types of products that contain a set of alternative atoms.

Example: I want to find all records for the synthesis of cyclopentanes with one of three defined heteroatoms, N, S, or O.

You can do this example in ISIS/Base only or in ISIS/Base with Reaction Browser. Each method requires a unique strategy.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the specific type of product (in this example, cyclopentanes) and that it contains a set of alternative atoms at a specified position (in this example, one of three defined heteroatoms, N, S, or O at one position in the ring).

You need to do the following (for which you will receive step-by-step instructions when you need them):

*	Create a search query with the structure as the reactant (Query 1). To create Query 1, draw the type of reactant with the reaction arrow, and then and add the ISIS atom-query feature List to allow specific atoms (such as N, O, and S) at the specified position:

*	Place Query 1 into the RXNSTRUCTURE box on the form, execute a search, and then save the search results.

*	Clear Query 1 from the RXNSTRUCTURE box on the form.

*	Create a search query with the structure as the product (Query 2). To create Query 2, draw the type of product with the reaction arrow, and then and add the ISIS atom-query feature List to allow specific atoms (such as N, O, and S) at the specified position:

*	Place Query 2 into the RXNSTRUCTURE box on the form, execute a search, and then save the search results.

*	Subtract the search results of Query 1 from the search results of Query 2. You want the search results that remain.

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Using ISIS/Base with IRDAS

The ISIS Reaction Database Access System 1.1 or 1.2 (IRDAS) is a specialized ISIS application that eliminates structurally similar reactants in the search results. With ISIS/Base only, you retrieve both structurally similar reactants and products. If IRDAS is available at your site, you need to install it, and then refer to the following manual for instructions on how to conduct a By Form search: "ISIS Reaction Database Access System" (Version 1.1 or 1.2).

To create the query for this example, draw the reaction component and add the ISIS atom-query feature List to allow specific atoms (such as N, O, and S) at the specified position. In the IRDAS form, click Struc, SSS, and Prod for the product and NOT, Struc, SSS, and Reac for the reactant.

The IRDAS query:


Using ISIS/Base With the Reaction Browser

The Reaction Browser is a specialized ISIS application that is designed to replace the ISIS application IRDAS 1.2. The Reaction Browser allows you to do the example in a single search instead of two searches. If the Reaction Browser is available at your site, you need to install it. For information on installing the Reaction Browser, see your ISIS Administrator.

To conduct the search in this example, select the Query Assistant in Reaction Browser. Then, follow the instructions on the screen to choose [image] No information for the REACTANT and [image] Substructure search for the PRODUCT. Then, click OK. You see the Query Assistant Form with a form box for the product molecule. The type of molecule search is Substructure (SSS)¸ and the role of the molecule in the reaction is Product not Reactant.

Double-click the form box and draw the following molecule query (without the reaction arrow) in ISIS/Draw:

Click [image] to return to Reaction Browser, then click SEARCH to conduct the search.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Question 2d: "I want to find..."
     Question 2e: I want to find all records for the synthesis of specific types of products that exclude a set of alternative atoms.

Example: I want to find all records for the synthesis of nicotinic acids that exclude bromine and chlorine at Position 5 in the ring.

You can do this example in ISIS/Base only or in ISIS/Base with Reaction Browser. Each method requires a unique strategy.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the specific type of product (in this example, nicotinic acids) and that it excludes a set of alternative atoms at a specified position (in this example, bromine and chlorine at Position 5 in the ring).

You need to do the following (for which you will receive step-by-step instructions when you need them):

*	Create a search query with the structure as the reactant (Query 1). To create Query 1, draw the type of reactant with the reaction arrow, and then and add the ISIS atom-query feature NOT List to exclude specific atoms (such as Br and Cl) at the specified position:

*	Place Query 1 into the RXNSTRUCTURE box on the form, execute a search, and then save the search results.

*	Clear Query 1 from the RXNSTRUCTURE box on the form.

*	Create a search query with the structure as the product (Query 2). To create Query 2, draw the type of product with the reaction arrow, and then and add the ISIS atom-query feature NOT List to exclude specific atoms (such as Br and Cl) at the specified position:

*	Place Query 2 into the RXNSTRUCTURE box on the form, execute a search, and then save the search results.

*	Subtract the search results of Query 1 from the search results of Query 2. You want the search results that remain.

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Using ISIS/Base with IRDAS

The ISIS Reaction Database Access System 1.1 or 1.2 (IRDAS) is a specialized ISIS application that eliminates structurally similar reactants in the search results. With ISIS/Base only, you retrieve both structurally similar reactants and products. If IRDAS is available at your site, you need to install it, and then refer to the following manual for instructions on how to conduct a By Form search: "ISIS Reaction Database Access System" (Version 1.1 or 1.2).

To create the query for this example, draw the reaction component and add the ISIS atom-query feature NOT List to exclude specific atoms (such as Br and Cl) at the specified position. In the IRDAS form, click Struc, SSS, and Prod for the product and NOT, Struc, SSS, and Reac for the reactant.

The IRDAS query:


Using ISIS/Base With the Reaction Browser

The Reaction Browser is a specialized ISIS application that is designed to replace the ISIS application IRDAS 1.2. The Reaction Browser allows you to do the example in a single search instead of two searches. If the Reaction Browser is available at your site, you need to install it. For information on installing the Reaction Browser, see your ISIS Administrator.

To conduct the search in this example, select the Query Assistant in Reaction Browser. Then, follow the instructions on the screen to choose [image] No information for the REACTANT and [image] Substructure search for the PRODUCT. Then, click OK. You see the Query Assistant Form with a form box for the product molecule. The type of molecule search is Substructure (SSS)¸ and the role of the molecule in the reaction is Product not Reactant.

Double-click the form box and draw the following molecule query (without the reaction arrow) in ISIS/Draw:

Click [image] to return to Reaction Browser, then click SEARCH to conduct the search.


Question 2e: "I want to find..."
     Question 2f: I want to find all records for the synthesis of specific types of products that contain a specific functional group.

Example: I want to find all records for the synthesis of primary amines.

You can do this example in ISIS/Base only or in ISIS/Base with Reaction Browser. Each method requires a unique strategy.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the specific type of product and functional group (in this example, primary amines).

You need to do the following (for which you will receive step-by-step instructions when you need them):

*	Create a search query with the structure as the reactant (Query 1). To create Query 1, draw the type of reactant with the reaction arrow, and then add the explicit hydrogens to prevent substitution at the specified position:

*	Place Query 1 into the RXNSTRUCTURE box on the form, execute a search, and then save the search results.

*	Clear Query 1 from the RXNSTRUCTURE box on the form.

*	Create a search query with the structure as the product (Query 2). To create Query 2, draw the type of product with the reaction arrow, and then add the explicit hydrogens to prevent substitution at the specified position:

*	Place Query 2 into the RXNSTRUCTURE box on the form, execute a search, and then save the search results.

*	Subtract the search results of Query 1 from the search results of Query 2. You want the search results that remain.

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Using ISIS/Base with IRDAS

The ISIS Reaction Database Access System 1.1 or 1.2 (IRDAS) is a specialized ISIS application that eliminates structurally similar reactants in the search results. With ISIS/Base only, you retrieve both structurally similar reactants and products. If IRDAS is available at your site, you need to install it, and then refer to the following manual for instructions on how to conduct a By Form search: "ISIS Reaction Database Access System" (Version 1.1 or 1.2).

To create the query for this example, draw the reaction component, and then add the explicit hydrogens to prevent substitution at the specified position. In the IRDAS form, click Struc, SSS, and Prod for the product and NOT, Struc, SSS, and Reac for the reactant.

The IRDAS query:


Using ISIS/Base With the Reaction Browser

The Reaction Browser is a specialized ISIS application that is designed to replace the ISIS application IRDAS 1.2. The Reaction Browser allows you to do the example in a single search instead of two searches. If the Reaction Browser is available at your site, you need to install it. For information on installing the Reaction Browser, see your ISIS Administrator.

To conduct the search in this example, select the Query Assistant in Reaction Browser. Then, follow the instructions on the screen to choose [image] No information for the REACTANT and [image] Substructure search for the PRODUCT. Then, click OK. You see the Query Assistant Form with a form box for the product molecule. The type of molecule search is Substructure (SSS)¸ and the role of the molecule in the reaction is Product not Reactant.

Double-click the form box and draw the following molecule query (without the reaction arrow) in ISIS/Draw:

Click [image] to return to Reaction Browser, then click SEARCH to conduct the search.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

I have one specific product of interest.  I want to find all reported routes of synthesis for:

1.	This one specific product. (Example: Synthesis of the single product Penicillin G)

2.	Closely related structures of this one specific product, such as all salts, isomers, tautomers, or alternative representations. (Example: Stereochemical isomers, tautomers, and salts of Penicillin G)

3.	This one specific product and other products that are structurally similar and/or that contain similar reacting centers. (Example: All products that are structurally similar to Penicillin G)


Question 1: "I want to find..."
     Question 1: I want to find all routes of synthesis for a specific product.

Example: I want to find all routes of synthesis for the product Penicillin G.

You can do this example in ISIS/Base only or in ISIS/Base with Reaction Browser. Each method requires a unique strategy.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the product (in this example, Penicillin G).

You need to do the following (for which you will receive step-by-step instructions when you need them):

*	Create a search query with the structure as the reactant (Query 1). To create Query 1, draw the reactant with the reaction arrow (You will later place the query into the RXNSTRUCTURE box on the form.):

*	Place Query 1 into the RXNSTRUCTURE box on the form, execute a search, and then save the search results.

*	Clear Query 1 from the RXNSTRUCTURE box on the form.

*	Create a search query with the structure as the product (Query 2). To create Query 2, draw the product with the reaction arrow (You will later place the query into the RXNSTRUCTURE box on the form.):

*	Place Query 2 into the RXNSTRUCTURE box on the form, execute a search, and then save the search results.

*	Subtract the search results of Query 1 from the search results of Query 2. You want the search results that remain.

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Using ISIS/Base With IRDAS

The ISIS Reaction Database Access System 1.1 or 1.2 (IRDAS) is a specialized ISIS application that allows you to do the example in a single search instead of two searches. If IRDAS is available at your site, you need to install it, and then refer to the following manual for instructions on how to conduct a By Form search: "ISIS Reaction Database Access System" (Version 1.1 or 1.2).

To create the query for this example, draw the reaction component. In the IRDAS form, click Struc, EXACT, and Prod for the product and NOT, Struc, EXACT, and Reac for the reactant:

The IRDAS query:


Using ISIS/Base With the Reaction Browser

The Reaction Browser is a specialized ISIS application that is designed to replace the ISIS application IRDAS 1.2. The Reaction Browser allows you to do the example in a single search instead of two searches. If the Reaction Browser is available at your site, you need to install it. For information on installing the Reaction Browser, see your ISIS Administrator.

To conduct the search in this example, select the Query Assistant in Reaction Browser. Then, follow the instructions on the screen to choose [image] No information for the REACTANT and [image] Full structure for the PRODUCT. Then, click OK. You see the Query Assistant Form with a form box for the product molecule. The type of molecule search is Exact Match, and the role of the molecule in the reaction is Product not Reactant.

Double-click the form box and draw the molecule query for Penicillin G (without the reaction arrow) in ISIS/Draw:

Click [image] to return to Reaction Browser, then click SEARCH to conduct the search.


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* REXACT/Comp


Question 2: "I want to find..."
     Question 2: I want to find all routes of synthesis for closely related structures of a specific product.

Example: I want to find all routes of synthesis for stereochemical isomers, tautomers, and salts of Penicillin G.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the product (in this example, Penicillin G).

You need to create a search query that is the product (You will later place the query into the PRODUCT_STRUCTURE box or table cell on the form.):

Example of a product retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Product Retrieved

The salt form of Penicillin G:

Note: Salts might be represented in a different form in your database.


Graphical Query For a Remote Database

These are the correct searches for this query. Click any of them to see a definition and step-by-step instructions:

* FLEX

* ISOMER

* TAUT

* PARENT


Question 3: "I want to find..."
     Question 3: I want to find all routes of synthesis for a specific product and for products that are structurally similar to it.

Example: I want to find all routes of synthesis for Penicillin G and for products that are structurally similar to it.

Note: This example is for remote searching only.

You can do this example in ISIS/Base only or in ISIS/Base with Reaction Browser. Each method requires a unique strategy.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the product (in this example, Penicillin G).

You need to create a search query that is the product with a reaction arrow (You will later place the query into the RXNSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Using ISIS/Base with IRDAS

The ISIS Reaction Database Access System 1.1 or 1.2 (IRDAS) is a specialized ISIS application that eliminates structurally similar reactants in the search results. With ISIS/Base only, you retrieve both structurally similar reactants and products. If IRDAS is available at your site, you need to install it, and then refer to the following manual for instructions on how to conduct a By Form search: "ISIS Reaction Database Access System" (Version 1.1 or 1.2).

To create the query for this example, draw the reaction component. In the IRDAS form, click Struc, Sim, and Prod for the product and click NOT, Struc, Sim, and Reac for the reactant.

The IRDAS query:


Using ISIS/Base With the Reaction Browser

The Reaction Browser is a specialized ISIS application that is designed to replace the ISIS application IRDAS 1.2. The Reaction Browser allows you to do the example in a single search instead of two searches. If the Reaction Browser is available at your site, you need to install it. For information on installing the Reaction Browser, see your ISIS Administrator.

To conduct the search in this example, select the Query Assistant in Reaction Browser. Then, follow the instructions on the screen to choose [image] No information for the REACTANT and [image] Full structure for the PRODUCT. Then, click OK. You see the Query Assistant Form with a form box for the product molecule. The type of molecule search is Exact Match and the role of the molecule in the reaction is Product not Reactant.

Double-click the form box and draw the molecule query for Penicillin G (without the reaction arrow) in ISIS/Draw:

Click [image] to return to Reaction Browser.

Next, you need to change the full-structure search from Exact Match to Similarity. To do this, click the Down arrow next to Exact Match to display the Select Role and Type for Molecule Search dialog. In the Type of search box, highlight Similarity to select it. Then, click OK. You see the form box with Similarity <70> as the type of search. Click SEARCH to conduct the search.

Note: In this query, the number 70 is the structural similarity value, which specifies the degree of structural similarity between your query and the structures retrieved. The structural similarity is an arbitrary value between 0 and 100 (these are not actual units). The higher the value, the more similarity.


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSim


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

I want explore the chemistry of specific reactants.  For these specific reactants, I want to find:

1.	All reported transformations that use:

(a) This exact reactant. (Example: The reactant cinnamaldehyde)

(b) Specific types of reactants. (Example: All lactams in the database)

(c) This exact reactant and closely related structures, such as all salts, isomers, tautomers, or alternative representations. (Example: Stereochemical isomers, tautomers, and salts of the reactant 1-hydroxy-5, 6-dimethyl-1, 3-cyclohexadiene)

(d) This exact reactant and other reactants that are structurally similar to it. (Example: Reactants that are structurally similar to Penicillin G)

2.	Transformations that contain reactants with the following structural constraint:

(a) Must be aromatic. (Example: Aromatic aldehydes, where an aromatic bond is attached to the aldehyde)

(b) Must contain a specific reacting center that makes or breaks a bond or that changes the bond type. (Example: Cleavage of the CO-NH amide bond in benzamides)

(c) Must contain a specific atom. (Example: A bromine that is 1 carbon from the amide nitrogen in lactams)

(d) Must contain one of a set of alternative atoms. (Example: One of 3 defined heteroatoms, N, S, or O at a single position in cyclopentanes)

(e) Must exclude one of a set of alternative atoms. (Example: Excludes Br and Cl at Position 5 in 3-methylpyridines)


Question 1a: "I want to find..."
     Question 1a: I want to find all transformations that use this exact reactant.

Example: I want to find all transformations that use the reagent/catalyst cinnamaldehdye.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the exact reactant (in this example, cinnamaldehyde).

You need to create a search query that is the exact reactant with a reaction arrow (You will later place the query into the RXNSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* REXACT/Comp


Question 1b: "I want to find..."
     Question 1b: I want to find all transformations that use specific types of reactants.

Example: I want to find all transformations that use any lactam in the database.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the specific type of reactant (in this example, all lactams in the database).

You need to create a search query that allows solely ring bond attachments at specified positions on a reactant.

To create the query for this example, draw the reactant with a reaction arrow, and then add the ISIS bond-query feature Rn to allow solely ring bonds at the specified positions (You will later place the query into the RXNSTRUCTURE box on the form.):

Example of a reactant retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Reactant Retrieved


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Question 1c: "I want to find..."
     Question 1c: I want to find all closely related reactants to the reactant of interest.

Example: I want to find all reactants that are stereochemical isomers, tautomers, and salts of the reactant 1-hydroxy-5, 6-dimethyl-1, 3-cyclohexadiene.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the reactant (in this example, the reactant 1-hydroxy-5, 6-dimethyl-1, 3-cyclohexadiene).

You need to create a search query that is the reactant without a reaction arrow (You will later place the query into the REACTANT_STRUCTURE box or table cell on the form.):

Example of a reactant retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Reactant Retrieved

The salt form of 1-hydroxy-5, 6-dimethyl-1, 3-cyclohexadiene:

Note: Salts might be represented in a different form in your database.


Graphical Query For a Remote Database

These are the correct searches for this query. Click any of them to see a definition and step-by-step instructions:

* FLEX

* ISOMER

* PARENT

* TAUT


Question 1d: "I want to find..."
     Question 1d: I want to find all transformations that contain this exact reactant and other reactants that are structurally similar to this reactant.

Example: I want to find all transformations that contain reactants that are structurally similar to the reactant Penicillin G.

Note: This example is for remote searching only.

You can do this example in ISIS/Base only or in ISIS/Base with Reaction Browser. Each method requires a unique strategy.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the reactant (in this example, Penicillin G).

You need to create a search query that is the reactant without a reaction arrow (You will later place the query into the RXNSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Using ISIS/Base With IRDAS

The ISIS Reaction Database Access System 1.1 or 1.2 (IRDAS) is a specialized ISIS application that allows you to do the example in a single search instead of two searches. If IRDAS is available at your site, you need to install it, and then refer to the following manual for instructions on how to conduct a By Form search: "ISIS Reaction Database Access System" (Version 1.1 or 1.2).

To create the query in this example, draw the reactant without a reaction arrow. In the IRDAS form, click Struc, Sim, and Reac:


Using ISIS/Base With the Reaction Browser

The Reaction Browser is a specialized ISIS application that is designed to replace the ISIS application IRDAS 1.2. The Reaction Browser allows you to do the example in a single search instead of two searches. If the Reaction Browser is available at your site, you need to install it. For information on installing the Reaction Browser, see your ISIS Administrator.

To conduct the search in this example, select the Query Assistant in Reaction Browser. Then, follow the instructions on the screen to choose [image] Full structure for the REACTANT and [image] No information for the PRODUCT. Click OK. You see the Query Assistant Form with a form box for the reactant molecule. The type of molecule search is Exact Match and the role of the molecule in the reaction is Reactant not Product.

Double-click the form box and draw the molecule query for Penicillin G (without the reaction arrow) in ISIS/Draw:

Click [image] to return to Reaction Browser.

Next, you need to change the full-structure search from Exact Match to Similarity. To do this, click the Down arrow next to Exact Match to display the Select Role and Type for Molecule Search dialog. In the Type of search box, highlight Similarity to select it. Then, click OK. You see the form box with Similarity <70> as the type of search. Click SEARCH to conduct the search.

Note: In this query, the number 70 is the structural similarity value, which specifies the degree of structural similarity between your query and the structures retrieved. The structural similarity is an arbitrary value between 0 and 100 (these are not actual units). The higher the value, the more similarity.


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* MSim


Question 2a: "I want to find..."
     Question 2a: I want to find all transformations that contain reactants that are aromatic.

Example: I want to find all transformations that contain reactants that are aromatic aldehydes.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the type of reactant (in this example, aromatic aldehydes).

You need to create a search query that is an aromatic reactant.

To create the query for this example, draw the reactant with a reaction arrow, add the ISIS bond-query feature AROMATIC (adjacent solid and dashed lines) to allow solely an aromatic bond at the specified position, and then add the ISIS atom-query feature A to allow any atom except hydrogen at that position (You will later place the query into the RXNSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Question 2b: "I want to find..."
     Question 2b: I want to find all transformations that contain types of reactants with a specific reacting center.

Example: I want to find all transformations that contain solely those benzamides as reactants that are cleaved at the CO-NH bond.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the type of reactant (in this example, benzamides) and the reacting center (in this example, cleavage at the CO-NH bond).

You need to create a search query that is a reactant with a specific reacting center.

To create the query for this example, draw the reactant with a reaction arrow, and then add the ISIS reaction-query feature Make/Break (bonds marked with //) to specify that the bond at this specified position (the reacting center bond) is formed or broken (You will later place the query into the RXNSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Question 2c: "I want to find..."
     Question 2c: I want to find all transformations that contain reactants with a specific atom.

Example: I want to find all transformations that contain solely those 5-membered lactams as reactants that contain a bromine that is 1 carbon from the amide nitrogen.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the type of reactant (in this example, a 5-membered lactam) and the specific atom (in this example, a bromine that is 1 carbon from the amide nitrogen).

You need to create a search query that is a reactant with a specific atom at a specified position. The reactant contains a reaction arrow (You will later place the query into the RXNSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Question 2d: "I want to find..."
     Question 2d: I want to find all transformations that contain reactants with a set of alternative atoms.

Example: I want to find all transformations that contain solely those cyclopentanes as reactants that contain one of 3 defined heteroatoms, N, S, O at a single position.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the type of reactant (in this example, cyclopentanes with one of 3 defined heteroatoms, N, S, or O, at a single position).

You need to create a search query that is a reactant that allows alternative atoms at a specified position.

To create the query for this example, draw the reactant with a reaction arrow, and then add the ISIS atom-query feature List to allow specific atoms (such as N, S, and O) at the specified position (You will later place the query into the RXNSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Comp


Question 2d: "I want to find..."
     Question 2e: I want to find all transformations that exclude reactants with a set of alternative atoms.

Example: I want to find all transformations that contain solely those 3-methylpyridines as reactants that exclude bromine and chlorine at a single position.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the type of reactant (in this example, 3-methylpyridines that exclude bromine and chlorine at a single position).

You need to create a search query that is a reactant that excludes alternative atoms at a specified position.

To create the query for this example, draw the reactant with a reaction arrow, and then add the ISIS atom-query feature NOT List to exclude specific atoms (such as Br and Cl) at the specified position (You will later place the query into the RXNSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

I have some specific data.  For these data, I want to find:

1.	All transformations with journal references by a specific author. (Example: The author Mark Smythe)

2.	Specific transformations that also contain a specific product yield. (Example: The conversion of the reactant 2-methyl-2-propenamide to the product N-(3, 4-dichlorophenyl)methacrylamide with a greater than 90% yield)

3.	Specific transformations that also contain a specific reaction temperature. (Example: The conversion of the reactant 1-bromo-2-phenylethylene to the product 1-trimethyl-2-phenylethylene with a reaction temperature of less than 10 degrees Centigrade)


Question 1: "I want to find..."
     Question 1: I want to find all transformations that are associated with the specific data ‘all journal references by a specific author.’

Example: I want to find all transformations with journal references by Mark Smythe.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the author (in this example, Mark Smythe).

You need to create a search query that contains a search operator, the entire name of the author or a portion of it. (You will later place the query into the AUTHOR box or table cell on the form.). To retrieve solely those records that contain exactly the target value that you specified, enter the following search query:

LIKE "Mark Smythe"

To retrieve those records that contain exactly the target value that you specified and any additional words or phrases that are stored with the database field ACTIVITY, enter either of the following search queries with wildcards:

LIKE "%Mark Smythe%"

LIKE "%Smythe%"

LIKE "%Sm_th%"

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Text String Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Text String Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Question 2: "I want to find..."
     Question 2: I want to find specific transformations that are also associated with the specific data ‘product yield.’

Example: I want to find all transformations that convert 2-methyl-2-propenamide to N-(3, 4-dichlorophenyl)methacrylamide with a yield that is greater than 90%.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the transformation (in this example, the conversion of 2-methyl-2-propenamide to N-[3, 4-dichlorophenyl]methacrylamide) and the product yield that you want to exceed (in this example, a greater than 90% yield).

You need to create a search query that contains both a transformation and text and/or numeric data.

To create the transformation for this example query, draw the functional groups in the transformation and add the ISIS reaction-query feature Make/Break (bonds marked with //) to specify that the bonds at these specified positions (the reacting center bonds) are formed or broken. Then add the atom-atom maps (You will later place the query into the RXNSTRUCTURE box on the form.):

Note: If you use the automap feature, the reacting center bonds and the atom-atom maps are added automatically.

To create the text and/or numeric data for this example query, enter a search operator and the product yield that you want to exceed (You will later place the query into the PRODUCT_YIELD box or table cell on the form.):

> 90

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Graphical + Text String Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Question 3: "I want to find..."
     Question 3: I want to find specific transformations that are also associated with the specific data ‘reaction temperature.’

Example: I want to find all transformations that convert 1-bromo-2-phenyl-ethylene to 1-trimethyl-2-phenylethylene with a reaction temperature that is less than 10 degrees Centigrade.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the transformation (in this example, the conversion of 1-bromo-2-phenyl-ethylene to 1-trimethyl-2-phenyl-ethylene) and the reaction temperature (in this example, less than 10 degrees Centigrade).

You need to create a search query that contains both a transformation and text and/or numeric data.

To create the transformation for this example query, draw the functional groups in the transformation and add the ISIS reaction-query feature Make/Break (bonds marked with //) to specify that the bonds at these specified positions (the reacting center bonds) are formed or broken. Then add the atom-atom maps (You will later place the query into the RXNSTRUCTURE box on the form.):

Note: If you use the automap feature, the reacting center bonds and the atom-atom maps are added automatically.

To create the text and/or numeric data for this example query, enter a search operator and a reaction temperature (You will later place the query into the REACTION_TEMPERATURE box or table cell on the form.):

< 10

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Graphical + Text String Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

I have a specific transformation of interest.  For this transformation, I want to find:

1.	All reports of this exact transformation (including all associated data, such as reaction conditions and journal references), if there are any. (Example: The transformation of the reactant propylene to the product n-propyl bromide)

2.	All other transformations that contain similar substrates and/or reacting centers. (Example: Similar reacting centers to the reactant cyclopentene and the product cyclopentene oxide)

3.	All transformations that convert stereospecifically. (Example: Synthesis of 1-methylcyclopentene oxide from 2-chloro-2-methylpentanol with the retention and inversion of specific stereo bonds)


Question 1: "I want to find..."
     Question 1: I want to find all reports of this exact transformation.

Example: I want to find all reports of the conversion of the reactant propylene to the product n-propyl bromide.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the exact transformation (in this example, the conversion of the reactant propylene to the product n-propyl bromide).

You need to create a search query that is the exact transformation, including any stereochemistry that you expect to see in the transformations retrieved (You will later place the query into the RXNSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* REXACT/Rxn


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* REXACT/Rxn


Question 2: "I want to find..."
     Question 2: I want to find all transformations that contain structurally similar substrates and/or similar reacting centers to my transformation of interest.

Example: I want to find all transformations that contain reacting centers that are similar to those in the conversion of cyclopentene to cyclopentene oxide.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the transformation (in this example, the transformation of cyclopentene to cyclopentene oxide).

You need to create a search query that is a transformation with reacting centers on the reactants and products.

To create the query for this example, draw the transformation and add the ISIS reaction-query feature Make/Break (bonds marked with //) to specify that the bonds at these specified positions (the reacting center bonds) are formed or broken. (You will later place the query into the RXNSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSim


Question 3: "I want to find..."
     Question 3: I want to find all records for the synthesis of specific types of products that are converted stereospecifically.

Example: I want to find all records for the synthesis of 1-methylcyclopentene oxide from 2-chloro-2-methylpentanol with the retention and inversion of specific stereo bonds.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the transformation (in this example, the synthesis of 1-methylcyclopentene oxide from 2-chloro-2-methylpentanol with the retention and inversion of specific stereo bonds).

You need to create a search query that is a transformation.

To create the query for this example, draw the transformation with the Up and Down stereo bonds. Add the ISIS bond-query features .Ret. to specify that you want to retain the stereo bonds at the specified position and .Inv. to specify that you want to invert the stereo bonds at the specified position. Add the atom-atom maps. Then add the stereochemical designation CHIRAL to specify the retrieval of solely the absolute stereoconfigurations (You will later place the query into the RXNSTRUCTURE box on the form.):

Note: If you use the automap feature, the retention and inversion marks on the stereo bonds and the atom-atom maps are added automatically.

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Rxn


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* RSS/Rxn


  I Want To Find Information on Molecules

Click one of these items:

*	I have a specific, fully defined molecule of interest. I want to find this molecule and closely related molecules (such as salts, isomers, tautomers, and alternative representations).

*	I have a specific portion of a molecule (fragment, substructure) of interest. I want to find molecules that contain this substructure wholly embedded within them.

*	I have a specific structural constraint of interest. I want to find molecules that contain this constraint.

*	I have specific data of interest. I want to find all molecules that are associated with this data.

*	I have a specific combination of structural features and data of interest. (Structural features can be a molecule, a fragment, or a structural constraint.) I want to find all molecules that have this combination of structural features and data in common.

What to do if you could not find a suitable sample question


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

I have a specific, fully defined molecule (such as a salt, an isomer, a tautomer, or an alternative representation) of interest.  I want to find:

1.	This exact molecule and duplicates (extra copies of the exact same molecule) in the database. (Example: Adenine)

2.	This exact molecule and its stereochemical isomers. (Example: The cis and trans forms of 1,2-dimethylcyclopropane)

3.	This exact molecule and its tautomer representation. (Example: 2-Pyridone and 2-hydroxypyridine)

4.	This exact molecule and closely related structures. (Example: Benzoic acid and its isotopes and salts)

5.	All other molecules with a specified degree of structural similarity to the molecule of interest. (Example: 6-Bromopurine has a specified degree of structural similarity to adenine, the molecule of interest.)


Question 1: "I want to find..."
     Question 1: I want to find this exact molecule and all duplicates of it in the database.

Example: I want to find all records of the molecule adenine.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the exact molecule (in this example, adenine).

You need to create a search query that is the exact molecule, including any stereochemistry that you expect to see in the molecules retrieved (You will later place the query into the MOLSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* MEXACT


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* MEXACT


Question 2: "I want to find..."
     Question 2: I want to find this exact molecule and its stereochemical isomers in the database.

Example: I want to find all stereochemical isomers of the molecule 1,2-dimethylcyclopropane.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the molecule (in this example, 1,2-dimethylcyclopropane).

You need to create a search query that is either the cis or the trans form of this exact fragment. For example, create the cis stereoconfiguration of 1,2-dimethylcyclopropane (You will later place the query into the MOLSTRUCTURE box on the form.):

Examples of molecules retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Molecule Retrieved
Examples of Molecules Retrieved

Both the cis and the trans stereoconfigurations:


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* ISOMER


Question 3: "I want to find..."
     Question 3: I want to find this exact molecule and its tautomer representation in the database.

Example: I want to find all tautomers of the molecule 2-pyridone.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the exact molecule (in this example, 2-pyridone).

You need to create a search query that is the exact molecule (You will later place the query into the MOLSTRUCTURE box on the form.):

Examples of molecules retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Examples of Molecules Retrieved

Both 2-pyridone and the tautomer 2-hydroxypyridine:


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* TAUT


Question 4: "I want to find..."
     Question 4: I want to find this exact molecule and closely related structures in the database.

Example: I want to find all isotopes and salts of the molecule benzoic acid.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the exact molecule (in this example, benzoic acid).

You need to create a search query that is the exact molecule (You will later place the query into the MOLSTRUCTURE box on the form.):

Example of a molecule retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Molecule Retrieved

Sodium Benzoate:

Note: Salts might be represented in a different form in your database.


Graphical Query For a Remote Database

This is the correct remote search for the query that you chose. Click it to see a definition and step-by-step instructions:

* FLEX


Question 5: "I want to find..."
     Question 5: I want to find all other molecules with a specified degree of structural similarity to the molecule of interest.

Example: I want to find all molecules with a specified degree of structural similarity to adenine.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the molecule of interest (in this example, adenine).

You need to create a search query that is the molecule of interest (You will later place the query into the MOLSTRUCTURE box on the form.):

Example of a molecule retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Molecule Retrieved

You retrieve all other molecules that are structurally similar to your molecule of interest. (You specify the degree of structural similarity prior to the search.) For example, you might retrieve 6-bromopurine:

Note: If you do not also retrieve your molecule of interest, it is not in the database.


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* MSim


Question 6: "I want to find..."
     Question 6: I want to find some specific data that is associated with the molecule of interest.

Example: I want to find the formula, molecular weight, and melting point of the molecule oxybenzone.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the molecule of interest (in this example, oxybenzone).

You need to create a search query that is the molecule of interest (You will later place the query into the MOLSTRUCTURE box on the form.):

Example of a record retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Record Retrieved

You retrieve records that contain molecules and associated data. For example, you might retrieve the following record:


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* MEXACT


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* MEXACT


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

I have a specific portion of a molecule (substructure, fragment) of interest.  For this substructure, I want to find all molecules that contain:

1.	This exact substructure OR this exact substructure with unspecified substituents at any open valence. (Example: All molecules that contain a 5-membered lactam ring as a substructure wholly within a larger molecule)

2.	This exact substructure with limited substituents at specific positions. (Example: All benzoic acids, but not esters, where the benzoic acids are substituted solely at position 4)

3.	This exact substructure with one or more specific substitutions at one or more positions. (Example: 3, 6-Dihydroxypyridine in which the substituent at position 3 can be COOH, CN, or Ph, and in which the substituent at position 6 can be OH or CH3)


Question 1: "I want to find..."
     Question 1: I want to find this exact substructure OR this exact substructure with unspecified substituents at any open valence.

Example: I want to find all molecules that contain a 5-membered lactam ring.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the exact substructure (in this example, a 5-membered lactam ring).

You need to create a search query that is the exact substructure with unspecified substituents at any open valence (You will later place the query into the MOLSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Question 2: "I want to find..."
     Question 2: I want to find this exact substructure with limited substitutions at specific positions.

Example: I want to find all benzoic acids, but not esters, where the benzoic acids are substituted solely at position 4.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the exact substructure (in this example, benzoic acids) and the positions on that substructure where you want substitutions to occur (in this example, substitution of benzoic acids solely at position 4).

You need to create a search query that is the exact substructure with limited substitutions at the specified positions. There are 2 ways to create your search query. The one you choose is strictly your own preference and does not affect the search results.

3.	To identify the type of search that you need to do and to see the step-by-step instructions, click the type of query that you prefer to use:

*	Query 1

The preferred query: Draw the structure, and then add explicit hydrogens to prevent substitutions at specific positions (You will later place the query into the MOLSTRUCTURE box on the form.):

*	Query 2

An alternative query for remote searching only: Draw the structure, and then add the ISIS atom-query feature s* to prevent substitutions at specific positions (You will later place the query into the MOLSTRUCTURE box on the form.):


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Graphical Query 1 For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Graphical Query 2 For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Question 3: "I want to find..."
     Question 3: I want to find this exact substructure with one or more specific substitutions at one or more positions.

Example: I want to find 3, 6-Dihydroxypyridine in which the substituent at position 3 can be COOH, CN, or Ph, and the substituent at position 6 can be OH or CH3.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the exact substructure (in this example, 3, 6-Dihydroxypyridine) and the specific substituents and their positions (COOH, CN, or Ph at position 3 and OH or CH3 at position 6).

You need to create a search query that is the exact substructure with one or more specific substitutions at one or more positions.

To create the query for this example, you draw the root structure with the Rgroup label R1 at position 3 and the Rgroup label R2 at position 6. Then you draw the Rgroup substituents and specify that they are members of the Rgroup R1 or R2. Then you add the ISIS atom-query feature s* to prevent substitutions at specific positions on the root structure and on the Rgroup substituents. Finally, you specify the Rgroup conditions (You will later place the query into the MOLSTRUCTURE box on the form.):

Example of a molecule retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


The Root Structure

The root structure is that portion of the query that must be present in all the structures retrieved. For example, the root structure is:

Note: Each Rgroup label (R1 and R2) on the root structure corresponds to a list of substituents that are allowed at that position in the molecules retrieved.


Rgroup Substituents

Rgroup substituents are the functional groups or atoms that you allow on the root structure at specific positions (R1 and R2) in the molecules retrieved. For example, the Rgroup substituents:

*	COOH, CN, or Ph are allowed at position 3 (R1) on the root structure.

*	OH or CH3 are allowed at position 6 (R2) on the root structure.

Note: An attachment point (marked with an arrow and an asterisk) designates the atom on the Rgroup substituent that is attached to the root structure.


Rgroup Conditions

Rgroup conditions are the set of restrictions on each Rgroup in your query. For example, the Rgroup condition:

*	R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved.

*	R2 > 0 specifies that an Rgroup substituent from the R2 list occupies at least one R2 site on the root structure in the records retrieved.


Example of a Molecule Retrieved


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* RGROUP


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

I have a specific structural constraint of interest.  For this constraint, I want to find specific types of molecules that:

1.	Are aromatic. (Example: Aromatic aldehydes, where an aromatic bond is attached to an aldehyde)

2.	Contain a specific atom or a specific list of atoms. (Example: Containing all 4-halo-substituted sodium benzoates)

3.	Excluding a specific atom or a specific list of atoms. (Example: Excluding halogen substituents from 2, 6-disubstituted pyridines)

4.	Are heterocyclic. (Example: Six-membered heterocyclic compounds that contain one nitrogen)

5.	Contain any relative stereochemistry. (Example: Geometric isomers and stereoisomers of 1,2-cyclohexanediol)

6.	Contain specific relative stereochemistry. (Example: All cis cinnamic acids)

7.	Contain specific absolute stereochemistry. (Example: All D-amino acids)

8.	Are unsubstituted aliphatic chains of a specific length. (Example: Unsubstituted aliphatic chains that are between 3 and 7 carbons in length)

9.	Contain multiple functional groups. (Example: An aromatic sulfonamide group and a carboxylic acid group at unspecified positions)

10.	Contain a single carbon atom that is attached to four ring bonds. (Example: All spiro-substituted saturated pyrimidines)


Question 1: "I want to find..."
     Question 1: I want to find specific types of molecules that are aromatic.

Example: I want to find all aldehydes that are aromatic.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the type of molecule and that it is aromatic (in this example, aldehydes that are aromatic, where an aromatic bond is attached to an aldehyde).

You need to create a search query that is a type of molecule with a specific structural constraint on one or more bonds (You will later place the query into the MOLSTRUCTURE box on the form.):

To create the query for this example, draw the aldehyde, add an explicit hydrogen to block substitution at that position, add the ISIS bond-query feature AROMATIC (adjacent solid and dashed lines) to allow solely an aromatic bond at the specified position, and then add the ISIS atom-query feature A to allow any atom except hydrogen at that position (You will later place the query into the MOLSTRUCTURE box on the form.):

Examples of molecules retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Examples of Molecules Retrieved


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Question 2: "I want to find..."
     Question 2: I want to find specific types of molecules that contain an atom or a list of atoms.

Example: I want to find all sodium benzoates that are 4-halo substituted.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the type of molecule and the atom or the list of atoms that you want to allow in the molecules retrieved (in this example, sodium benzoates with halogen substituents at position 4).

You need to create a search query that is a type of molecule with a specific structural constraint on one or more atoms. There are 2 ways to create your search query. The one you choose is strictly your own preference and does not affect the search results.

3.	To identify the type of search that you need to do and to see the step-by-step instructions, click the type of query that you prefer to use:

*	Query 1

The preferred query: Draw the structure, add the ISIS atom-query feature List to allow specific atoms (such as Br, Cl, I, and F) at the specified position, and then add explicit hydrogens to prevent substitutions at other specified positions (You will later place the query into the MOLSTRUCTURE box on the form.):

*	Query 2

An alternative query for remote searching only: Draw the structure, add the ISIS atom-query feature List to allow specific atoms (such as Br, Cl, I, and F) at the specified position, and then add the ISIS atom-query feature s* to prevent substitutions at other specific positions (You will later place the query into the MOLSTRUCTURE box on the form.):


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Local Database
Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Graphical Query 1 For a Remote Database
Query 1 For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Graphical Query 2 For a Remote Database
Query 2 For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Question 3: "I want to find..."
     Question 3: I want to find specific types of molecules that exclude an atom or a list of atoms.

Example: I want to find all 2, 6-disubstituted pyridines that are not substituted with halogens.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the type of molecule and that it excludes an atom or a list of atoms (in this example, 2, 6-disubstituted pyridines that exclude halogen substituents).

You need to create a search query that is a type of molecule with a specific structural constraint on one or more atoms. There are 2 ways to create your search query. The one you choose is strictly your own preference, although you might retrieve N-oxides with Query 1.

3.	To identify the type of search that you need to do and to see the step-by-step instructions, click the type of query that you prefer to use:

*	Query 1

The preferred query: Draw the structure, add the ISIS atom-query feature NOT List to exclude specific atoms (such as the halogens) at the specified positions, and then add explicit hydrogens to prevent substitutions at other specified positions (You will later place the query into the MOLSTRUCTURE box on the form.):

*	Query 2

An alternative query for remote searching only: Draw the structure, add the ISIS atom-query feature NOT List to exclude specific atoms (such as the halogens) at the specified positions, and then add the ISIS atom-query feature s* to prevent substitutions at the specified positions (You will later place the query into the MOLSTRUCTURE box on the form.):


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Graphical Query 1 For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Graphical Query 2 For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Question 4: "I want to find..."
     Question 4: I want to find specific heterocyclic molecules.

Example: I want to find all 6-membered heterocyclic compounds that contain one nitrogen.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the type of molecule and the position of specific atoms (in this example, all 6-membered heterocyclic compounds that contain one nitrogen).

You need to create a search query that is a heterocyclic molecule with atoms in a specific position, and then add the ISIS bond-query feature ANY (dashed lines) to allow any bond type at the specified positions (You will later place the query into the MOLSTRUCTURE box on the form.):

Example of a molecule retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Molecule Retrieved


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SSS


Question 5: "I want to find..."
     Question 5: I want to find specific types of molecules that contain any relative stereochemistry.

Example: I want to find all geometric isomers and stereoisomers of 1, 2-cyclohexanediol.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the type of molecule (in this example, 1, 2-cyclohexanediol) and that the database might contain geometric isomers and stereoisomers.

You need to create a search query that is a type of molecule that allows the retrieval of any relative stereochemistry.

To create the query for this example, draw the structure (You will later place the query into the MOLSTRUCTURE box on the form.):

Examples of molecules retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Examples of Molecules Retrieved

Both the cis and the trans stereoconfigurations:


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* ISOMER


Question 6: "I want to find..."
     Question 6: I want to find specific types of molecules that contain specific relative stereochemistry.

Example: I want to find all cinnamic acids with the cis stereoconfiguration.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the type of molecule and its relative stereochemistry (in this example, all cinnamic acids with the cis stereoconfiguration). You need to create a search query that is a type of molecule with a structural constraint that allows the retrieval of specific relative stereoconfigurations.

There are 2 ways to create your search query. The one you choose is strictly your own preference and does not affect the search results.

3.	To identify the type of search that you need to do and to see the step-by-step instructions, click the type of query that you prefer to use:

*	Query 1

The preferred query: Draw the structure with the stereochemistry that you expect to see in the molecules retrieved, add the ISIS atom-query feature Stereo Box ( [image]) to allow the retrieval of solely the cis stereoconfiguration, and then add explicit hydrogens to prevent substitutions at other specified positions (You will later place the query into the MOLSTRUCTURE box on the form.):

*	Query 2

An alternative query for remote searching only: Draw the structure with the stereochemistry that you expect to see in the molecules retrieved, and then add the ISIS atom-query features Stereo Box ( [image]) to allow the retrieval of solely the cis stereoconfiguration and s* to prevent substitutions at other specific positions (You will later place the query into the MOLSTRUCTURE box on the form.):


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Graphical Query 1 For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Graphical Query 2 For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Question 7: "I want to find..."
     Question 7: I want to find specific types of molecules that contain specific absolute stereochemistry.

Example: I want to find all D-amino acids.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the type of molecule and its absolute stereochemistry (in this example, all D-amino acids).

You need to create a search query that is a type of molecule with a structural constraint that allows the retrieval of specific solely absolute stereoconfigurations.

To create the query for this example, draw the structure with the stereochemistry that you expect to see in the molecules retrieved, add explicit hydrogens to prevent substitutions at other specified positions, and then add the chiral flag (You will later place the query into the MOLSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Question 8: "I want to find..."
     Question 8: I want to find all molecules that are unsubstituted aliphatic chains of a specific length.

Example: I want to find all unsubstituted aliphatic chains that are between 3 and 7 carbons in length.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the length of the unsubstituted aliphatic chain (in this example, between 3 and 7 carbons).

You need to create a search query that is an unsubstituted aliphatic chain of a specific length.

To create the query for this example, draw the minimum length aliphatic chain, add the ISIS bond-query feature ANY (dashed lines) to allow any bond type at the specified positions, and then add the ISIS atom-query features s* to prevent substitutions at specific positions and Link Node to allow additional repeating units that lengthen the chain (You will later place the query into the MOLSTRUCTURE box on the form.):

Example of a molecule retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Molecule Retrieved


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SSS


Question 9: "I want to find..."
     Question 9: I want to find all molecules that contain multiple functional groups.

Example: I want to find all molecules that contain both an aromatic sulfonamide group and a carboxylic acid group at unspecified positions.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the functional groups (in this example, an aromatic sulfonamide group and a carboxylic acid group at unspecified positions).

You need to create a search query that is a set of unattached functional groups.

To create the query for this example, draw the unattached functional groups. To the sulfonamide group, add the ISIS bond-query feature AROMATIC (adjacent solid and dashed lines) to allow solely an aromatic bond at the specified position, and then add the ISIS atom-query feature A to allow any atom except hydrogen at that position (You will later place the query into the MOLSTRUCTURE box on the form.):

Examples of molecules retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Examples of Molecules Retrieved


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SSS


Question 10: "I want to find..."
     Question 10: I want to find specific types of molecules that contain a single carbon atom that is attached to four ring bonds.

Example: I want to find all spiro-substituted saturated pyrimidines.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the type of molecule and that a single carbon atom is attached to four ring bonds (in this example, all spiro-substituted saturated pyrimidines).

You need to create a search query that allows only a specific number of ring bond attachments at the given positions on the molecule.

To create the query for this example, draw the structure, and then use the ISIS atom-query features r2 (two ring bond attachments) and r4 (at least four ring bond attachments) to specify the number of ring bond attachments at the given positions (You will later place the query into the MOLSTRUCTURE box on the form.):

Example of a molecule retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Molecule Retrieved

Spirothiobarbital:


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SSS


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

I have specific data of interest.  I want to find all molecules that are associated with a specific:

1.	ID number. (Example: MUSE00000009)

2.	CAS number. (Example: All molecules in the ACD database with the CAS number 87-82-1)

3.	Company. (Example: All molecules in the MDDR database that were developed by Pfizer Limited)

4.	Formula and no other atoms. (Examples: C17H19N3)

5.	Subformula and any additional atoms. (Examples: C5H10)

6.	Subformula and any additional atoms except a specific atom. (Examples: C5H10N0, where N0 represents zero nitrogens)

7.	Molecular weight or molecular weight range. (Examples: Molecular weight, 350; molecular weight ranges, >350, 200-250)

8.	Compound name. (Example: Aspirin)

9.	Text string in their compound name. (Example: Acid)

10.	Type of activity. (Example: Cardiotonic activity)

11.	Combination of data. (Example: Molecular weight, < 180, and activity, cardiotonic)


Question 1: "I want to find..."
     Question 1: I want to find a molecule that is associated with a specific ID number.

Example: I want to find the molecule with the ID number MUSE000000009.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the ID number (in this example, MUSE000000009).

You need to create a search query that contains a search operator and the exact ID number (You will later place the query into the CORPORATE ID box or equivalent on the form.):

Example of a record retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Record Retrieved


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Text String Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Text String Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Question 2: "I want to find..."
     Question 2: I want to find all molecules that are associated with a specific CAS number.

Example: I want to find all molecules with the CAS number 87-82-1.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the CAS number (in this example, 87-82-1).

You need to create a search query that contains a search operator and the exact CAS number (You will later place the query into the CAS_NUMBER box or equivalent on the form.):

= 87-82-1

Example of a record retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Record Retrieved


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Text String Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Text String Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Question 3: "I want to find..."
     Question 3: I want to find all molecules that are associated with a specific company.

Example: I want to find all molecules in the database that were developed by Pfizer Limited.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the company name (in this example, Pfizer Limited).

You need to create a search query that contains a search operator and either the entire company name or a portion of it (You will later place the query into the COMPANY_NAME box or equivalent on the form.). To retrieve solely those records that contain exactly the target value that you specified, enter the following search query:

LIKE "Pfizer Limited"

To retrieve those records that contain exactly the target value that you specified and any additional words or phrases that are stored with the database field COMPANY_NAME, enter either of the following search queries with wildcards:

LIKE "%Pfizer Limited%"

LIKE "%Pfizer%"

Example of a record retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Record Retrieved


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Text String Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Graphical Query For a Local Database
Text String Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Question 4: "I want to find..."
     Question 4: I want to find all molecules that are associated with a specific formula and no other atoms.

Example: I want to find all molecules with the formula C17H19N3.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the exact formula (in this example, C17H19N3).

You need to create a search query that contains the exact formula in upper- or lower-case characters (You will later place the query into the Query text box in the Formula dialog box.):

C17H19N3

Example of a record retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Record Retrieved


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Formula Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* FMLA


Formula Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* FMLA


Question 5: "I want to find..."
     Question 5: I want to find all molecules that are associated with a specific subformula and any additional atoms.

Example: I want to find all molecules with the subformula C5H10.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the subformula (in this example, C5H10).

You need to create a search query that contains the subformula in upper- or lower-case characters (You will later place the query into the Query text box in the Formula dialog box.):

C5H10

Example of a record retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Record Retrieved


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Formula Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* FMLA


Formula Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* FMLA


Question 6: "I want to find..."
     Question 6: I want to find all molecules that are associated with a specific subformula and any additional atoms except a specific atom.

Example: I want to find all molecules with the subformula C5H10 that do not contain any nitrogens.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the subformula and the atoms that you want to exclude (in this example, the subformula is C5H10, and the excluded atoms are nitrogens).

You need to create a search query that contains the subformula with a zero after each excluded atom (such as N0 for zero nitrogens) in upper- or lower-case characters (You will later place the query into the Query text box in the Formula dialog box.):

C5H10N0

Example of a record retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Record Retrieved


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Formula Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* FMLA


Formula Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* FMLA


Question 7: "I want to find..."
     Question 7: I want to find all molecules that are associated with a specific molecular weight or a range of molecular weights.

Example: I want to find all molecules with a molecular weight of 350 or a molecular weight greater than 350 or a molecular weight between 200 and 250.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the molecular weight (in this example, it is 350 or greater than 350 or between 200 and 250).

You need to create a search query that contains a search operator and the molecular weight (You will later place the query into the MOLECULAR.WEIGHT box or equivalent on the form.):

A search query with a specific molecular weight:

= 350

A search query that is greater than a specific molecular weight:

> 350

A search query that is between (and including) two molecular weights:

BETWEEN 200 250

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Text String Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Graphical Query For a Local Database
Text String Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Question 8: "I want to find..."
     Question 8: I want to find all molecules that are associated with a specific compound name.

Example: I want to find all molecules that contain the name “aspirin.”

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the compound name (in this example, aspirin).

You need to create a search query that contains a search operator and the compound name (You will later place the query into the COMPOUND_NAME box or equivalent on the form.). The following search query retrieves solely those records that contain exactly the target value that you specified:

LIKE "aspirin"

Example of a record retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Record Retrieved


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Text String Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Graphical Query For a Local Database
Text String Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Question 9: "I want to find..."
     Question 9: I want to find all molecules that are associated with a specific text string in their compound name.

Example: I want to find all molecules that contain the term “acid” in their compound name.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know a portion of the compound name (in this example, acid).

You need to create a search query that contains a search operator, the portion of the compound name that you know, and wildcards (You will later place the query into the COMPOUND_NAME box or equivalent on the form.). The following search query retrieves those records that contain exactly the target value that you specified and any additional words or phrases that are stored with the database field COMPOUND_NAME:

LIKE "%acid%"

Example of a record retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Record Retrieved


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Text String Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Graphical Query For a Local Database
Text String Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Question 10: "I want to find..."
     Question 10: I want to find all molecules that are associated with a specific type of activity.

Example: I want to find all molecules that contain cardiotonic activity.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the type of activity (in this example, cardiotonic).

You need to create a search query that contains a search operator and either the entire type of activity or a portion of it (You will later place the query into the ACTIVITY box or equivalent on the form.). To retrieve solely those records that contain exactly the target value that you specified, enter the following search query:

LIKE "cardiotonic"

To retrieve those records that contain exactly the target value that you specified and any additional words or phrases that are stored with the database field ACTIVITY, enter either of the following search queries with wildcards:

LIKE "%cardiotonic%"

LIKE "%cardio%"

Example of a record retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Record Retrieved


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Text String Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Graphical Query For a Local Database
Text String Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Question 11: "I want to find..."
     Question 11: I want to find all molecules that are associated with a combination of data.

Example: I want to find all molecules with a molecular weight less than 180 and all molecules that contain cardiotonic activity.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the molecular weight and the type of activity (in this example, the molecular weight is < 180 and the activity is cardiotonic).

You need to create a search query that contains a search operator and the molecular weight, and search operator and either the entire type of activity or a portion of it. To retrieve solely those records with a molecular weight less than 180 and that contain exactly the target value in the ACTIVITY box that you specified: Enter the following search query:

< 180	(into the MOLECULAR.WEIGHT box on the form)

LIKE "cardiotonic"	(into the ACTIVITY box on the form)

To retrieve those records with a molecular weight less than 180 and that contain exactly the target value in the ACTIVITY box that you specified and any additional words or phrases that are stored with that database field: Enter < 180 and either of the following text strings with wildcards:

< 180	(into the MOLECULAR.WEIGHT box on the form)

LIKE "%cardiotonic%"	(into the ACTIVITY box on the form)

LIKE "%cardio%"	(into the ACTIVITY box on the form)

Example of a record retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Record Retrieved

Note: You might retrieve molecules that satisfy solely one specification in your search query and not the other.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Text String Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Graphical Query For a Local Database
Text String Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

I have a specific combination of structural features and data of interest.  I want to find all molecules with a specific:

1.	Functional group and a specific melting point. (Example: All molecules that contain benzoic acid embedded wholly within them and that have a melting point >150)

2.	Functional group and a specific molecular weight. (Example: All heterocyclic compounds with a molecular weight between 250 and 350)


Question 1: "I want to find..."
     Question 1: I want to find all molecules that contain a specific functional group and that are associated with specific data.

Example: I want to find all molecules that contain benzoic acid embedded wholly within them and that have a melting point greater than 150.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the functional group (in this example, benzoic acid) and the data (in this example, a melting point greater than 150).

You need to create a single search query that contains both a functional group component and a specific data component. There are 2 ways to create your search query. The one you choose is strictly your own preference and does not affect the search results.

3.	To identify the type of search that you need to do and to see the step-by-step instructions, click the type of query that you prefer to use:

*	Query 1

The preferred query:

The functional group component: Draw the structure, and then add the explicit hydrogen to prevent substitutions at that position (You will later place this query component into the MOLSTRUCTURE box on the form.):

The specific data component: Enter a search operator and the melting point (You will later place this query component into the MELTING.PT box or equivalent on the form.):

> 150

*	Query 2

An alternative query for remote searching only:

The functional group component: Draw the structure, and then add the ISIS atom-query feature s* to prevent substitution at that position (You will later place this query component into the MOLSTRUCTURE box on the form.):

The specific data component: Enter a search operator and the melting point (You will later place this query component into the MELTING.PT box or equivalent on the form.):

> 150


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Local Database
Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SBF


Graphical Query 1 For a Remote Database
Query 1 For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SBF


Graphical Query 2 For a Remote Database
Query 2 For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* SBF


Question 2: "I want to find..."
     Question 2: I want to find all molecules that contain a specific functional group and that are associated with specific data.

Example: I want to find all 5-membered heterocyclic compounds with a molecular weight that is between 250 and 350.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the functional group (in this example, 5-membered heterocyclic rings) and the data (in this example, a molecular weight between 250 and 350).

You need to create a single search query that contains both a functional group component with allowed heteroatoms at a specified position and a specific data component.

The functional group component: Draw the structure, and then add the ISIS atom-query feature List to allow specific heteroatoms (such as N, O, and S) at the specified position (You will later place this query component into the MOLSTRUCTURE box on the form.):

The specific data component: Enter a search operator and the molecular weight range (You will later place this query component into the MOLECULAR.WEIGHT box or equivalent on the form.):

BETWEEN 250 350

Example of a record retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Record Retrieved

Note: You might retrieve molecules that satisfy solely one specification in your search query and not the other.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Text String Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Graphical Query For a Local Database
Text String Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


What To Do If You Could Not Find...
   What To Do If You Could Not Find a Suitable Sample Question

We hope that you were able to find a suitable sample question. We believe that these sample questions illustrate all the searches that you can perform with ISIS. If you did not find a question, please look again because this is the best method to find the most suitable search.

If you are still unable to find a suitable sample question, the only thing that we can do now is to show you a list of all the searches and their definitions. But first, do you have a remote or local database?

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to obtain network access information. A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to obtain network access information. (If you do not know which type of database you have, see your ISIS Administrator.)

To view the searches and their definitions, click one of the following:

*	I want to search a remote database

*	I want to search a local database


   I Want to Search a Remote Molecule Database

For a remote molecule database, there are 14 possible searches that you can conduct.

Click any item to see a definition of that search:

Exact Match of a Molecule (MEXACT)

Flexmatch (FLEX)

Formula (FMLA)

ID

Isomer of a Molecule (ISOMER)

Parent of a Molecule That is a Salt (PARENT)

Query Builder (QB)

Retrieve All (ALL)

Search By Form (SBF)

Structurally Similar Molecule (MSim)

Substituents of the Root Structure of a Molecule (RGROUP)

Substructure of a Biopolymer (SSS/Biopoly)

Substructure of a Molecule (SSS)

Tautomer of a Molecule (TAUT)


   I Want to Search a Local Molecule Database

For a local molecule database, there are 8 possible searches that you can conduct.

Click any item to see a definition of that search:

Exact Match of a Molecule (MEXACT)

Formula (FMLA)

ID

Query Builder (QB)

Retrieve All (ALL)

Search By Form (SBF)

Substructure of a Biopolymer (SSS/Biopoly)

Substructure of a Molecule (SSS)


What To Do If You Could Not Find...
   What To Do If You Could Not Find a Suitable Sample Question

We hope that you were able to find a suitable sample question. We believe that these sample questions illustrate all the searches that you can perform with ISIS. If you did not find a question, please look again because this is the best method to find the most suitable search.

If you are still unable to find a suitable sample question, the only thing that we can do now is to show you a list of all the searches and their definitions. But first, do you have a remote or local database?

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to obtain network access information. A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to obtain network access information. (If you do not know which type of database you have, see your ISIS Administrator.)

To view the searches and their definitions, click one of the following:

*	I want to search a remote database

*	I want to search a local database


   I Want to Search a Remote Reaction Database

For a remote reaction database, there are 19 possible searches that you can conduct.

Click any item to see a definition of that search:

Exact Match of a Reaction (REXACT/Rxn)

Exact Match of a Reaction Component With a Reaction Arrow (REXACT/Comp)

Exact Match of a Reaction Component Without a Reaction Arrow (MEXACT)

Find Related Reactions (RELATED)

Flexmatch of a Reaction Component (FLEX)

Formula of a Reaction Component (FMLA)

ID

Isomer of a Reaction Component (ISOMER)

Parent of a Reaction Component That is a Salt (PARENT)

Query Builder (QB)

Retrieve All (ALL)

Search By Form (SBF)

Structurally and/or Transformationally Similar Reactions or Structurally Similar Reaction Components With a Reaction Arrow (RSim)

Structurally Similar Reaction Components Without a Reaction Arrow (MSim)

Substituents of the Root Structure of a Reaction Component (RGROUP)

Substructure of a Reaction (RSS/Rxn)

Substructure of a Reaction Component With a Reaction Arrow (RSS/Comp)

Substructure of a Reaction Component Without a Reaction Arrow (SSS)

Tautomer of a Reaction Component (TAUT)


   I Want to Search a Local Reaction Database

For a local reaction database, there are 11 possible searches that you can conduct.

Click any item to see a definition of that search:

Exact Match of a Reaction (REXACT/Rxn)

Exact Match of a Reaction Component Without a Reaction Arrow (MEXACT)

Formula of a Reaction Component (FMLA)

ID

QB

RELATED

Retrieve All (ALL)

Search By Form (SBF)

Substructure of a Reaction Component Without a Reaction Arrow (SSS)

Substructure of a Reaction (RSS/Rxn)

Substructure of a Reaction Component With a Reaction Arrow (RSS/Comp)


I Want To Find Information on Molecules
  I Want To Find Information on 3D Structures

Click one of these items:

*	I have a fully defined 3D structure (such as a ligand) of interest. I want to find this 3D structure and closely related 3D structures (such as exact matches within specific tolerance limits or duplicate 2D structures with different 3D conformations).

*	I have a portion of a 3D structure (such as a fragment or a substructure of a ligand) of interest. I want to find 3D structures that contain this substructure embedded wholly within them in specific 3D conformations.

*	I have information about portions of a receptor site that interacts with ligands of interest. I want to find 3D structures that can interact with this receptor site.

*	I have a pharmacophore hypothesis of interest. I want to find 3D structures that contain this pharmacophore in specific 3D conformations.

*	I have specific data of interest for a 3D structure (such as a ligand or receptor). I want to find all 3D structures that are associated with this data.

What to do if you could not find a suitable sample question


What To Do If You Could Not Find...
   What To Do If You Could Not Find a Suitable Sample Question

We hope that you were able to find a suitable sample question. We believe that these sample questions illustrate all the searches that you can perform with ISIS. If you did not find a question, please look again because this is the best method to find the most suitable search.

If you are still unable to find a suitable sample question, the only thing that we can do now is to show you a list of all the searches and their definitions. But first, do you have a remote or local database?

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to obtain network access information. A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to obtain network access information. (If you do not know which type of database you have, see your ISIS Administrator.)

To view the searches and their definitions, click one of the following:

*	I want to search a remote database

*	I want to search a local database


   I Want to Search a Remote 3D Database

For a remote 3D database, there are 10 possible 3D searches that you can conduct.

Click any item to see a definition of that search:

3D Substructure (SSS3D)

3D Substructure (SSS3D/Biopoly)

Conformationally Flexible Substructure (CFS)

Conformationally Flexible Substructure (CFS/Biopoly)

Exact Match of a 3D Structure (3DEXACT)

ID

Query Builder (QB)

Retrieve All (ALL)

Search By Form in a Protein or 3D Database (SBF)

Structurally Similar Molecule (MSim)


   I Want to Search a Local 3D Database

For a local 3D database, there are 5 possible 3D searches that you can conduct.

Click any item to see a definition of that search:

Exact Match of a Molecule (3DEXACT)

ID

Query Builder (QB)

Retrieve All (ALL)

Search By Form in a Protein or 3D Database (SBF)


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

I have a specific, fully defined 3D structure (such as a ligand) of interest.  I want to find all 3D structures that:

1.	Are duplicates. (Example: All 3D representations in the database of the molecule Felodipine)

2.	Are exact matches within specific tolerance limits. (Example: All 3D structures that differ from Felodipine by no more than 0.1 Angstroms for individual atoms and by no more than 0.5 Angstroms for the overall fit of the structure)

3.	Contain the same 2D structure. (Example: All 3D structures that contain the 2D structure Spirapril)


Question 1: "I want to find..."
     Question 1: I want to find this exact 3D structure and all duplicates of it in the database.

Example: I want to find all 3D representations in the database of the molecule Felodipine.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the name of the 3D structure (in this example, Felodipine).

You need to obtain a search query that is the exact 3D structure, as follows:

*	Conduct a search for the 3D structure using its name as the query: Enter the text-string search query LIKE "felodipine" into the box or table cell on the form in ISIS/Base that is connected to the database field MOLNAME. Execute an SBF search (choose Search > By Form.) After the search, click Browse if necessary. You see the 3D structure in the MODELSTRUCTURE box or table cell on the form.

*	Transfer the 3D structure to the appropriate box or table cell on the form: Click the MODELSTRUCTURE box that contains the 3D structure. Choose Edit > Copy. Click Query. To clear the form, choose Edit > Clear Data > Form. Click the MODELSTRUCTURE box or table cell. Choose Edit > Paste. You see Felodipine in the MODELSTRUCTURE box or table cell on the form in Query mode.

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Graphical Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* Exact 3D Structure (3DEXACT)


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* Exact 3D Structure (3DEXACT)


Question 1: "I want to find..."
     Question 2: I want to find this exact 3D structure in the database within specific tolerance limits.

Example: I want to find all 3D structures that differ from Felodipine by no more than 0.1 Angstroms for individual atoms and by no more than 0.5 Angstroms for the overall fit of the structure.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the name of the 3D structure (in this example, Felodipine) and the allowed tolerance limits for both the individual atoms (in this example, no more than 0.1 Angstroms) and for the overall atoms (in this example no more than 0.5 Angstroms).

You need to obtain a search query that is the exact 3D structure, as follows:

*	Conduct a search for the 3D structure using its name as the query: Enter the text-string search query LIKE "felodipine" into the box or table cell on the form in ISIS/Base that is connected to the database field MOLNAME. Execute an SBF search (choose Search > By Form.) After the search, click Browse if necessary. You see the 3D structure in the MODELSTRUCTURE box or table cell on the form.

*	Transfer the 3D structure to the appropriate box or table cell on the form: Click the MODELSTRUCTURE box that contains the 3D structure. Choose Edit > Copy. Click Query. To clear the form, choose Edit > Clear Data > Form. Click the MODELSTRUCTURE box or table cell. Choose Edit > Paste. You see Felodipine in the MODELSTRUCTURE box or table cell on the form in Query mode (You will later enter the allowed tolerance limits.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions:

* Exact 3D Structure (3DEXACT)


Question 1: "I want to find..."
     Question 3: I want to find all 3D conformations of this exact 2D structure in the database.

Example: I want to find all 3D conformations of the 2D structure Spirapril.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the 2D structure (in this example, Spirapril).

You need to create a search query that contains the 2D structure, as follows (for which you will receive further step-by-step instructions when you need them):

*	Conduct a search for the 2D structure using its name as the query: Enter the text-string search query LIKE "spirapril" into the box or table cell on the form in ISIS/Base that is connected to the database field MOLNAME. Execute an SBF search (choose Search > By Form.) After the search, click Browse if necessary. You see the 2D structure in the MOLSTRUCTURE box or table cell on the form in the Browse mode.

*	Click the MOLSTRUCTURE box that contains the 2D structure. Choose Edit > Copy. Click Query. To clear the form, choose Edit > Clear Data > Form. Click the MOLSTRUCTURE box or table cell. Choose Edit > Paste. You see the 2D structure in the MOLSTRUCTURE box or table cell on the form in the Query mode:

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Graphical Query For a Remote Database

These are the correct searches for this query. Click either of them to see a definition and step-by-step instructions:

*	CFS

*	SSS3D


Graphical Query For a Remote Database

This is the correct search for this query. Click it to see a definition and step-by-step instructions:

*	SSS3D


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

I have a portion of a 3D structure (such as a portion of a ligand) of interest.  I want to find all 3D structures that:

1.	Contain this hydrogen-bond donor in a specific spatial arrangement. (Example: All 3D structures with a hydrogen-bond donor that is 6 to 10 Angstroms from the terminal carbon of an alkyl group of 3 to 13 carbons in length)

2.	Contain this hydrogen-bond acceptor in a specific spatial arrangement. (Example: All 3D structures with a hydrogen-bond acceptor, basic nitrogen, that is 3 to 8 Angstroms from the center of a phenyl ring)

3.	Contain this acidic center in a specific spatial arrangement. (Example: All 3D structures with an acidic center that is 5 to 8 Angstroms from an amide nitrogen)

4.	Contain this set of functional groups and/or atoms in a specific spatial arrangement. (Example: All 3D structures with phenyl and phenol groups whose centers are 6 to 10 Angstroms from each other)

5.	Exclude this set of functional groups and/or atoms in a specific spatial arrangement. (Example: All 3D structures that exclude any atoms within two spherical regions of 3.5 Angstroms in diameter above and below a phenyl ring)

6.	Contain this submodel. (Example: All 3D structures with a subset of the 3D structure of Spirapril)

7.	Contain this submodel but with a different 3D conformation. (Example: All 3D structures with a subset of the 3D structure of Spirapril in which there are two interatomic distance constraints)


Question 1: "I want to find..."
     Question 1: I want to find all 3D structures in the database that contain this hydrogen-bond donor and a functional group embedded wholly within them in a specific spatial arrangement.

Example: I want to find all 3D structures with a hydrogen-bond donor that is 6 to 10 Angstroms from the terminal carbon of an alkyl group of 3 to 13 carbons in length.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the portions of the 3D structure that you want to find in all 3D structures retrieved and their spatial arrangement (in this example, a hydrogen-bond donor that is 6 to 10 Angstroms from the terminal carbon of an alkyl group of 3 to 13 carbons in length).

You need to create a search query that contains the portions of the 3D structures and the 3D constraint that specifies the spatial arrangement. Do the following (for which you will receive further step-by-step instructions when you need them):

*	Draw the hydrogen-bond donor with the ISIS atom-query feature List that allows specific atoms (such as O, N, and S) at the specified position:

Note: You might define a hydrogen-bond donor differently.

*	Draw the minimum-length aliphatic chain, and then add the ISIS atom-query features Link Node to allow additional repeating units that lengthen the chain, A to allow any atom except hydrogen at that position, and s* to prevent substitutions at specific positions.

*	Add the 3D distance constraint (in Angstroms) between the hydrogen-bond donor and the terminal carbon of the alkyl group (You will later place the query into the MODELSTRUCTURE box on the form.):

Examples of 3D Structures Retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Examples of 3D Structures Retrieved


Question 1: "I want to find..."
     Question 2: I want to find all 3D structures in the database that contain this hydrogen-bond acceptor and a functional group embedded wholly within them in a specific spatial arrangement.

Example: I want to find all 3D structures with basic nitrogen, a hydrogen-bond acceptor, that is 3 to 8 Angstroms from the center of a phenyl ring.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the portions of the 3D structure that you want to find in all 3D structures retrieved and their spatial arrangement (in this example, a hydrogen-bond acceptor, basic nitrogen, that is 3 to 8 Angstroms from the center of a phenyl ring).

You need to create a search query that contains the portions of the 3D structures and the 3D constraint that specifies the spatial arrangement. Do the following (for which you will receive further step-by-step instructions when you need them):

*	Retrieve the following MDL ISIS/Draw sketch file of the hydrogen-bond acceptor basic nitrogen: BSC_N_2.SKC. (Alternatively, you can use the MDL sketch file BSC_N_1.SKC or H_ACCEPT.SKC).

This file contains: A root structure with the Rgroup label R1; the Rgroup substituents with the nested Rgroup R2; and Rgroup conditions. The ISIS bond-query feature AROMATIC (adjacent solid and dashed lines) allows solely aromatic bonds at the specified position. The ISIS atom-query feature List allows specific atoms (such as O, S, and N) at the specified position.

Note: You might define a hydrogen-bond acceptor differently. Thus, you might want to modify this sketch file to create your own query.

*	Draw the phenyl ring.

*	Add the 3D Object (a centroid, represented by the triangle) that allows a distance constraint to be drawn to a functional group. (In this example, a centroid was created from all atoms in the ring.)

*	Add the 3D distance constraint (in Angstroms) between the hydrogen-bond acceptor, basic nitrogen, and the centroid of the phenyl ring.

For clarity, the following query displays solely two of the members of the Rgroup substituent R1 in the basic nitrogen component (You will later place the query into the MODELSTRUCTURE box on the form.):

Examples of 3D Structures Retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


The Root Structure

The root structure is that portion of the query that must be present in all the structures retrieved. In this example, the root structure is:

Note: The Rgroup label (R1) on the root structure corresponds to a list of substituents that are allowed or excluded at that position in the molecules retrieved.


Rgroup Substituents

Rgroup substituents are the functional groups or atoms that you allow (or exclude) on the root structure at a specific position (R1 or R2) in the molecules retrieved. In this example:

*	Substituents in list R1 (for example, amides and anilines) are excluded at position R1 on the root structure (R1=0).

*	NO2 and C=O are allowed on Rgroup substituents on list R1 that have an R2 site (R2 > 0).

Note: An attachment point (marked with an arrow and an asterisk) designates the atom on the Rgroup substituent that is attached to the root structure or Rgroup substituent.


Rgroup Conditions

Rgroup conditions are the set of restrictions on each Rgroup in your query. In this example, the Rgroup condition:

*	R1 = 0 specifies that no Rgroup substituents from the R1 list can occupy the R1 site on the root structure in the records retrieved.

*	R2 > 0 specifies that an Rgroup substituent from the R2 list must occupy at least one R2 site on the Rgroup substituents on the R1 list that have an R2 site.


Nested Rgroup

A nested Rgroup is an Rgroup that is a place holder within another Rgroup rather than within the root structure. (You cannot nest an Rgroup any lower than this level.) In the following example, Rgroup R2 is nested within the Rgroup R1:

The nested Rgroups in this example are equivalent to the following structures:


Nested Rgroup

A nested Rgroup is an Rgroup that is a place holder within another Rgroup rather than within the root structure. (You cannot nest an Rgroup any lower than this level.) In the following example, Rgroup R2 is nested within the Rgroup R1:

Nested Rgroups are equivalent to the following structures:


Examples of 3D Structures Retrieved


BSC_N_1.SKC File

The file BSC_N_1.SKC contains a definition of a basic nitrogen that includes alkyl amines (nsp3), amidines (nsp2), and guanidines (nsp2). This definition excludes other nitrogens such as aromatic nitrogens, aniline-type nitrogens, N=O, NHC=O, and NHC=C:


BSC_N_2.SKC File

The definition of basic nitrogen in the file BSC_N_2.SKC excludes all amides or anilines, and other conjugated systems that reduce the accessibility of the electron pair on the nitrogen atom:


H_ACCEPT.SKC File

The definition of a hydrogen-bond acceptor in the file H_ACCEPT.SKC extends the definition of a basic nitrogen to include oxygen and sulfur:


Question 1: "I want to find..."
     Question 3: I want to find all 3D structures in the database that contain this acidic center and a functional group embedded wholly within them in a specific spatial arrangement.

Example: I want to find all 3D structures with an acidic center that is 5 to 8 Angstroms from an amide nitrogen.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the portions of the 3D structure that you want to find in all 3D structures retrieved and their spatial arrangement (in this example, an acidic center that is 5 to 8 Angstroms from an amide nitrogen).

You need to create a search query that contains the portions of the 3D structures and the 3D constraint that specifies the spatial arrangement. Do the following (for which you will receive further step-by-step instructions when you need them):

*	Retrieve the following MDL ISIS/Draw sketch file of an acidic center: ACID_CTR.SKC.

This file contains: A root structure with the Rgroup labels R1 and R2; the Rgroup substituents; and Rgroup conditions.

The ISIS atom-query features List allows specific atoms (such as N and O) at the specified position; UNSATURATED (u) requires at least one multiple bond (double, triple, or aromatic) to be attached to the atom at the specified position; and s2 allows solely two non-hydrogen attachments of any bond type at the specified positions.

The ISIS bond-query features SINGLE/AROMATIC (two lines, one line with long and short dashes) allows solely single or aromatic bonds at the specified positions; ANY (single dashed line) allows any bond type at the specified position; and Rn allows solely ring bonds at the specified positions.

Note: You might define an acidic center differently. Thus, you might want to modify this sketch file to create your own query.

*	Draw the amide nitrogen group.

*	Add the 3D distance constraint (in Angstroms) between the acidic center and the amide nitrogen (You will later place the query into the MODELSTRUCTURE box on the form.):

Examples of 3D Structures Retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Examples of 3D Structures Retrieved


Acidic Center

In this example, an acidic center as either an oxygen of a carboxylic acid or any nitrogen of an unsubstituted tetrazole.


ACID_CTR.SKC File

The file ACID_CTR.SKC contains the following definition of an acidic center:

Together, R1 and R2 allow solely the following:

*	When the atom at the [O,N] site is oxygen, R1 and R2 specify a hydroxy group that is attached to an unsaturated carbon atom.

*	When the atom at the [O,N] site is nitrogen, R1 and R2 specify a tetrazole ( [image]) in which the unsaturated carbon in the root structure of the Rgroup is included in the tetrazole ring. The condition R2 < 2 excludes amines.


The Root Structure

The root structure is that portion of the query that must be present in all the structures retrieved. In this example, the root structure is:

Note: The Rgroup labels (R1 and R2) on the root structure correspond to lists of substituents that are allowed at that position in the molecules retrieved.


Rgroup Substituents

Rgroup substituents are the functional groups or atoms that you allow (or exclude) on the root structure at a specific position (R1 and R2) in the molecules retrieved. In this example:

*	Substituents in list R1 are allowed at position R1 on the root structure.

*	Substituents in list R2 are allowed at position R2 on the root structure.

Note: An attachment point (marked with an arrow and an asterisk) designates the atom on the Rgroup substituent that is attached to the root structure.


Rgroup Conditions

Rgroup conditions are the set of restrictions on each Rgroup in your query. In this example:

*	R1 < 2 (Rest H) specifies that the Rgroup substituent from the R1 list must occupy either 0 or 1 sites on the root structure. Rest H excludes all non-hydrogen functional groups except the Rgroup substituent from the R1 list.

*	R2 < 2 specifies that the Rgroup substituent from the R2 list (a hydrogen atom) must occupy fewer than two sites on the root structure in the records retrieved.

Together, the two Rgroup conditions specify that either hydrogen or the Rgroup substituent from the R1 list must occupy the R1R2 site on the root structure.


Question 1: "I want to find..."
     Question 4: I want to find all 3D structures in the database that contain this set of functional groups and/or atoms in a specific spatial arrangement.

Example: I want to find all 3D structures with phenyl and phenol groups whose centers are 6 to 10 Angstroms from each other.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the portions of the 3D structure that you want to find in all 3D structures retrieved and their spatial arrangement (in this example, phenyl and phenol groups whose centers are 6 to 10 Angstroms from each other).

You need to create a search query that contains the portions of the 3D structures and the 3D constraint that specifies the spatial arrangement. Do the following (for which you will receive further step-by-step instructions when you need them):

*	Draw the phenol group.

*	Draw the phenyl group.

*	Add the 3D Object (a centroid, represented by the triangle) that allows a distance constraint to be drawn between functional groups. (In this example, each centroid was created from all atoms in the ring.)

*	Add the 3D distance constraint (in Angstroms) between the centroid of the phenol group and the centroid of the phenyl group (You will later place the query into the MODELSTRUCTURE box on the form.):

Example of a 3D Structure Retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a 3D Structure Retrieved


Question 1: "I want to find..."
     Question 5: I want to find all 3D structures in the database that exclude this set of functional groups and/or atoms in a specific spatial arrangement.

Example: I want to find all 3D structures that exclude any atoms within two spherical regions of 3.5 Angstroms in diameter above and below a phenyl ring.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the portions of the 3D structure that you want to exclude in all 3D structures retrieved and their spatial arrangement (in this example, the exclusion of any atoms within two spherical regions of 3.5 Angstroms in diameter above and below a phenyl ring).

You need to create a search query that contains the portions of the 3D structures that you want to exclude and the 3D constraint that specifies the spatial arrangement. Do the following (for which you will receive further step-by-step instructions when you need them):

*	Draw the phenyl ring. For illustration purposes, the ring in this example was 3D rotated. (3D rotation is unnecessary.)

*	Add the following 3D Objects (which you must add now so that you can add the 3D constraints later):

(a) A centroid (a triangle at the center of the phenyl ring) and a plane to allow a normal to be drawn through the plane of the phenyl ring. The default thickness of the plane is 0.5 Angstroms.

(b) A normal (a line with an arrow) to specify two points along the plane. (If you do not see the normal, you might need to 3D rotate the query.)

(c) Two points (triangles on the normal) on the normal at distances of 2 Angstroms above and below the plane. Each point will be the center of an exclusion sphere (3D constraint).

*	Add the 3D constraints (two exclusion spheres, each 1.5 Angstroms in diameter) around the points along the normal (You will later place the query into the MODELSTRUCTURE box on the form.):

Examples of 3D Structures Retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Examples of 3D Structures Retrieved


Question 1: "I want to find..."
     Question 6: I want to find all 3D structures in the database that contain this submodel portion of the 3D structure.

Example: I want to find all 3D structures that contain a specific submodel portion of the 3D structure Spirapril.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know name of the 3D structure and the submodel portion that you want to find in all 3D structures retrieved (in this example, a specific submodel portion of the 3D structure Spirapril).

You need to create a search query that is a submodel portion of the 3D structure, as follows:

*	Conduct a search for the 3D structure using its name as the query: Enter the text-string search query LIKE "spirapril" into the box or table cell on the form in ISIS/Base that is connected to the database field MOLNAME. Execute an SBF search (choose Search > By Form.) After the search, click Browse if necessary. You see the 3D structure in the MODELSTRUCTURE box or table cell on the form:

*	Transfer the 3D structure to the appropriate box or table cell on the form: Click the MODELSTRUCTURE box that contains the 3D structure. Choose Edit > Copy. Click Query. To clear the form, choose Edit > Clear Data > Form. Click the MODELSTRUCTURE box or table cell. Choose Edit > Paste. You see Spirapril in the MODELSTRUCTURE box or table cell on the form in Query mode.

*	Create the submodel: Transfer to ISIS/Draw. Add the fixed-atom tolerances (F) to specific atoms and delete the portions of the 3D structure that you do not want in the records retrieved. Then transfer the query back to ISIS/Base. You see your search query in the MODELSTRUCTURE box or table cell on the form:

Examples of 3D Structures Retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Examples of 3D Structures Retrieved


Question 1: "I want to find..."
     Question 7: I want to find all 3D structures in the database that contain this submodel portion of the 3D structure but with a different 3D conformation.

Example: I want to find all 3D structures that contain a specific submodel portion of the 3D structure Spirapril with two interatomic distance constraints.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know name of the 3D structure, the submodel portion that you want to find in all 3D structures retrieved, and the 3D constraints (in this example, a specific submodel portion of the 3D structure Spirapril with two interatomic distance constraints).

You need to create a search query that is a submodel portion of the 3D structure, as follows:

*	Conduct a search for the 3D structure using its name as the query: Enter the text-string search query LIKE "spirapril" into the box or table cell on the form in ISIS/Base that is connected to the database field MOLNAME. Execute an SBF search (choose Search > By Form.) After the search, click Browse if necessary. You see the 3D structure in the MODELSTRUCTURE box or table cell on the form:

*	Transfer the 3D structure to the appropriate box or table cell on the form: Click the MODELSTRUCTURE box that contains the 3D structure. Choose Edit > Copy. Click Query. To clear the form, choose Edit > Clear Data > Form. Click the MODELSTRUCTURE box or table cell. Choose Edit > Paste. You see Spirapril in the MODELSTRUCTURE box or table cell on the form in Query mode.

*	Create the submodel and add the 3D constraints: Transfer to ISIS/Draw. Add the fixed-atom tolerances (F) to specific atoms and delete the portions of the 3D structure that you do not want in the records retrieved. Add the 3D constraints (the two distances in Angstroms). Then transfer the query back to ISIS/Base. You see your search query in the MODELSTRUCTURE box or table cell on the form:

Examples of 3D Structures Retrieved

Example of a 3D Structure That is NOT Retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Examples of 3D Structures Retrieved


Example of a 3D Structure That is NOT Retrieved


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

I have information about portions of a receptor site that interacts with ligands of interest. I want to find 3D structures that interact with receptors that:

1.	Contain this hydrogen-bond donor and hydrogen-bond acceptor in a specific spatial arrangement to each other. (Example: All 3D structures that can interact with a receptor site that contains a hydrogen-bond acceptor 8 to 10 Angstroms from a hydrogen-bond donor)

2.	Contain this hydrogen-bond donor or hydrogen-bond acceptor in a specific spatial arrangement to another group on the receptor. (Example: All 3D structures that can interact with a receptor site that contains a hydrogen-bond donor 6 to 10 Angstroms from an aromatic group. The aromatic group on the receptor interacts with a phenyl ring on the ligand through a planar hydrophobic (pi-pi) bond.)


Question 1: "I want to find..."
     Question 1: I want to find all 3D structures in the database that can interact with a receptor site that contains this hydrogen-bond donor and hydrogen-bond acceptor in a specific spatial arrangement to each other.

Example: I want to find all 3D structures that can interact with a receptor site that contains a hydrogen-bond acceptor 8 to 10 Angstroms from a hydrogen-bond donor.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know that the receptor site contains a hydrogen-bond donor and a hydrogen-bond acceptor in a specific spatial arrangement (in this example, the receptor site contains a hydrogen-bond acceptor 8 to 10 Angstroms from a hydrogen-bond donor). The 3D structures that you retrieve must contain functional groups that can interact with the groups on the receptor (in this example, the structures that you retrieve must contain a hydrogen-bond donor and a hydrogen-bond acceptor that can interact with the complementary groups on the receptor).

You need to create a search query that contains portions of the 3D structures and the 3D constraints that specify the spatial arrangements (You will later place the query into the MODELSTRUCTURE box on the form.):

*	To specify the hydrogen-bond acceptor on the receptor site, you draw an exclusion sphere around a point that you construct from two atoms of the complementary hydrogen-bond donor on the ligand:

Where the ISIS atom-query feature List allows specific atoms (such as O, N, and S) at the specified position.

*	To specify the hydrogen-bond donor on the receptor site, you draw an exclusion sphere around a point that you construct from two atoms of the complementary hydrogen-bond acceptor on the ligand:

Note: You might define hydrogen-bond donors and acceptors on the ligand differently.

*	Add the 3D constraint between the two groups on the receptor (a distance of 8 to 10 Angstroms).

For clarity, the Rgroup label (R1) and the list of Rgroup members is omitted from the H-bond donor on receptor site:

Examples of 3D Structures Retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Examples of 3D Structures Retrieved


Question 1: "I want to find..."
     Question 2: I want to find all 3D structures in the database that can interact with a receptor site that contains this hydrogen-bond donor or hydrogen-bond acceptor in a specific spatial arrangement with another group on the receptor.

Example: I want to find all 3D structures that can interact with a receptor site that contains a hydrogen-bond donor 6 to 10 Angstroms from an aromatic group. The aromatic group on the receptor interacts with a phenyl ring on the ligand through a planar hydrophobic (pi-pi) bond.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know that the receptor site contains a hydrogen-bond donor and an aromatic group in specific spatial arrangement (in this example, a hydrogen-bond donor on a receptor that is 6 to 10 Angstroms from an aromatic group). The 3D structures that you retrieve must also contain functional groups that can interact with the groups on the receptor [in this example, the structures that you retrieve must contain a hydrogen-bond acceptor that can interact with the hydrogen-bond donor on the receptor, and a phenyl group that can interact with the aromatic group on the receptor through a planar hydrophobic (pi-pi) bond].

You need to create a search query that contains portions of the 3D structures that can interact with the receptor and the 3D constraints that specify the spatial arrangements of groups on the receptor. Do the following (for which you will receive further step-by-step instructions when you need them):

*	Draw the phenyl ring. For illustration purposes, the ring in this example was rotated in three dimensions with the 3D Rotate tool: . (Rotation does not affect the search results.)

*	Add the following 3D Objects (which you must add now so that you can add the 3D constraints later):

(a) A centroid (a triangle at the center of the phenyl ring) and a plane to allow a normal to be drawn through the plane of the phenyl ring. Specify a planarity constraint of 0.5 Angstroms for the plane.

(b) A normal (a line with an arrow) to specify two points along the plane. (If you do not see the normal, you might need to 3D rotate the query.)

(c) Two points (triangles on the normal) on the normal at distances of 2 Angstroms above and below the plane. Each point will be the center of an exclusion sphere (3D constraint).

(d) An additional point (a triangle on the normal) on the normal at a distance of 3.5 Angstroms above the plane. This point will specify the location of the aromatic group.

*	To create the hydrogen-bond donor as part of the receptor site, first draw the complementary hydrogen-bond acceptor basic nitrogen on the ligand. To draw the basic nitrogen, retrieve the following MDL ISIS/Draw sketch file: BSC_N_2.SKC. (Alternatively, you can use the MDL sketch file BSC_N_1.SKC or H_ACCEPT.SKC).

This file contains: A root structure with the Rgroup label R1; the Rgroup substituents with the nested Rgroup R2; and Rgroup conditions. The ISIS bond-query feature AROMATIC (adjacent solid and dashed lines) allows solely aromatic bonds at the specified position. The ISIS atom-query feature List allows specific atoms (such as O, S, and N) at the specified position.

You need to add a lone pair (LP) to the nitrogen atom.

Note: You might define a hydrogen-bond acceptor on the ligand differently. Thus, you might want to modify this sketch file to create your own query.

*	Add the 3D constraints:

(a) Two exclusion spheres (each 1.5 Angstroms in diameter) around the points along the normal.

(b) A distance constraint (a distance of 6 to 10 Angstroms) between the hydrogen-bond donor on the receptor and the aromatic group on the receptor.

For clarity, the following query displays solely two of the members of the Rgroup substituent R1 in the hydrogen-bond donor as part of the receptor site (You will later place the query into the MODELSTRUCTURE box on the form.):

Examples of 3D Structures Retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Examples of 3D Structures Retrieved


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

I have a pharmacophore hypothesis of interest.  I want to find all 3D structures that:

1.	Contain a functional group embedded wholly within them (Example: All 3D structures that contain purines or pyrimidines)

2.	Contain this set of functional groups and/or atoms in a specific spatial arrangement. Examples:

(a) All 3D structures with an aliphatic amine nitrogen that is both 6 to 8 Angstroms from a carbonyl oxygen and 4 to 6 Angstroms from a phenyl group, and the carbonyl oxygen and the phenyl group are 4.5 to 6 Angstroms apart

(b) All 3D structures with an aliphatic amine nitrogen that is both 4.2 to 7.3 Angstroms from the centroid of a phenyl group and 4.9 to 7.3 Angstroms from the centroid of a phenyl or a pyridyl group, and the phenyl and/or pyridyl groups are 4.7 to 5.1 Angstroms apart

(c) All 3D structures with an acidic center that is 5 to 8 Angstroms from an amide nitrogen


Question 1: "I want to find..."
     Question 1: I want to find all 3D structures in the database that contain a functional group embedded wholly within them.

Example: I want to find all 3D structures that contain purines or pyrimidines embedded wholly within them.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the functional group that you want to find in all 3D structures retrieved (in this example, purines or pyrimidines).

You need to create a search query that contains the functional groups.

To create the query for this example, draw a substructure that generally defines purines and pyrimidines. (Hint: The minimum structural features include a hetero-substituted six-membered ring with two nitrogen atoms and variable bond types.) Add the ISIS atom-query feature Q to specify the two heteroatoms. Add the ISIS bond-query feature ANY (dashed lines) to allow any bond type at the specified positions and Ch to allow solely an acyclic attachment at the specified position (You will later place the query into the MODELSTRUCTURE box on the form.):

Examples of 3D Structures Retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Examples of 3D Structures Retrieved


Question 1: "I want to find..."
     Question 2a: I want to find all 3D structures in the database that contain this set of functional groups and/or atoms embedded wholly within them in a specific spatial arrangement.

Example: I want to find all 3D structures with an aliphatic amine nitrogen that is both 6 to 8 Angstroms from a carbonyl oxygen and 4 to 6 Angstroms from a phenyl group, and the carbonyl oxygen and the phenyl group are 4.5 to 6 Angstroms apart.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the set of functional groups that you want to find in all 3D structures retrieved and their spatial arrangements (in this example, an aliphatic amine nitrogen that is both 6 to 8 Angstroms from a carbonyl oxygen and 4 to 6 Angstroms from a phenyl group, and the carbonyl oxygen and the phenyl group are 4.5 to 6 Angstroms apart).

You need to create a search query that contains the set of functional groups and the 3D constraints that specify the spatial arrangements. Do the following (for which you will receive step-by-step instructions when you need them):

*	Draw the aliphatic amine, the carbonyl oxygen, and the phenyl group.

*	Add the ISIS atom-query feature List on the aliphatic amine that allows specific atoms (such as H and C) at the specified positions.

*	Add the 3D distance constraints (in Angstroms) between each chemical group (You will later place the query into the MODELSTRUCTURE box on the form.):

Example of a 3D Structure Retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a 3D Structure Retrieved


Question 1: "I want to find..."
     Question 2b: I want to find all 3D structures in the database that contain this set of functional groups and/or atoms embedded wholly within them in a specific spatial arrangement.

Example: I want to find all 3D structures with an aliphatic amine nitrogen that is both 4.2 to 7.3 Angstroms from the centroid of a phenyl group and 4.9 to 7.3 Angstroms from the centroid of a phenyl or a pyridyl group, and the phenyl and/or pyridyl groups are 4.7 to 5.1 Angstroms apart

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the set of functional groups that you want to find in all 3D structures retrieved and their spatial arrangements (in this example, all 3D structures with an aliphatic amine nitrogen that is both 4.2 to 7.3 Angstroms from the centroid of a phenyl group and 4.9 to 7.3 Angstroms from the centroid of a phenyl or a pyridyl group, and the phenyl and/or pyridyl groups are 4.7 to 5.1 Angstroms apart).

You need to create a search query that contains the set of functional groups and the 3D constraints that specify the spatial arrangements. Do the following (for which you will receive step-by-step instructions when you need them):

*	Draw the two phenyl groups and the aliphatic amine.

*	Add the ISIS atom-query feature List on both the aliphatic amine and one of the phenyl groups that allows specific atoms (such as H and C on the aliphatic amine and C and N on the phenyl group) at the specified positions.

*	Add the 3D Objects (two centroids, represented by the triangles) that allows a distance constraint to be drawn between functional groups. (In this example, each centroid was created from all atoms in the ring.)

*	Add the 3D distance constraints (in Angstroms) between each chemical group (You will later place the query into the MODELSTRUCTURE box on the form.):

Examples of 3D Structures Retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Examples of 3D Structures Retrieved


Question 1: "I want to find..."
     Question 2c: I want to find all 3D structures in the database that contain this set of functional groups and/or atoms embedded wholly within them in a specific spatial arrangement.

Example: I want to find all 3D structures that contain an acidic center that is 5 to 8 Angstroms from an amide nitrogen.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the set of functional groups that you want to find in all 3D structures retrieved and their spatial arrangements (in this example, an acidic center that is 5 to 8 Angstroms from an amide nitrogen).

You need to create a search query that contains the set of functional groups and the 3D constraints that specify the spatial arrangements. Do the following (for which you will receive step-by-step instructions when you need them):

*	Retrieve the following MDL ISIS/Draw sketch file of an acidic center: ACID_CTR.SKC.

This file contains: A root structure with the Rgroup label R1; the Rgroup substituents; and Rgroup conditions.

The ISIS atom-query features List allows specific atoms (such as N and O) at the specified position; UNSATURATED (u) allows at least one multiple bond (double, triple, or aromatic) to be attached to the atom at the specified position; and s2 allows solely two non-hydrogen attachments of any bond type at the specified positions.

The ISIS bond-query features SINGLE/AROMATIC (two lines, one line with long and short dashes) allows solely single or double bonds at the specified positions; ANY (single dashed line) allows any bond type at the specified position; and Rn allows solely ring bonds at the specified positions.

Note: You might define an acidic center differently. Thus, you might want to modify this sketch file to create your own query.

*	Draw the amide nitrogen group.

*	Add the 3D distance constraint (in Angstroms) between the acidic center and the amide nitrogen (You will later place the query into the MODELSTRUCTURE box on the form.):

Examples of 3D Structures Retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

I have specific data of interest for a 3D structure (such as a ligand or receptor).  I want to find all 3D structures that:

1.	Are associated with a specific ID number. (Example: All 3D structures that contain the ID number MUSE33300002)

2.	Are associated with a specific biological activity. [Example: All 3D structures that are inhibitors of angiotensin-converting enzyme (ACE)]

3.	Share the same data for specific atoms. (Example: All 3D structures that contain a Gasteiger charge of -0.30 to -0.31 on a single oxygen atom within a ring)

4.	Share the same data for specific pairs of atoms. (Example: All 3D structures that contain the proton spin-spin couplings of 1.0 Hz (for protons 3 and 5), 2.0 Hz (for protons 4 and 5), and 3.5 Hz (for protons 3 and 4) in the furanyl group of the substructure methyl 2-furoate)


Question 1: "I want to find..."
     Question 1: I want to find a 3D structure that is associated with a specific ID number.

Example: I want to find the molecule with the ID number MUSE33300002.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the ID number (in this example, MUSE33300002).

You need to create a search query that contains a search operator and the exact ID number (You will later place the query into the CORPORATE ID box or equivalent on the form.):

LIKE "MUSE33300002"

Example of a record retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Record Retrieved


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Text String Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Text String Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Question 10: "I want to find..."
     Question 2: I want to find all 3D structures that are associated with a specific type of activity.

Example: I want to find all 3D structures that are inhibitors of angiotensin-converting enzyme (ACE).

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the type of activity (in this example, ACE inhibitors).

You need to create a search query that contains a search operator and either the entire type of activity or a portion of it (You will later place the query into the ACTIVITY box or equivalent on the form.). To retrieve solely those records that contain exactly the target value that you specified, enter one of the following search queries:

LIKE "ACE"

LIKE "ACE inhibitor"

LIKE "angiotensin-converting enzyme"

To retrieve those records that contain exactly the target value that you specified and any additional words or phrases that are stored with the database field ACTIVITY, enter one of the following search queries with wildcards:

LIKE "%ACE%"

LIKE "%angiotensin%"

Example of a record retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Record Retrieved


Do you have a local database or remote database?

A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to input network information.

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to input network information.

Click one of the following:

*	I have a local database

*	I have a remote database.

(If you do not know which type you have, see your ISIS Administrator)


Text String Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Text String Query For a Local Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SBF


Question 1: "I want to find..."
     Question 3: I want to find all 3D structures in the database that share the same data for specific atoms.

Example: I want to find all 3D structures contain a Gasteiger charge of -0.30 to -0.31 on a single oxygen atom within a ring.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the data that you want to find on specific atoms in the 3D structures retrieved (in this example, a Gasteiger charge of -0.30 to -0.31 on a single oxygen atom within a ring).

You need to create a search query that contains the data for specific atoms.

To create the query for this example, draw the oxygen atom attached to a bond. Add the ISIS bond-query feature Rn to allow solely a ring bond at the specified position (You will later place the query into the MODELSTRUCTURE box on the form.):

Example of a record retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Record Retrieved


Question 1: "I want to find..."
     Question 4: I want to find all 3D structures in the database that share the same data for specific pairs of atoms.

Example: I want to find all 3D structures with proton spin-spin couplings of 1.0 Hz (for protons 3 and 5), 2.0 Hz (for protons 4 and 5), and 3.5 Hz (for protons 3 and 4) in the furanyl group of the substructure methyl 2-furoate.

Note: This example is for remote searching only.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the data that you want to find on specific pairs of atoms in the 3D structures retrieved [in this example, proton spin-spin couplings of 1.0 Hz (for protons 3 and 5), 2.0 Hz (for protons 4 and 5), and 3.5 Hz (for protons 3 and 4) in the furanyl group of the substructure methyl 2-furoate].

You need to create a search query that contains the data for specific pairs of atoms (You will later place the query into the MODELSTRUCTURE box on the form.):

Example of a record retrieved

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Example of a Record Retrieved


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

For a specific reagent/catalyst of interest, I want to find:

1.	A suitable supplier and price. (Example: The supplier and price of dinitroaniline)

2.	The CAS Registry Number. (Example: The CAS Registry Number of peroxybenzoic acid)

What to do if you could not find a suitable sample question


Question 1: "I want to find..."
     Question 1: I want to find a suitable supplier and price for a specific reagent/catalyst of interest.

Example: I want to find a suitable supplier and price for the reagent/catalyst dinitroaniline.

You can do this example in ISIS/Base only or in ISIS/Base with ACD Finder. Each method provides a unique way to view the search results.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the reagent/catalyst (in this example, dinitroaniline).

You need to create a search query that is the reagent/catalyst. There are 2 ways to create your search query. The one you choose is strictly your own preference and does not affect the search results. However, if you create a query that contains solely a portion of the compound name, you might retrieve additional search results.

3.	To identify the type of search that you need to do and to see the step-by-step instructions, click the type of query that you prefer to use:

*	Graphical Query

Draw the graphical structure:

*	Compound Name Query

Enter a text string that contains a search operator and either the entire name of the compound or a portion of it:

A search query with the entire compound name:

A search query with a portion of the compound name and wildcards:


Using ISIS/Base With ACD Finder

ACD Finder is a specialized ISIS application that simplifies and enhances the searching and view capabilities of ISIS/Base for the ACD, ACDRX, and ACD-3D databases. If ACD Finder is available at your site, you need to install it, and then refer to the following manual for instructions on how to conduct a By Form search: “Available Chemicals Directory, Available Chemicals Directory RX, Available Chemicals Directory 3D." For more information, see your ISIS Administrator.


Which database do you use?

Use either your proprietary database or any one of the MDL databases that allow you to search for catalog and supplier information on commercially available chemicals.

Click one of the following:

Remote molecule database

Remote reaction database

Remote 3D database

Local molecule database

Local reaction database

Local 3D database


Remote Molecule Database

A remote molecule database is a database with information on molecules that typically exists on a mainframe computer. To do a remote search, you need to obtain network access information.

An MEXACT search finds all records that match your structure query exactly.

Click here for step-by-step instructions


Local Molecule Database

A local molecule database is a database with information on molecules that typically exists on your hard disk. To do a local search on your hard disk, you do not need to access network information.

An MEXACT search finds all records that match your structure query exactly.

Click here for step-by-step instructions


Remote Reaction Database

A remote reaction database is a database with information on reactions and reaction components that typically exists on a mainframe computer. To do a remote search, you need to obtain network access information.

An MEXACT search finds all records that match your structure query exactly.

Click here for step-by-step instructions


Local Reaction Database

A local reaction database is a database with information on reactions and reaction components that typically exists on your hard disk. To do a local search on your hard disk, you do not need to access network information.

An MEXACT search finds all records that match your structure query exactly.

Click here for step-by-step instructions


Remote 3D Database

A remote 3D database is a database with information on 3D structures that typically exists on a mainframe computer. To do a remote search, you need to obtain network access information.

A 3DEXACT search finds all records that match your structure query exactly.

Click here for step-by-step instructions


Local 3D Database

A local 3D database is a database with information on 3D that typically exists on your hard disk. To do a local search on your hard disk, you do not need to access network information.

A 3DEXACT search finds all records that match your structure query exactly.

Click here for step-by-step instructions


Which database do you use?

Use either your proprietary database or any one of the MDL databases that allow you to search for catalog and supplier information on commercially available chemicals.

Click one of the following:

Remote molecule database

Remote reaction database

Remote 3D database

Local molecule database

Local reaction database

Local 3D database


Remote Molecule Database

A remote molecule database is a database with information on molecules that typically exists on a mainframe computer. To do a remote search, you need to obtain network access information.

A Search By Form (SBF) search finds all records that match your compound name query.

Click here for step-by-step instructions


Local Molecule Database

A local molecule database is a database with information on molecules that typically exists on your hard disk. To do a local search on your hard disk, you do not need to access network information.

A Search By Form (SBF) search finds all records that match your compound name query.

Click here for step-by-step instructions


Remote Reaction Database

A remote reaction database is a database with information on reactions and reaction components that typically exists on a mainframe computer. To do a remote search, you need to obtain network access information.

A Search By Form (SBF) search finds all records that match your compound name query.

Click here for step-by-step instructions


Local Reaction Database

A local reaction database is a database with information on reactions and reaction components that typically exists on your hard disk. To do a local search on your hard disk, you do not need to access network information.

A Search By Form (SBF) search finds all records that match your compound name query.

Click here for step-by-step instructions


Remote 3D Database

A remote 3D database is a database with information on 3D structures that typically exists on a mainframe computer. To do a remote search, you need to obtain network access information.

A Search By Form (SBF) search finds all records that match your compound name query.

Click here for step-by-step instructions


Local 3D Database

A local 3D database is a database with information on 3D that typically exists on your hard disk. To do a local search on your hard disk, you do not need to access network information.

A Search By Form (SBF) search finds all records that match your compound name query.

Click here for step-by-step instructions


Question 2: "I want to find..."
     Question 2: I want to find a suitable supplier and price for a specific reagent/catalyst of interest.

Example: I want to find the CAS Registry Number for the reagent/catalyst peroxybenzoic acid.

You can do this example in ISIS/Base only or in ISIS/Base with ACD Finder. Each method provides a unique way to view the search results.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the reagent/catalyst (in this example, peroxybenzoic acid).

You need to create a search query that is the reagent/catalyst. There are 2 ways to create your search query. The one you choose is strictly your own preference and does not affect the search results. However, if you create a query that contains solely a portion of the compound name, you might retrieve additional search results.

3.	To identify the type of search that you need to do and to see the step-by-step instructions, click the type of query that you prefer to use:

*	Graphical Query

Draw the graphical structure:

*	Compound Name Query

Enter a text string that contains a search operator and either the entire name of the compound or a portion of it:

A search query with the entire compound name:

A search query with a portion of the compound name and wildcards:


What To Do If You Could Not Find...
   What To Do If You Could Not Find a Suitable Sample Question

We hope that you were able to find a suitable sample question. We believe that these sample questions illustrate all the searches that you can perform with ISIS. If you did not find a question, please look again because this is the best method to find the most suitable search.

If you are still unable to find a suitable sample question, the only thing that we can do now is to show you a list of all the searches and their definitions.

Click here for a list of all the searches and their definitions


  I Want To Find Information on Biopolymers

Click one of the following items:

*	I have a specific biopolymer fragment of interest. I want to find biopolymers that contain this fragment.

*	I have a specific structural constraint of interest. I want to find biopolymers that contain this constraint.

What to do if you could not find a suitable sample question


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

I have a specific amino acid or nucleic acid fragment of interest.  For this fragment, I want to find all biopolymers that contain:

1.	The fragment anywhere wholly within them. (Example: All biopolymers that contain the sequence FRCAT anywhere wholly within them)


Question 1: "I want to find..."
     Question 1: I want to find biopolymers that contain a specific fragment wholly within them.

Example: I want to find those biopolymers that contain the amino acid sequence FRCAT anywhere wholly within them.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the fragment (in this example, the amino acid sequence FRCAT).

You need to create a search query that is a fragment. Do the following in the order shown (for which you will receive step-by-step instructions when you need them):

(a)	To draw the fragment FRCAT, type in the residue codes F, R, C, A, and T. You see the following contracted amino acid residues and leaving groups:

(b)	Expand the entire fragment.

(c)	Add the ISIS atom-query feature s* to all the expanded residues to prevent substitutions at all positions.

(d)	Contract the entire fragment.

(e)	To retrieve structures with FRCAT embedded anywhere wholly within them, delete the leaving groups on F, C, and T.

Alternatively, to retrieve structures with FRCAT embedded solely at a specific end, do not delete the specific terminal leaving group. For example, to retrieve structures with FRCAT embedded solely at the acid end, do not delete the COOH leaving group.

(f)	Expand those residues whose leaving groups you deleted in Step (e). (In this example, expand solely F and T).

(g)	To retrieve structures with FRCAT embedded anywhere wholly within them, remove the s* marks from the nitrogen atom at the N-terminus and the carbonyl carbon atom at the C-terminus.

Alternatively, to retrieve structures with FRCAT embedded solely at a specific end, remove the s* mark at the opposite terminus of the leaving group you retained in Step (e). For example, to retrieve structures with FRCAT embedded solely at the C-terminus, remove the s* mark on the nitrogen atom at the amino end.

(h)	(Optional) Contract the two terminal residues of the fragment (contract F and T).

(I)	Place the query into the MOLSTRUCTURE box on the form.

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Graphical Query For a Remote Database

This is the correct search for the query that you chose. Click it to see a definition and step-by-step instructions.

* SSS/Biopoly


Click the number of the sample question...
  Click the number of the sample question that most closely resembles your question.

I have a specific structural constraint of interest.  For this constraint, I want to find biopolymers that:

1.	Contain atoms at specific distances from each other. (Example: Reduced sulfur atoms that are between 1 and 4 Angstroms apart)


Question 1: "I want to find....."
     Question 1: I want to find biopolymers that contain a specific structural constraint.

Example: I want to find those biopolymers that contain reduced sulfur atoms that are 1 to 4 Angstroms apart.

Instructions For Searching in ISIS/Base

Do these steps in the order shown:

1.	Click the printer icon (above) to print this screen now because you will need to refer to this printed example later.

2.	Read the strategy now. You will receive step-by-step instructions on how to do this example later. The strategy is as follows:

You know the specific atoms and the structural constraint (in this example, reduced sulfur atoms that are between 1 and 4 Angstroms apart).

You need to create a search query that is the atoms with the structural constraint.

To create the query for this example, draw the two sulfur atoms with explicit hydrogens to show the reduced condition. Select the two sulfur atoms and add the ISIS 3D query feature Distance to specify a structural constraint that is a distance of 1-4 Angstroms (You will later place the query into the MODELSTRUCTURE box on the form.):

3.	Click here to identify the type of search that you need to do and to see the step-by-step instructions.


Graphical Query For a Remote Database

These are the correct searches for this query. Click either of them to see a definition and step-

* CFS/Biopoly

* SSS3D/Biopoly


What To Do If You Could Not Find...
   What To Do If You Could Not Find a Suitable Sample Question

We hope that you were able to find a suitable sample question. We believe that these sample questions illustrate all the searches that you can perform with ISIS. If you did not find a question, please look again because this is the best method to find the most suitable search.

If you are still unable to find a suitable sample question, the only thing that we can do now is to show you a list of all the searches and their definitions. But first, do you have a remote or local database?

A typical remote database is one that exists on a mainframe computer. To search a remote database, you need to obtain network access information. A typical local database is one that exists on your hard disk. To search a local database on your hard disk, you do not need to obtain network access information. (If you do not know which type of database you have, see your ISIS Administrator.)

To view the searches and their definitions, click one of the following:

*	I want to search a remote database

*	I want to search a local database


   I Want to Search a Remote Molecule Database

For a remote biopolymer database, there are 9 possible searches that you can conduct.

Click any item to see a definition of that search:

* 2D Substructure for Biopolymers (SSS/Biopoly)

* 3D Substructure for Biopolymers (SSS3D/Biopoly)

* Conformationally Flexible Substructure for Biopolymers (CFS/Biopoly)

* Exact Match of a 3D Structure (3DEXACT)

* ID

* Query Builder (QB)

* Retrieve All (ALL)

* Search By Form in a Protein or 3D Database (SBF)

* Structurally Similar Molecule (MSim)

Note: You cannot conduct a sequence search to compare sequence homologies in this version of ISIS.


   I Want to Search a Local Molecule Database

For a local biopolymer database, there are 6 possible searches that you can conduct.

Click the following item to see a definition of that search:

* 2D Substructure for Biopolymers (SSS/Biopoly)

* Exact Match of a 3D Structure (3DEXACT)

* ID

* Query Builder (QB)

* Retrieve All (ALL)

* Search By Form in a Protein or 3D Database (SBF)

Note: You cannot conduct a sequence search to compare sequence homologies in this version of ISIS.


How To Use ISIS/Desktop Help

Invest 15 minutes of your time to learn how to use the online help effectively!

Click these 5 green, underlined items in the order shown:

1.	How to Navigate in the Help System (4 min.)

2.	How to Use the Help and ISIS at the Same Time (3 min.)

3.	How to Find Information on Searching in ISIS/Base (4 min.)

4.	Adding Your Own Notes and Bookmarks to the Help (3 min.)

5.	Printing Help Screens (1 min.)

If you prefer, click here to print the above information (4 pages).


How to Navigate in the Help System

In addition to underlined items, you see some items with dotted underlines (-------). When you click a dotted underlined item, you see a help screen on top of the original help screen. To remove it, click anywhere outside it with the mouse.

Click these 6 items in the order shown:

1.	The Back button

2.	Choose Hyperlinks Carefully

3.	The Contents button

4.	The Index

5.	Bookmarks

6.	History

When you have read all six items, click the Back button to return to the previous screen.


Choose Hyperlinks Carefully

It is easy to become lost in the help system if you click the wrong hyperlinks. (Hyperlinks are the green, underlined items that you click to go to another help screen). We designed the help system so that the hyperlink choices on every screen are distinct from each other. Thus, if you choose carefully you will not become lost. If you do become lost, click the Back button until you return to your starting position.


The Back Button

This is one of the most important buttons in the help system. You will use it frequently! Often, you arrive at a help screen where there are no green items (“hyperlinks”) to click. You must click the Back button with the mouse until you return to a help screen that has suitable choices.

Click the Back button now to go back to the previous help screen. (The button is near the top of this help screen.)


The Contents button

This button appears at the top of most help screens. Click the Contents button to go to the Desktop Table of Contents. From there, you can go to the ISIS/Draw or the ISIS/Base Table of Contents. From there, you can find information on all the functionality of ISIS/Draw and ISIS/Base. If you are a new user of ISIS, we recommend that you use the tables of contents.


The Index

There are two methods to access the Index: (1) Choose Help > Index (Draw + Base only) in ISIS/Draw or ISIS/Base; or (2) Click the Search button that you see on most help screens.

Note: The index is for information on ISIS/Draw and ISIS/Base only: For information on other MDL products and ISIS applications, you must use the index in the appropriate help file. Choose Help > MDL Help Files: Overview for more information.


Bookmarks

Bookmarks provide an excellent method to navigate directly to those help screens that you use frequently. (You will learn how to create your personal bookmarks later.)


History

This button appears at the top of most help screens. Click the History button to go to the History window, where you see a list of all the help screens you have seen. Double-click any title to go directly to that help screen.

Windows 95/NT Users: To display the History window, choose Options > Display History Window.


How to use the help and ISIS at the same time

The technique that you use to see the help and ISIS at the same time depends on the type of computer that you have.

Click one of the following:

PC

Macintosh


PC

Click these items in the order shown:

1.	Default size recommended

2.	Keep the help window “always on top”

3.	Moving the help window out of the way


Default size recommended

When you first access help, you see a help window appear in the default size. (This is the size you see now.) We strongly recommend that you keep this default size: The help windows are designed for reading this way; they take up less space on the screen; and they require little or no scrolling.


Keep the help window "always on top"

For the PC (only), the help window is set to be always on top. This means that it will not disappear behind either the ISIS/Draw or ISIS/Base application windows when you work in them. Thus, the help is always available: You do not have to search for it among all the windows that are open.

If the help window disappears, find it and then choose Help > Always on Top (Windows 95/NT: Options > Keep Help On Top > On Top) on the help-window menu bar.


Moving the help window out of the way:

If the help window obscures the ISIS/Draw or ISIS/Base window, drag the title bar with your mouse:

You can drag the help window to its original position when you need it again.


Macintosh

Click these items in the order shown:

1.	Default size recommended

2.	Switching between the help window and the ISIS window


Default size recommended

When you first access help, you see a help window appear in the default size. (This is the size you see now.) We strongly recommend that you keep this default size: The help windows are designed for reading this way; they take up less room on the screen; and they require little or no scrolling.


Switching between the help window and the ISIS window

Position the help window behind and to one side of the ISIS/Draw or ISIS/Base window:

Click the visible portion of the help window to bring it to the front when you need it. Click in the ISIS/Draw or ISIS/Base window to push the help window behind it.


How to Find Information on Searching in ISIS/Base

Click these items in the order shown:

Deciding on the Most Effective and Efficient Search

Finding Information for a Specific Search Type


Deciding on the Most Efficient and Effective Search

The Two Questions

For a new or occasional user, there are two questions:

1.	Which is the best type of ISIS/Base search for my particular chemistry question? The search must be effective (give me all the chemically suitable hits and not leave any in the database), and it must be efficient (not give me any irrelevant or extraneous hits).

2.	When I find the best type of search, how do I do it?

The ISIS SearchSelector

You use the SearchSelector (TM) to find the most suitable type of ISIS search for your particular chemistry question. To access the SearchSelector, choose Help > SearchSelector on the Help menu in ISIS/Base.

The SearchSelector asks you a number of chemistry-oriented questions. With the answers you give, the SearchSelector finds the best type of search for your particular chemistry question. It also gives you a graphical search query from which you can easily extrapolate the query that you need for your particular search! You do not require any previous knowledge of ISIS to do this.

Sixty Ways to Search in ISIS/Base

Note that there are over 60 chemically significant ways to search in ISIS/Base. There are, for example, four different ways to conduct a substructure search: You can search for molecule records in a remote database, molecule records in a local database, reaction components in a remote database, and reaction components in a local database. Each of these searches has significant differences from the others. The SearchSelector helps you to choose between all these similar but different searches.

All Searching Instructions on One Help Screen

After it finds the best type of search, the SearchSelector shows you the specific help screen for that search. This type of help screen (identified by a logo; see below) is the searching hub screen. From this hub, you can find all the information and only the information that you need to do that specific search, including searching examples (A) and step-by-step instructions (B):

Using the Hub Screen

To use the step-by-step instructions, click each item in the order shown. The help explains all your choices at every step. When you finish a step, click the Back button on the help screen to return to the screen shown above. Then click on the next step.

When you find your specific search, we recommend that you place a bookmark on that screen so that you can easily find it again.


Finding Information for a Specific Search Type

The existing ISIS user might know exactly which type of search they want to do. Therefore, they do not need to use the SearchSelector: They want to go directly to the information for a particular search. To do this, choose Help > Search Types. You see all the searches available in ISIS/Base on one help screen. Click any one to see a brief definition of the search. You can then also go to either the specific searching examples for that search or the complete step-by-step instructions.

Note: Ensure that you choose carefully between molecule records and reaction records, and between local and remote searches. Each of these searches has significant differences from the others.


Adding Your Own Notes and Bookmarks to the Help

It is very simple to customize the help system! You can add your own notes to any help screen, and you can put a bookmark on any help screen so that you can easily find it again.

To add notes to a help screen (PC only)

To add notes to a help screen (Mac only)

To add bookmarks to a help screen (PC only)

To add bookmarks to a help screen (Mac only)


To add notes to a help screen (PC only)

1.	Choose Edit > Annotate on the help menu bar. You see the Annotate dialog box.

2.	Type your information in the box.

3.	Click Save. You see a new symbol in the top left corner of the screen.

To read your note at any time, click the symbol.

Follow the above instructions to experiment with this feature now!


To add notes to a help screen (Mac only)

1.	There is a yellow note icon near the top of the help screen. Press and drag this icon onto the help screen.

2.	Type your information into the note.

3.	Then click anywhere outside the note.

To hide all your notes (but not delete them), you require View > Show Notes. If you see [image] Show Notes, choose the command.

To delete a note, delete all the text in the note and then click outside the note.

Follow the above instructions to experiment with this feature now!


To add bookmarks to a help screen (PC only)

1.	Choose Bookmark > Define on the help menu bar. In the Bookmark Define dialog box, you see the title of the help screen.

2.	Click OK to accept this title, or type any title you choose. The title then appears on the Bookmark menu.

To find a help screen with a bookmark, click Bookmark and choose the title of the help screen from the list on the menu.

Follow the above instructions to experiment with this feature now!


To add bookmarks to a help screen (Mac only)

1.	Choose Bookmarks > Set Bookmark on the help menu bar. In the Set Bookmark dialog box, you see the title of the help screen.

2.	Click OK to accept this title, or type any title you choose. The title then appears on the Bookmark menu.

To find a help screen with a bookmark, click Bookmark and choose the title of the help screen from the list on the menu.

Follow the above instructions to experiment with this feature now!


Printing Help Screens

Although most help screens are designed to be read online, you can print any help screen at any time: Choose File > Print Topic on the PC, File > Print on the Macintosh.

Some help screens are very long and complex. Most of these screens have a blue area at the top of the screen:

The blue area contains an icon (picture) of a printer. We recommend that you click this icon to print these help screens.


How to Use ISIS/Desktop Help

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	How To Navigate in the Help System	1.1

*	How To Use Help And ISIS At The Same Time	1.2

*	How to Find Information on Searching in ISIS/Base	1.3

*	Adding Your Own Notes and Bookmarks to the Help	1.4

*	Printing Help Screens	1.5

We recommend that you print this 5-page Request-A-Document, and then browse through it. To print this document, click the printer icon at the top of the screen.

1.1 How to Navigate in the Help System

Choose hyperlinks carefully: It is easy to become lost in the help system if you click the wrong hyperlinks. (Hyperlinks are the green, underlined items that you click to go to another help screen). We designed the help system so that the hyperlink choices on every screen are distinct from each other. Thus, if you choose carefully you will not become lost. If you do become lost, click the Back button until you return to your starting position.

The Back button: This is one of the most important buttons in the help system. You will use it frequently! Often, you arrive at a help screen where there are no green items (hyperlinks) to click. You must click the Back button with the mouse until you return to a help screen that has suitable choices.

The Contents button: This button appears at the top of most help screens. Click the Contents button to go to the Desktop Table of Contents. From there, you can go to the ISIS/Draw or the ISIS/Base Table of Contents. From there, you can find information on all the functionality of ISIS/Draw and ISIS/Base. If you are a new user of ISIS, we recommend that you use the tables of contents.

Pop-up screens: On many help screens, you see a number of green items with dotted underlines (--------). When you click a dotted, underlined item with the mouse, you see a small help screen appear on top of the original help screen. To remove the small help screen, click anywhere outside it with the mouse.

Index: There are two methods to access the Index: (1) Choose Help > Index (Draw + Base only) in ISIS/Draw or ISIS/Base; or (2) Click the Search button that you see on most help screens.

Note: The index is for information on ISIS/Draw and ISIS/Base only: For information on other MDL products and ISIS applications, you must use the index in the appropriate help file. Choose Help > MDL Help Files: Overview for more information.

Bookmarks: Bookmarks provide an excellent method to navigate directly to those help screens that you use frequently. (See Section 1.4, below.)

History: This button appears at the top of most help screens. Click the History button to go to the History window, where you see a list of all the help screens you have seen. Double-click any title to go directly to that help screen.

Windows 95/NT Users: To display the History window, choose Options > Display History Window.

1.2 How to Use the Help and ISIS at the Same Time

The technique that you use to see the help and ISIS at the same time depends on the type of computer that you have.

1.21 Default size recommended

When you first access help, you see a help window appear in the default size. We strongly recommend that you keep this default size: The help windows are designed for reading this way; they take up less space on the screen; and they require little or no scrolling.

1.22 Keep the help window "always on top" (PC only)

For the PC (only), the help window is set to be always on top. This means that it will not disappear behind either the ISIS/Draw or ISIS/Base application windows when you work in them. Thus, the help is always available: You do not have to search for it among all the windows that are open.

If the help window disappears, find it and then choose Help > Always on Top (Windows 95/NT: Options > Keep Help On Top > On Top) on the help-window menu bar.

1.23 Moving the help window out of the way (PC only)

If the help window obscures the ISIS/Draw or ISIS/Base window, drag the title bar with your mouse:

You can drag the help window to its original position when you need it again.

1.24 Switching between the help window and the ISIS window (Mac)

Although we recommend that you drag the help window out of the way on PC computers (see section 1.23), this technique is not available on the Macintosh

Instead, position the help window behind and to one side of the ISIS/Draw or ISIS/Base window:

Click the visible portion of the help window to bring it to the front when you need it. Click the ISIS/Draw or ISIS/Base window to push the help window behind them.

1.3 How to Find Information on Searching in ISIS/Base

1.31 Deciding the Most Effective and Efficient Search in ISIS/Base

The Two Questions

For a new or occasional user, there are two questions:

1.	Which is the best type of ISIS/Base search for my particular chemistry question? The search must be effective (give me all the chemically suitable hits and not leave any in the database), and it must be efficient (not give me any irrelevant or extraneous hits).

2.	When I find the best type of search, how do I do it?

The ISIS SearchSelector

You use the SearchSelector (TM) to find the most suitable type of ISIS search for your particular chemistry question. To access the SearchSelector, choose Help > SearchSelector on the Help menu in ISIS/Draw or ISIS/Base.

The SearchSelector asks you a number of chemistry-oriented questions. With the answers you give, the SearchSelector finds the best type of search for your particular chemistry question. It also gives you a graphical search query from which you can easily extrapolate the query that you need for your particular search! You do not require any previous knowledge of ISIS to do this.

Sixty Ways to Search in ISIS/Base

Note that there are over 60 chemically significant ways to search in ISIS/Base. There are, for example, four different ways to conduct a substructure search: You can search for molecule records in a remote database, molecule records in a local database, reaction components in a remote database, and reaction components in a local database. Each of these searches has significant differences from the others. The SearchSelector helps you to choose between all these similar but different searches.

All Searching Instructions on One Help Screen

After it finds the best type of search, the SearchSelector shows you the specific help screen for that search. This type of help screen (identified by a logo; see below) is the searching hub screen. From this hub, you can find all the information and only the information that you need to do that search, including searching examples (A) and step-by-step instructions (B):

Using the Hub Screen

To use the step-by-step instructions, click each item in the order shown. The help explains all your choices at every step. When you finish a step, click the Back button on the help screen to return to the screen shown above. Then click on the next step.

When you find your specific search, we recommend that you place a bookmark on that screen so that you can easily find it again. See Section 1.4, below, for details.

1.32 Finding Information for a Specific Search Type

The existing ISIS user might know exactly which type of search they want to do. Therefore, they do not need to use the SearchSelector: They want to go directly to the information for a particular search. To do this, choose Help > Search Types. You see all the searches available in ISIS/Base on one help screen. Click any one to see a brief definition of the search.. You can then also go to either the specific searching examples for that search or the complete step-by-step instructions.

Note: Ensure that you choose carefully between molecule records and reaction records, and between local and remote searches. Each of these searches has significant differences from the others.

1.4 Adding Your Own Notes and “Bookmarks”

It is very simple to customize the help system! You can add your own notes to any help screen, and you can put a bookmark on any help screen so that you can easily find it again.

1.41 Adding Notes to a Help Screen (PC only)

1.	Choose Edit > Annotate on the help menu bar. You see the Annotate dialog box.

2.	Type your information in the box.

3.	Click Save. You see a new symbol in the top left corner of the screen.

To read your note at any time, click the symbol.

1.42 Adding Notes to a Help Screen (Mac only)

1.	There is a yellow note icon near the top of the help screen. Press and drag this icon onto the help screen.

2.	Type your information into the note.

3.	Then click anywhere outside the note.

To hide all your notes (but not delete them), you require View > Show Notes. If you see [image] Show Notes, choose the command.

To delete a note, delete all the text in the note and then click outside the note.

1.43 Adding Bookmarks to a Help Screen (PC only)

1.	Choose Bookmark > Define on the help menu bar. In the Bookmark Define dialog box, you see the title of the help screen.

2.	Click OK to accept this title, or type any title you choose. The title then appears on the Bookmark menu.

To find a help screen with a bookmark, click Bookmark and choose the title of the help screen from the list on the menu.

1.44 Adding Bookmarks to a Help Screen (Mac only)

1.	Choose Bookmarks > Set Bookmark on the help menu bar. In the Set Bookmark dialog box, you see the title of the help screen.

2.	Click OK to accept this title, or type any title you choose. The title then appears on the Bookmark menu.

To find a help screen with a bookmark, click Bookmark and choose the title of the help screen from the list on the menu.

1.5 Printing Help Screens

Although most help screens are designed to be read online, you can print any help screen at any time: Choose File >Print Topic for the PC, File > Print for the Macintosh.

Some help screens are very long and complex. Most of these screens have a blue area at the top of the screen:

The blue area contains an icon (picture) of a printer. We recommend that you click this icon to print these help screens.


 ISIS Licensing/Documentation

ISIS, the Integrated Scientific Information System from MDL, consists of the following components.

Click any component for additional information:

Click here for a complete list of ISIS end-user documentation.


ISIS End-User Documentation

Note: For a complete list of the Request-A-Documents included with the ISIS/Desktop 2.3 Helps, click here. You can view Request-A-Documents online, however we recommend that you print them out.

ISIS/Draw: Online-only (in this help file).

ISIS/Base (Searching, Forms): Online-only (in this help file).

ISIS/Base (Database Creation; Registration): Online-only (Dbmaint.pdf).

File-Format Conversion: Online-only (Exographics.pdf).

SAR Table: Online-only. See Help > ISIS/Base Add-ins on the ISIS/Base menu bar, after installation of SAR Table.

Add-in Manager: Online-only. See the Help menu on the ISIS/Draw or ISIS/Base menu bar.

MDL Databases: The database documentation is available in Portable Document Format (PDF) for online viewing and printing. Use Adobe Acrobat Reader to read and print the books. Adobe Acrobat Reader is included in the Document folder of the ISIS installation CD. You can also download it for free from Adobe’s web site at http://www.adobe.com.

ISIS/ADK (ISIS/PL and ISIS/OL): Online-only. ISISDEV.HLP includes reference information on ISIS/PL and ISIS/PL. Adkusers.pdf is the User's Guide.


ISIS/Draw

Use ISIS/Draw to: (1) Draw search queries to use in ISIS/Base searches; or (2) Draw presentation graphics to use in presentations, lab reports, and so on.

Documentation for ISIS/Draw is online-only (in this help file).

Site licenses: All.


ISIS/Base

Use ISIS/Base to:

Search local or remote databases: To access remote databases, your ISIS Administrator must install a remote-access file on your PC or Macintosh. Then, choose File > Open Database and click the name of this file. You will also require a password.

Create forms: You can create new forms or edit existing ones.

Create local databases: You can create molecule or reaction databases and store them on your hard disk. You can import data from remote databases, or you can export data to RDfiles. A colleague can import your RDfile so that you can share data.

Register records to local or remote databases: Registration to remote databases may be restricted at your company. See your ISIS Administrator for details.

Documentation for searching and creating forms is online-only (in this help file). Documentation for creating local databases and registering records is available in the PDF file Dbmaint.pdf.

Site licenses: All. However, searching functionality is restricted for ISIS/Life Science and ISIS/Retrieval. See your ISIS Administrator for details.


Local Databases

MDL supplies small demonstration local molecule and reaction databases.

You can also create your own local databases in ISIS/Base.

Documentation for creating local databases, registering or updating records, and importing or exporting data, is available in the PDF file Dbmaint.pdf.


File-Format Conversion

MDL provides the two file-conversion programs, ConSystant and Chemeleon from ExoGraphics, Inc. These two programs convert ISIS and other files into over 25 commonly used file formats.

Documentation for ConSystant/Chemeleon is available in the PDF file Exographics.pdf.

Installation: Follow the instructions on the label of Disk 1 of the ISIS/Applications disk package.

Site licenses: All.


IRDAS/Reaction Browser

The ISIS Reaction Database Access System (IRDAS) application has been replaced with a new database application called the Reaction Browser.

The Reaction Browser is an information system that enables you to find the published information on synthetic reactions. This system consists of the Reaction Browser and one or more reaction databases that reside on a host computer.

The Reaction Browser system contains up-to-date information that will help you to:

*	Develop new synthetic methods for solution or solid-phase chemistry

*	Determine which reagents to use for synthesis reactions

*	Determine which solid supports to use for synthesis reactions

*	Develop combinatorial libraries

Documentation for the Reaction Browser is online only, and is accessed from the ISIS/Base Help menu.


SAR Table

The ISIS Structure-Activity Relationship Table (SAR Table) is an ISIS add-in that you can install via the Add-in Manager. It integrates the spreadsheet functionality of Microsoft Excel with the chemical information management functionality of ISIS/Base. It allows you to visualize the relationship between structure and activity in a familiar spreadsheet environment.

Documentation for SAR Table is online-only. When you have installed SAR Table, choose Help > ISIS/Base Add-ins on the ISIS/Base menu bar. You see the ISIS Add-ins Help dialog. Double-click any SAR Table-related item for information. If you do not see any SAR Table-related items, then SAR Table has not been installed. See Installation, below.

Installation: Follow the instructions on the label of Disk 1 of the ISIS/Applications disk package. You can install the add-ins of your choice, including SAR Table.

Site licenses: All.


Add-in Manager

The Add-in Manager is an ISIS Application. After you install it, you can easily install a large number of ISIS "add-ins." An add-in is a piece of computer code that adds functionality to ISIS/Draw or ISIS/Base.

Documentation for the Add-in Manager is online-only. When you install Add-in Manager, you see a new command, "ISIS/Draw (or ISIS/Base) Add-ins," on the Help menu. Choose this command to see the help file.

Installation: The Add-in Manager is installed at the same time as ISIS/Draw and/or ISIS/Base: Follow the instructions on the label of Disk 1 of the ISIS disk package. To install individual add-ins, follow the instructions on the label of Disk 1 of the ISIS/Applications disk package.

Site licenses: All.


ISIS/PL

ISIS/Procedural Language (ISIS/PL) is a high-level programming language that enables you to customize ISIS and its applications. It is a component of the ISIS/Application Development Kit (ISIS/ADK).

Documentation for ISIS/PL is available in the online-help file ISISDEV.HLP and the PDF file Adkusers.pdf.

Site licenses: ISIS/Development.


ISIS/OL

ISIS/Object Library (ISIS/OL) is a high-level, object-oriented application-programming language that enables you to create new applications that work with ISIS. It is a component of the ISIS/Application Development Kit (ISIS/ADK).

Documentation for ISIS/PL is available in the online-help file ISISDEV.HLP and the PDF file Adkusers.pdf.

Site licenses: ISIS/Development.


ISIS/Host

ISIS/Host receives search queries from ISIS/Base or ISIS applications and sends the queries to the relevant remote databases. It then returns the list of records that it finds to ISIS/Base. To the end user, ISIS/Host is invisible.


Proprietary Databases

Your company probably has a number of proprietary databases. See your ISIS Administrator for information on how to access these from ISIS/Base.


MDL Databases

MDL is a major supplier of commercial databases. See Information on MDL Databases for descriptions of the databases that are available.

MDL has two types of database documentation that are available online-only.

*	The databases are described in Portable Document Format (PDF) for online viewing and printing. Use Adobe Acrobat Reader to read and print the books. Adobe Acrobat Reader is included in the Document folder of the ISIS installation CD. You can also download it for free from Adobe’s web site at http://www.adobe.com.

*	The database applications, and how to use them, are described in online help. You access the online help for database applications from the ISIS/Base Help menu. For example, if you use the Metabolite database applications, Metabolite Browser and Metabolite Registrar, you see Metabolite Registrar and Metabolite Browser on the Help menu. Choose the name to access the help file for that application. To access the index specific to Metabolite Browser or Metabolite Registrar, click Search in the Help window.

Note: The Index (Draw + Base only) item shown on the Help menu is for ISIS/Draw and ISIS/Base only.


Writers

The following MDL technical writers created this help file. Areas of specialty are shown in parentheses:

Trevor Grayling, Sr. Team Manager (Design/Architecture)

Nicolette Davis, Sr. Scientist Writer (Chemistry)

Cate Larsen, Sr. Scientist Writer (Chemistry)

Frank Ripp, Sr. Technical Writer (Technical Resources)

Kimberly Steele, Sr. Technical Writer (Forms)


 MDL Customer Support

How you receive technical support depends on whether you purchased an individual, boxed copy of ISIS or are a user at a company with a site license. Please click one of the following:

User at a company with an ISIS site license

User who purchased an individual, boxed copy of ISIS

For general information about MDL products, see the MDL Web page at http://www.mdli.com.


User at a company with an ISIS site license

If you are a user at a company with an ISIS site license, you can receive technical support from your internal Help Desk or your ISIS Administrator. If these internal resources cannot answer your questions, they will contact MDL for the answers. They will then give the answers to you.

Users with site licenses should not contact MDL directly.


User who purchased an individual, boxed copy of ISIS

MDL technical support is included in the price of this release of ISIS. However, you must register to receive support! Either mail the Registration Card in the "Read This First" booklet, or register via MDL's web page at http://www.mdli.com. Click Support, then Contact Us!, and then Register.

You are eligible to receive technical support until MDL releases the next ISIS upgrade. To continue receiving support, you must purchase an upgrade. MDL only supports the current version of the product. For information on how to contact MDL Customer Support, click here

With technical support, you receive:

*	Technical assistance from experts in MDL software. Our staff also has experience in chemistry. You can receive support via our web site at http://www.mdli.com/supp, email, fax, or telephone.

*	New software release information complete with an order form and pricing information.


To contact MDL Customer Support

When you have registered, you can contact your regional office:

North America

Continental Europe (excluding UK)

United Kingdom

Japan

Korea

Singapore

Taiwan

People's Republic Of China

Poland

Hungary

Czech Republic

Slovakia


North America

MDL Information Systems, Inc.

14600 Catalina Street

San Leandro, California 94577

Phone	(800) 326-3002

(510) 895-2213

FAX	(510) 895-6092

Email	techsupp@mdli.com

Extended support hours are 6:00 AM to 4:00 PM (PT). Thus, we are available during standard business hours across the continental US.


Continental Europe (excluding UK)

MDL Information Systems AG

Gewerbestrasse 12

CH-4123 Allschwil 2

Switzerland

Phone	+41 61 486 8888

FAX	+41 61 486 8889

Email	hotline@ag.mdli.com


United Kingdom

MDL Information Systems (UK) Limited

Ground Floor, Building 4

Archipelago, Lyon Way

Camberley, Surrey GU16 5ER

England

Phone	+44 1 276 701520

FAX	+44 1 276 701501

Email	ukhotline@mdli.com


Japan

CTC Laboratory Systems Corporation

Tokyo, Japan

Phone	+81 3 3419 9171

FAX	+81 3 3419 9179


Korea

BITEK CHEMS INC.

Seoul, Korea

Phone	+82 2 822 9295

FAX	+82 2 822 9296


Singapore

Info Access and Distribution Pte Ltd.

Singapore

Phone	+65 74 1 84 22

FAX	+65 74 1 88 21


Taiwan

Cradle Technology Corporation

Taipei, Taiwan

Phone	+886 2 753 3535

Fax	+886 2 753 3237


People's Republic Of China

Trident Systems Pte Ltd.

Beijing, Peoples Republic of China

Phone	+86 10 62179929

Fax	+86 10 62179932 (call first)


Poland

ABB Poland SP.Z.O.O.

Krakow, Poland

Phone	+48 12 154074

+48 12 153836

Fax	+48 12 153443


Hungary

Creative Engineering LTD

Budaoers, Hungary

Phone	+36 23 416 832

Fax	+36 23 505 071


Slovakia

Dimension 5 Ltd.

Hlohovec, Slovakia

Phone	+42 1 804 21223

Fax	+42 1 804 21223


Czech Republic

OPENCAE Praha s.r.o.

Praha, Czech Republic

Phone	+420 2 2213 5581

Fax	+420 2 2213 5580


Remote SSS/Biopoly: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote SSS/Biopoly Search	96.1

*	Definition of Aromaticity	96.2

*	Specifying Query Features on Atoms and Bonds in
Expanded Residues	96.3

*	Specifying Stereochemistry in Expanded Residues	96.4

*	Guidelines for Revising the Query	96.5

*	Searching Example 1: Match Residues Anywhere
Within Rigid Biopolymers	96.6

We recommend that you print this 15-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote SSS/Biopoly search, click here.

96.1 Definition of a Remote SSS/Biopoly Search

A remote Biopolymer Substructure (SSS/Biopoly) search finds biopolymer records in your remote database that contain your query as a fragment (a set of residues of your choice) wholly within a larger, rigid biopolymer. The matching residues might be anywhere within the rigid biopolymer.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

96.1.1 What is a Biopolymer?

A biopolymer sequence is a linear chain of connected repeating structures that are called residues. In the following example, you see the residue codes for one of the protein Bovine Insulin, which contains 21 amino acid residues:

H2N-G I V E Q C C A S V C S L Y Q L E N Y C N-COOH

In ISIS, the list of residue codes that you can use are defined in a Residue Map file that uses the structures from a Residue Template file. In this example, the Residue Map file contains the list of 1-letter residue codes for the amino acid residues. MDL provides you with Residue Map files for 1- and 3-letter residue codes for amino acids and for the nucleic acids DNA and RNA. The sequence bond between each residue is formed by the connection of atoms that are specified within the Residue Template file.

If the list of residue codes or their underlying structures are not sufficient for your specific needs, you can edit an existing Residue Map file or Residue Template file or create your own.

To improve the readability of a sequence, you can group residues into suitably sized blocks, limit the number of residues per line, or change the spacing between blocks or residues:

96.2 Definition of Aromaticity

For remote databases: ISIS interprets the following ring systems as aromatic:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:

Note: The bonds of six-membered aromatic ring systems and the perimeter bonds of azulenes are stored as aromatic bonds in the database. The bonds of five-membered aromatic rings, however, are stored as single and double bonds and interpreted as aromatic during a search. The differences between five-membered rings and other types of aromatic rings can cause different search results for five- and six-membered rings/azulenes when you use the following bonds in queries: Single, Double, and Single/Double query bonds. For more information on the Single/Double query bond, see Section 96.3.7.

96.3 Specifying Query Features on Atoms and Bonds in Expanded Residues

A query feature on an atom and/or a bond in an expanded residue is a restriction that specifies the retrieval of certain types of biopolymer records from an ISIS/Base database.

If you do not use query features, the biopolymers retrieved contain solely your exact fragment query embedded wholly within them. For example:

96.3.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all biopolymers that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all biopolymers that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

96.3.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of hydrogens. For example:

96.3.3 Allowing an Unsaturated Atom

Use an atom query feature to specify that an atom is attached to at least one multiple bond (double, triple, or aromatic).

Atom Query Feature: Unsaturated Atom (u)

Specifies that the atom of your choice is attached to at least one multiple bond (double, triple, or aromatic). For example, the following query specifies both an unsaturated atom (u) and single or double bonds (the double dashed lines).

96.3.4 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

Atom Query Feature: Substitution Count of Zero, s0

Specifies that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of a single atom with attached hydrogens (if any).

Atom Query Feature: Substitution Count of One, s1

Specifies that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Two, s2

Specifies that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Three, s3

Specifies that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Four, s4

Specifies that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Five, s5

Specifies that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of at Least Six, s6

Specifies that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count as Drawn, s*

Specifies that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:

96.3.5 Allowing a Specific Number of Ring Bond Attachments

Use atom query features to specify the number of ring bond attachments.

Atom Query Feature: Ring Bond Count of Zero, r0

Specifies that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:

Atom Query Feature: Ring Bond Count of Two, r2

Specifies that the records retrieved have solely two ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of Three, r3

Specifies that the records retrieved have solely three ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of at Least Four, r4

Specifies that the records retrieved have at least four ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count as Drawn, r*

Specifies that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:

96.3.6 Allowing Additional Atoms and/or Bonds in a Chain or a Ring

Use a query feature that is for either atoms or bonds to specify the addition of atoms and/or bonds in a chain or a ring.

Atom or Bond Query Feature: Link Node

Use a link node to specify the addition of variable numbers repeating units (atoms and/or bonds) to a ring or chain. A repeating unit must be attached to two adjacent bonds. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the link node [L1-3]:

Or, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the link node [L1-3]:

96.3.7 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Note: An aromatic query bond hits any bond in all types of aromatic rings: 6-membered ring bonds, 5-membered ring bonds, and azulene perimeter bonds. For more information on the structures that ISIS interprets as aromatic, see Section 96.2.

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

Note: A Single/Double query bond does not hit bonds in 6-membered aromatic rings, or perimeter bonds of azulenes, because bonds in these structures are stored in the database as aromatic bonds. However, a Single/Double query bond does hit bonds in 5-membered rings that ISIS interprets as aromatic. For more information on the structures that ISIS interprets as aromatic, see Section 96.2.

Bond Query Feature: Single/Aromatic Bond

Specifies either a single or an aromatic bond at that position:

Bond Query Feature: Double/Aromatic Bond

Specifies either a double or an aromatic bond at that position:

96.3.8 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

96.3.9 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved biopolymers contain either single or aromatic bonds at the specified positions.)

96.4 Specifying Stereochemistry in Expanded Residues

For remote databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve biopolymers with matching stereochemistry. For example:

An SSS/Biopoly search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve biopolymers with matching cis or trans stereochemistry. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An SSS/Biopoly search produces the following results:

Chiral Flags on Biopolymers

In a remote database, you can create a query with a chiral flag on a biopolymer with at least one asymmetric center or on a biopolymer that is asymmetric to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

96.5 Guidelines for Revising the Query

If your SSS/Biopoly search retrieved no records or too few records, you might want to:

*	Conduct an SSS/Biopoly search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Make your query more general, and then search the same set of records. For example, for any expanded residues, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, remove substituent limits, or remove stereochemical requirements.

If your SSS/Biopoly search retrieved too many records, you might want to:

*	Refine your query, and then search the same set of records. For example, for expanded residues, you can limit substitution at specific positions, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional fragment to the query so that it is a multiple-fragment query.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for biopolymers that you want to exclude (and save them), and then subtract the two lists.

96.6 Searching Example 1: Match Residues Anywhere Within Rigid Biopolymers

This example shows you how to find rigid biopolymers that contain your fragment query anywhere wholly within them and that contain a specific structural constraint.

96.6.1 Problem

You want to retrieve all biopolymers that contain the fragment phenylalanyl-arginyl-cysteinyl-alanyl-threonyl- (FRCAT) wholly within them. You also want to include in your search results all FRCAT-containing biopolymers that contain oxygen in place of nitrogen on the double bond in the R residue of the FRCAT sequences.

96.6.2 Approach and Query

Draw the fragment FRCAT: Type in the residue codes F, R, C, A, and T. You see the following contracted amino acid residues and leaving groups:

Expand the entire fragment. Add the ISIS atom-query feature s* to all the expanded residues to prevent substitutions at all positions. Contract the entire fragment. Delete the leaving groups on F, C, and T. Expand residues F and T. Remove the s* marks from the nitrogen atom at the N-terminus and the carbonyl carbon atom at the C-terminus. Contract residues of the fragment F and T.

Place the query into the MOLSTRUCTURE box on the form. Then conduct an SSS/Biopoly search in the database of your choice. (You can search the 3D demo database ISISPDB if you create it locally from the remote version.)

96.6.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS/Biopoly, how to/examples.

96.6.4 Results

You retrieve all biopolymers that contain both one or more FRCAT fragments wholly within them.


Local SSS/Biopoly: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Local SSS/Biopoly Search	97.1

*	Definition of Aromaticity	97.2

*	Specifying Query Features on Atoms and Bonds in Expanded

Residues	97.3

*	Specifying Stereochemistry in Expanded Residues	97.4

*	Guidelines for Revising the Query	97.5

*	Searching Example 1: Match Residues Anywhere Within Rigid

Biopolymers	97.6

We recommend that you print this 9-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a local SSS/Biopoly search, click here.

97.1 Definition of a Local SSS/Biopoly Search

A remote Biopolymer Substructure (SSS/Biopoly) search finds biopolymer records in your remote database that contain your query as a fragment (a set of residues of your choice) wholly within a larger, rigid biopolymer. The matching residues might be anywhere within the rigid biopolymer.

A local search is a search over a database that typically exists on your hard disk. To do a local search on your hard disk, you do not need to input network information.

Note: To do a local search that is accessed from a shared network, you need to input network information.

97.1.1 What is a Biopolymer?

A biopolymer sequence is a linear chain of connected repeating structures that are called residues. In the following example, you see the residue codes for one of the protein Bovine Insulin, which contains 21 amino acid residues:

H2N-G I V E Q C C A S V C S L Y Q L E N Y C N-COOH

In ISIS, the list of residue codes that you can use are defined in a Residue Map file that uses the structures from a Residue Template file. In this example, the Residue Map file contains the list of 1-letter residue codes for the amino acid residues. MDL provides you with Residue Map files for 1- and 3-letter residue codes for amino acids and for the nucleic acids DNA and RNA. The sequence bond between each residue is formed by the connection of atoms that are specified within the Residue Template file.

If the list of residue codes or their underlying structures are not sufficient for your specific needs, you can edit an existing Residue Map file or Residue Template file or create your own.

To improve the readability of a sequence, you can group residues into suitably sized blocks, limit the number of residues per line, or change the spacing between blocks or residues:

97.2 Definition of Aromaticity

For local databases: A bond is aromatic if it is in a six-membered ring with alternating double and single bonds, such as benzene.

Note: Aromaticity is not perceived for fused rings in which the double bonds are arranged in a way that cannot be defined as aromatic.

97.3 Specifying Query Features on Atoms and Bonds in Expanded Residues

A query feature on an atom and/or a bond in an expanded residue is a restriction that specifies the retrieval of certain types of biopolymer records from an ISIS/Base database.

If you do not use query features, the biopolymers retrieved contain solely your exact fragment query embedded wholly within them. For example:

97.3.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

97.3.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature: H0

Prohibits the attachment of hydrogens. For example:

97.3.3 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

97.3.4 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

97.3.5 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

97.3.6 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

97.4 Specifying Stereochemistry in Expanded Residues

For local databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

An SSS/Biopoly search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve molecules with matching cis or trans stereochemistry. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An SSS/Biopoly search produces the following results:

97.5 Guidelines for Revising the Query

If your SSS/Biopoly search retrieved no records or too few records, you might want to:

*	Conduct an SSS/Biopoly search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Make your query more general, and then search the same set of records. For example, for any expanded residues, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, or remove stereochemical requirements.

If your SSS/Biopoly search retrieved too many records, you might want to:

*	Refine your query, and then search the same set of records. For example, for expanded residues, you can limit substitution at specific positions with explicit hydrogens, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional fragment to the query so that it is a multiple-fragment query.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for biopolymers that you want to exclude (and save them), and then subtract the two lists.

97.6 Searching Example 1: Match Residues Anywhere Within Rigid Biopolymers

This example shows you how to find rigid biopolymers that contain your fragment query anywhere wholly within them and that contain a specific structural constraint.

97.6.1 Problem

You want to retrieve all biopolymers that contain the fragment phenylalanyl-arginyl-cysteinyl-alanyl-threonyl- (FRCAT) wholly within them. You also want to include in your search results all FRCAT-containing biopolymers that contain oxygen in place of nitrogen on the double bond in the R residue of the FRCAT sequences.

97.6.2 Approach and Query

Draw the fragment FRCAT: Type in the residue codes F, R, C, A, and T. You see the following contracted amino acid residues and leaving groups:

Expand the entire fragment. Add explicit hydrogens to all the expanded residues to prevent substitutions at all positions except on the nitrogen atom at the N-terminus and the carbonyl carbon atom at the C-terminus. Contract the entire fragment. Delete the leaving groups on F, C, and T.

Place the query into the MOLSTRUCTURE box on the form. Then conduct an SSS/Biopoly search in the database of your choice. (You can search the 3D demo database ISISPDB if you create it locally from the remote version.)

97.6.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS/Biopoly, how to/examples.

97.6.4 Results

You retrieve all biopolymers that contain both one or more FRCAT fragments wholly within them.


Remote CFS/Biopoly: Searching Concepts/Examples, Part 1

Click [image] to print Part 1.    Click [image] to go to Part 2.    Click [image] to close this Request-A-Document.

This Request-A-Document contains:

Part 1:

*	Definition of CFS/Biopoly Search	95.1

*	Specifying Query Features on Atoms and Bonds	95.2

*	Specifying Rgroup Query Features	95.3

*	Specifying Chemical Environments	95.4

*	Specifying Submodel Components	95.5

*	Specifying 3D Objects and Constraints	95.6

*	Using Receptor Information	95.7

---------------------------------------------------------------------------------------------------------------------

Part 2:

*	The CFS/Biopoly Search Process and Its Options	95.8

*	Sprouting Hydrogens and Lone Pairs	95.9

*	Guidelines for Revising a CFS/Biopoly Search	95.10

*	Searching Example 1: Searching For Residues
Within Fitted Biopolymers	95.11

We recommend that you print this Request-A-Document, and then browse through it. For technical reasons, this 54-page Request-A-Document has been divided into two parts. To print Part 1, click the Printer icon at the top of the screen. To print Part 2, first click the Part 2 icon, and then click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a CFS/Biopoly search, click here.

95.1 Definition of a Remote CFS/Biopoly Search

A remote Conformationally Flexible Substructure (CFS/Biopoly) search finds 3D structures that contain your query as a fragment (a set of residues of your choice) wholly within a larger, unrigid biopolymer.

A CFS search attempts to fit residues to the query by rotating their single bonds. Consequently, the 3D structures that you obtain from a CFS search are not necessarily in the same conformations as the 3D structures in the database.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

95.1.1 What is a Biopolymer?

A biopolymer sequence is a linear chain of connected repeating structures that are called residues. In the following example, you see the residue codes for one of the protein Bovine Insulin, which contains 21 amino acid residues:

H2N-G I V E Q C C A S V C S L Y Q L E N Y C N-COOH

In ISIS, the list of residue codes that you can use are defined in a Residue Map file that uses the structures from a Residue Template file. In this example, the Residue Map file contains the list of 1-letter residue codes for the amino acid residues. MDL provides you with Residue Map files for 1- and 3-letter residue codes for amino acids and for the nucleic acids DNA and RNA. The sequence bond between each residue is formed by the connection of atoms that are specified within the Residue Template file.

If the list of residue codes or their underlying structures are not sufficient for your specific needs, you can edit an existing Residue Map file or Residue Template file or create your own.

To improve the readability of a sequence, you can group residues into suitably sized blocks, limit the number of residues per line, or change the spacing between blocks or residues:

95.1.2 CFS/Biopoly Search Queries

A CFS/Biopoly search query must contain at least one of the following 3D query features:

*	Submodel. A submodel is a three-dimensional (3D) representation of a portion of a molecule. A submodel contains two or more atoms in a fixed spatial arrangement (F). You construct a submodel from an existing 3D structure. For example:

For more information on submodels, see Section 95.5.

*	3D geometric constraints. You construct geometric constraints from atoms or from 3D objects such as points, lines, and centroids. For example, you can specify that the centers (centroids) of two rings must be separated by a distance of 2 to 10 Angstroms:

For more information on 3D geometric constraints, see Section 95.6.

*	3D data constraints that you apply to atoms or to pairs of atoms. The following example shows calculated values (in Hz) for the ring proton spin-spin couplings of methyl 2-furoate:

For more information on 3D data constraints, see Section 95.6.

A CFS/Biopoly search query can also contain 2D query features. A 2D query feature is a restriction on an atom or bond that specifies solely the number, type, and connectivity of atoms in a molecule, without any information on spatial arrangement. 2D query features can include:

*	Query features on atoms and bonds. You can allow or exclude specific atoms at certain locations, allow or exclude specific types of bonds, and so on. For example, the following query specifies that only carbon, nitrogen, or oxygen can be present at a specific position on the ring:

For more information on atom and bond query features, see Section 95.2.

*	Rgroups. An Rgroup query contains a root structure with defined Rgroup substituents attached to it at specific positions. An Rgroup consists of the molecule fragments (substituents) that can attach to the corresponding Rgroup sites on the root. That is, any Rgroup substituents that are members of the Rgroup R1 can attach to any position with the Rgroup label R1.

For example, you can specify that the Rgroup label R1 on the root structure allows a carboxyl group at its position and that R2 allows either a chlorine atom or a sulfonic acid group at its position:

For more information on Rgroups, see Section 95.3.

You can combine 2D and 3D query features to specify:

*	Chemical environments. You can use 2D query features to specify chemical environments such as basic nitrogens, acidic centers, hydrogen-bond donors, or hydrogen-bond acceptors on the molecules that you retrieve. For example, the following is a hydrogen-bond donor:

For more information on chemical environments, see Section 95.4.

*	Information on the receptor with which active structures interact. For example, you can specify a distance constraint between a hydrogen-bond donor and a hydrogen-bond acceptor on the receptor:

For more information on queries that use information on the receptor, see Section 95.7.

95.1.3 CFS/Biopoly Search Options

CFS/Biopoly searching provides many options that allow you to control how ISIS fits 3D structures to your query. For example, you can specify:

*	The algorithm (simplex or derivative) that ISIS uses to fit 3D structures to the query.

*	The number of times that ISIS attempts to fit (map) the query to each 3D structure.

*	The types of single bonds that ISIS can rotate when fitting 3D structures to the query. For example, you can specify whether single bonds in rings can be rotated, or whether to include single bonds between unsaturated centers (for example, biphenyls).

*	Whether to ignore nonbonded (van der Waals) interactions when fitting 3D structures to the query (bump checking). For example, you can ignore van der Waals interactions during the CFS/Biopoly search, then calculate van der Waals interactions on individual 3D structures as you view them.

*	Whether to rotate single bonds in other regions of a 3D structure so that the 3D structure can be fitted to the query (global relaxation).

*	Whether to calculate specific types of data that are derived from the fitted 3D structures. For example, you can calculate the difference in van der Waals interaction energy between the fitted 3D structure and the conformation that is stored in the database.

Caution: The CFS options subtly interact with each other and can produce undesirable results if improperly used. Therefore, we strongly recommend that you use the default CFS options, except for specific situations that are specified in the step-by-step instructions. For step-by-step instructions on conducting a CFS/Biopoly search, click here. Alternatively, choose Help > Index, and choose CFS, how-to/examples.

After you have more experience with CFS/Biopoly searching, you might want to experiment with CFS options. For information on the default CFS options, and on how to specify meaningful combinations of CFS options, see Section 95.8.

95.1.4 Choosing Between CFS/Biopoly and SSS3D/Biopoly Searches

A CFS/Biopoly search produces a set of 3D structures (hit list) whose fitted conformations might be different from the 3D conformations that are stored in the database. In contrast, an SSS3D/Biopoly search retrieves solely 3D conformations that are actually stored in the database.

Note: The 3D structures that you obtain from a CFS/Biopoly search (hits) are not necessarily low-energy conformations. You can, however, export the fitted structures to a modeling program for further processing.

Your choice of CFS/Biopoly or SSS3D/Biopoly search depends on your 3D searching strategy:

*	Use CFS/Biopoly when your database does not necessarily contain all possible conformations of each 3D structure, and you want to find additional conformations that fit the query. By deriving additional conformations during the search, CFS/Biopoly can find structures that SSS3D/Biopoly might miss.

*	Use SSS3D/Biopoly when your database already contains 3D structures with the desired conformations, and you want to find solely those conformations.

*	Use SSS3D/Biopoly when fast search speed is more important than retrieving all possible conformations. SSS3D/Biopoly is faster than a CFS/Biopoly search. In a preliminary study, for example, you might want to use a series of SSS3D/Biopoly searches to obtain a representative series of compounds and use this information to refine your query. After you have refined your query, you can perform a CFS/Biopoly search that retrieves as many structures as possible.

*	Use SSS3D/Biopoly when you want to find 3D structures that are rigid in the region that matches the query. For example, you might want to export rigid structures to a modeling software program so that you can use them in structure-activity studies. The SSS3D/Biopoly finds both rigid and flexible structures. However, you can remove the flexible structures by conducting a CFS/Biopoly search over the set of records that you retrieve from the SSS3D/Biopoly search. For more information on removing flexible structures, see Section 95.9.

95.2 Specifying 2D Query Features on Atoms and Bonds in Expanded Residues

A 2D query feature on an atom and/or a bond in an expanded residue is a restriction that specifies the retrieval of certain types of biopolymer records from an ISIS/Base database.

If you do not use query features, the biopolymers retrieved contain solely your exact fragment query embedded wholly within them. For example:

You can also define Rgroups that specify a root structure with defined Rgroup substituents attached to it at specific positions. For more information on Rgroups, see Section 95.4.

Caution: Atom and bond query features are 2D query features. 2D query features specify solely the number, type, and connectivity of atoms in a molecule. A CFS/Biopoly query must contain at least one component that specifies the spatial distribution of atoms in a 3D structure; otherwise, the query will fail. To specify the spatial distribution of atoms, you can use a submodel with two or more fixed atoms, and/or use 3D geometric constraints such as distances and angles. For more information on submodels, see Section 95.5. For more information on 3D geometric constraints, see Section 95.6.

95.2.1 Definition of Aromaticity

For remote databases: ISIS interprets the following ring systems as aromatic:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:

Note: The bonds of six-membered aromatic ring systems and the perimeter bonds of azulenes are stored as aromatic bonds in the database. The bonds of five-membered aromatic rings, however, are stored as single and double bonds and interpreted as aromatic during a search. The differences between five-membered rings and other types of aromatic rings can cause different search results for five- and six-membered rings/azulenes when you use the following bonds in queries: Single, Double, and Single/Double query bonds. For more information on the Single/Double query bond, see Section 95.3.7.

95.2.2 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except implicit or explicit hydrogens:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

95.2.3 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature: H0

Prohibits the attachment of implicit hydrogens. For example:

95.2.4 Allowing an Unsaturated Atom

Use an atom query feature to specify that an atom is unsaturated, or attached to at least one multiple bond: double, triple, or aromatic.

Atom Query Feature: Unsaturated Atom (u)

Specifies that the atom of your choice is unsaturated. For example, the following query specifies both an unsaturated atom and single or double bonds (the double dashed lines).

95.2.5 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

Use explicit hydrogens to block non-hydrogen attachments on atoms. For example:

Atom Query Feature: Substitution Count of Zero, s0

Specifies that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of an isolated atom.

Atom Query Feature: Substitution Count of One, s1

Specifies that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Two, s2

Specifies that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Three, s3

Specifies that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Four, s4

Specifies that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Five, s5

Specifies that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of at Least Six, s6

Specifies that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count as Drawn, s*

Specifies that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:

95.2.6 Allowing a Specific Number of Ring Bond Attachments

Use atom query features to specify the number of ring bond attachments.

Atom Query Feature: Ring Bond Count of Zero, r0

Specifies that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:

Atom Query Feature: Ring Bond Count of Two, r2

Specifies that the records retrieved have solely two ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of Three, r3

Specifies that the records retrieved have solely three ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of at Least Four, r4

Specifies that the records retrieved have at least four ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count as Drawn, r*

Specifies that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:

95.2.7 Allowing Additional Atoms and/or Bonds in a Chain or a Ring

Use a query feature that is for either atoms or bonds to specify the addition of atoms and/or bonds in a chain or a ring.

Atom or Bond Query Feature: Link Node

Use a link node to specify the addition of variable numbers repeating units (atoms and/or bonds) to a ring or chain. A repeating unit must be attached to two adjacent bonds. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the link node [L1-3]:

Or, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the link node [L1-3]:

95.2.8 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Note: An aromatic query bond hits any bond in all types of aromatic rings: 6-membered ring bonds, 5-membered ring bonds, and azulene perimeter bonds. For more information on the structures that ISIS interprets as aromatic, see Section 95.2.1.

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

Note: A Single/Double query bond does not hit bonds in 6-membered aromatic rings, or perimeter bonds of azulenes, because bonds in these structures are stored in the database as aromatic bonds. However, a Single/Double query bond does hit bonds in 5-membered rings that ISIS interprets as aromatic. For more information on the structures that ISIS interprets as aromatic, see Section 95.2.1.

Bond Query Feature: Single/Aromatic Bond

Specifies either a single or an aromatic bond at that position:

Bond Query Feature: Double/Aromatic Bond

Specifies either a double or an aromatic bond at that position:

95.2.9 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is attached to a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

95.2.10 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is attached to a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

95.3 Specifying Rgroup Query Features

An Rgroup query finds structures that contain your query as a root structure with defined Rgroup substituents attached to it at specific positions. Your query can contain restrictions on the Rgroup substituents, called Rgroup conditions: You can specify the number of Rgroup sites that must be occupied in the records retrieved, specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site, or specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

Your Rgroup query can also contain restrictions on atoms and bonds of the root structure and Rgroup substituents. For example, you can use the atom query feature H(0) to prohibit the attachment of implicit hydrogens on a specific atom in the structures retrieved.

An example of an Rgroup query is as follows:

You can use Rgroups and atom and bond query features to specify chemical environments such as basic nitrogens and acidic centers. For more information on chemical environments, see Section 95.4.

Caution: Like atom and bond query features, Rgroup queries contain no information about the spatial distribution of atoms in a 3D structure. A CFS/Biopoly query must contain at least one component that specifies the spatial distribution of atoms in a 3D structure; otherwise, the query will fail. To specify the spatial distribution of atoms, you can use a submodel with two or more fixed atoms, and/or use 3D constraints such as distances and angles. For more information on submodels, see Section 95.5. For more information on 3D constraints, see Section 95.6.

95.3.1 The Root Structure

The root structure contains the portion of the structure that does not vary among the structures retrieved. For example, if you want to find 2, 5-Dihydroxypyridine in which the substituent at position 2 can be COOH, CN, or Ph, and the substituent at position 5 can be OH or CH3, the root structure is 2, 5-Dihydroxypyridine with Rgroups (such as R1 and R2):

Rgroups

On the root structure, Rgroups (R1 through R32) are placeholders that designate where the lists of functional groups and atoms that can attach to the root structure. In the example above, the Rgroup R1 designates that the members of the list R1 (the Rgroup substituents) are allowed at position 5 on the root structure. The Rgroup R2 designates that the members of the list R2 (the Rgroup substituents) are allowed at position 2 on the root structure.

Multiple Rgroups at One Position

You can specify multiple Rgroups at a single site on the root structure. For example:

One Rgroup at Multiple Positions

You can specify a single Rgroup (such as R1) at multiple positions on the root structure. For example:

Note: For information on how to restrict the number of Rgroups that must be occupied in the records retrieved, See Section 95.2.3, "Rgroup Conditions." A molecule need not satisfy all the Rgroup sites on the root structure to be retrieved. For example, the Rgroup condition R1 > 0 specifies that any molecule in which at least one of the R1 sites is filled by an R1 member will be retrieved. In addition, the Rgroup condition RestH determines whether the unsatisfied sites must be filled with hydrogen atoms or if other molecule fragments are allowed to be attached if they are not on the list.

95.3.2 Rgroup Substituents

Rgroup substituents are the members of the list of Rgroups. You define the Rgroup substituents that you will allow to be found at specified positions in the molecules retrieved. Rgroup substituents can be any structural fragment, including functional groups and single atoms.

In the example below, the Rgroup substituents COOH, CN, or Ph are allowed at position 5 (R1) on the root structure and the Rgroup substituents OH or CH3 are allowed at position 2 (R2) on the root structure:

Attachment Points

An attachment point (marked with an arrow and an asterisk) designates the atom on the Rgroup substituent that is attached to the root structure:

You must designate an attachment point on an Rgroup substituent for each bond that is attached to the substituent. If an Rgroup is attached to two bonds on the root structure, you must designate two attachment points. The bond on the root structure that is marked with double quotes corresponds to the attachment point on the Rgroup substituent that is marked with double quotes. The other attachment point on the Rgroup substituent is marked with a single quote:

Nested Rgroups

A nested Rgroup is an Rgroup that is a placeholder within another Rgroup rather than within the root structure. (You cannot nest an Rgroup any lower than this level.) In the following example, Rgroup R2 is nested within the Rgroup R1:

Nested Rgroups are equivalent to the following structures:

95.3.3 Rgroup Conditions

You can apply restrictions to each Rgroup in your query after you assemble all the Rgroups. The set of restrictions is called the Rgroup conditions.

If you do not apply Rgroup conditions, ISIS assigns the default conditions: Occurrence > 0 and RestH off for each Rgroup.

Occurrence

With the Rgroup condition Occurrence, you can specify the number of Rgroup sites that must be occupied in the records retrieved. For example, the occurrence designation R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved. Type one of the following values in the Occurrence range text box:

Value	Explanation

0	All members of the Rgroup are excluded from the Rgroup site (such as R1). To allow any other Rgroup substituent at the Rgroup site, set RestH to off.

> 0	At least one Rgroup must be satisfied. If RestH is off, any other substituent can attach to unsatisfied sites. If RestH is on, unsatisfied sites must be filled solely by hydrogens.

n	Exactly n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

< n	Less than n number of sites (including zero) must be satisfied. RestH controls substitution at unsatisfied sites.

m - n	Any number of sites falling within the range of m to n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

m,n,...	Any combination of the above expressions, separated by commas. For example: 1, 3-5, 9, >12.

For example, the Rgroup condition R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved.

In another example, the Rgroup condition R1 > 0 and R2 > 0 specifies that an Rgroup substituent from the R1 list AND an Rgroup substituent from the R2 list must occupy at least one site on the root structure in the records retrieved.

Finally, the Rgroup conditions R1 = 1, 3-5, 9, >12 specify that either 1, 3, 4, 5, 9, or more than 12 sites must be satisfied:

RestH

With the Rgroup condition RestH, you can specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site.

An unsatisfied Rgroup site is an Rgroup site on the root structure that does not have an Rgroup member attached: If RestH is off, any functional group or atom may be attached at unsatisfied Rgroup sites on the root structure. If RestH is on, solely hydrogens are allowed to be attached at unsatisfied Rgroup sites on the root structure.

If/Then

With the Rgroup condition If/then, you can specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

For example, If R1 then R2 specifies that if the conditions for R1 are satisfied, then the conditions for R2 must also be satisfied. (If the conditions for R1 are not satisfied, then the conditions for R2 are ignored.) The If/then condition implies that a molecule may be retrieved even though R1 is not satisfied.

In the following query, R1 contains a nitro group and a sulfonic acid group. R2 contains a chlorine atom. The condition If R1 then R2 specifies that if a nitro group or a sulfonic acid group is attached at R1 on the root structure, then a chlorine must also be attached at R2. However, if the R1 site on the root structure does not have either the nitro or the sulfonic acid group (R1 is unsatisfied), then R2 can have any substituent (R2 is ignored):

95.4 Specifying Chemical Environments

You can incorporate specific chemical environments into your CFS/Biopoly query. This section contains examples of chemical environments that you can create with 2D query features and Rgroups. MDL supplies ISIS/Draw sketch files that contain specific types of chemical environments. You can incorporate these structures into your own queries and modify them if desired.

Note: There are two different conventions for defining hydrogen-bond donors and acceptors. This help file uses the definition of a hydrogen-bond donor that is generally used by medicinal chemists. By this convention, the donor of a hydrogen bond is the group to which the hydrogen atom is attached:

An alternative definition of hydrogen-bond donors and acceptors defines a hydrogen-bond donor as the group that provides the lone-pair electrons (LP) to the hydrogen bond.

95.4.1 Acidic Center

The file ACID_CTR.SKC contains the following definition of an acidic center:

This query defines an acidic center as either an oxygen of a carboxylic acid or any nitrogen of an unsubstituted tetrazole.

95.4.2 Basic Nitrogen

BSC_N_1.SKC File

The file BSC_N_1.SKC contains a definition of a basic nitrogen that includes alkyl amines (nsp3), amidines (nsp2), and guanidines (nsp2). This definition excludes other nitrogens such as aromatic nitrogens, aniline-type nitrogens, N=O, NHC=O, and NHC=C:

You can change this definition to fit your needs. For example, if you want to include aromatic nitrogens, delete R2 from the definition.

BSC_N_2.SKC File

The definition of basic nitrogen in the file BSC_N_2.SKC excludes all amides or anilines, and other conjugated systems that reduce the accessibility of the electron pair on the nitrogen atom:

Simple Definition

The following is a simple definition of a basic nitrogen:

95.4.3 Hydrogen-Bond Acceptor

The definition of a hydrogen bond acceptor in the file H_ACCEPT.SKC extends the definition of a basic nitrogen to include oxygen and sulfur:

95.4.4 Hydrogen-Bond Donor

The following is an example of a hydrogen bond donor:

95.5 Specifying Submodel Components

A submodel is a three-dimensional (3D) representation of a portion of a molecule. A submodel search retrieves all models that contain the same spatial arrangement of atoms as those specified in your submodel query, within specified deviations of the individual and overall atoms.

You specify the spatial arrangement of atoms in a submodel query by fixing the 3D coordinates of two or more atoms in the structure. To create a submodel, you eliminate parts of an existing 3D structure until you have the submodel that you want to find in other 3D structures. Then, you fix the positions of the atoms of your choice. The figure below shows how you create a submodel query from the 3D structure of Trandolapril. Circles mark the atoms in Trandolapril that are fixed (F) in the query:

When you conduct a search with a submodel query, you must specify how closely the 3D structures that you retrieve must match the spatial arrangement of the fixed atoms in the submodel query. Two fixed-atom tolerances specify how closely the structures must match the query:

*	Maximum atomic displacement specifies the maximum allowed deviation of individual fixed atoms in the query from those in the structures that you retrieve.

*	Maximum RMS deviation specifies the maximum allowed deviation of all fixed atoms in the query from fixed atoms in the structures that you retrieve. During the search, ISIS superimposes the fixed atoms in the 3D structure on those of the query and performs a least-squares calculation.

When your query contains fixed atoms, you must specify at least one fixed-atom tolerance for the SSS3D search. You can specify:

*	Maximum atomic displacement only (structures with 2 or 3 fixed atoms)

*	Maximum RMS deviation only (structures with at least 4 fixed atoms)

*	Both fixed-atom tolerances (structures with at least 4 fixed atoms)

Your ISIS Administrator sets default fixed-atom tolerances that your site uses to register 3D structures to the database. These tolerances are specified in the Session Settings file that your ISIS Administrator supplies you. To change fixed-atom tolerances for searching, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for fixed-atom tolerances, changing.

Caution: If you change the default fixed-atom tolerances for searching, you must restore the default fixed-atom tolerances before you register 3D structures.

The following are examples of the 3D structures that you retrieve from a search with the query that you derive from Trandolapril, with both fixed-atom tolerances set to 0.5:

Note: Queries that contain fixed atoms produce slower search speeds than queries that do not contain fixed atoms. As an alternative to the fixed-atom query shown previously, you can use a query with distance constraints that incorporate the fixed-atom tolerances:

You can also use other 3D query features to specify the spatial distribution of atoms within a 3D structure. For more information on distance constraints and other 3D constraints, see Section 95.6.

95.6 3D Objects and Constraints

To specify the spatial relationships between atoms, you can construct 3D objects and create 3D constraints that use atoms and/or constructed 3D objects.

95.6.1 Specifying 3D Objects

You can set geometric constraints on various molecular or constructed geometric 3D objects. These objects can be points, lines, planes, centroids, and normal vectors. Lines, planes, and normal vectors actually extend infinitely, but are represented in ISIS as shown below:

Centroid

Use a centroid to define the geometric center of a set of reference points or atoms of your choice. For example, the centroids in the structures below (depicted by the triangles) are the geometric centers of selected atoms. The centroid on the left is created when all six ring atoms are selected. The centroid on the right is created when the atoms in the box are selected (the box is used here to indicate atoms selected, and does not appear in the query):

Line

Use a line to define a path through two or more reference positions, such as points, atoms, or centroids:

ISIS derives a best-fit line if you use at least three reference positions to define the line. You can specify a linearity constraint for a best-fit line. For more information, see 95.6.2.

Normal

Use a normal to specify a line (with an arrowhead) that is perpendicular to a plane and that passes through a reference position (a point, atom, or centroid):

In ISIS, the direction of the normal arrow is defined by the sequence in which you selected the first three components of the plane. To reverse the direction of the arrow, simply reverse the order in which you define the components of a plane.

Note: If you define a normal through a point that lies in the same plane, the direction of the normal is undefined.

Plane

Use a plane to define a surface that consists of three or more reference positions (points, atoms, or centroids). A plane actually extends infinitely in all directions, but is depicted in ISIS as a small rectangular surface. In the following figure, the entire molecule specifies the plane:

ISIS derives a best-fit plane if you use at least four reference positions to define the line. You can specify a planarity constraint for a best-fit plane. For more information, see Section 95.6.2.

Point

A point is a reference position. You specify a point at a defined distance and direction from a distance reference position (another point, atom or centroid). To specify the direction, you can use either another reference position (called the direction reference position) or a normal.

You can specify the distance from the distance reference position to the direction reference position in Angstroms or as a percentage. Angstrom distances must lie between -100 and +100 Angstroms. Percentage distances must lie between -1,000% and +1,000%, and must include the % sign.

The following example defines a point at a distance of 1.4 Angstroms from a ring nitrogen (the distance reference position) to a ring oxygen (the direction reference position):

The point that you specify need not lie between the two reference positions. The following example shows a point projected 2.8 Angstroms along a line between the nitrogen atom (the distance reference position) and the hydrogen (the direction reference position):

When you use a normal to specify the direction of the point from the distance reference position, you must specify the distance from the distance reference position in Angstroms.

The following example uses a normal to create points that lie 2.8 Angstroms above and below the center of a phenyl ring. The normal is perpendicular to the plane of the ring and passes through the ring centroid. The direction of the normal is undefined, because the point that defines it lies in the plane. To define points on both sides of the plane, use plus (+) and minus (-) signs with Angstrom values to specify the distances:

To create a point on only one side of the plane, specify a distance of 2.8 Angstroms without the plus (+) or minus (-) sign:

Note: You can use points to represent features on a receptor. For examples, see Section 95.7.

95.6.2 Specifying 3D Constraints

You can apply 3D geometric constraints to 3D objects. 3D geometric constraints include distances, angles, dihedral angles, exclusion spheres, linearity constraints, and planarity constraints:

You can also apply 3D data constraints to atoms and atom pairs. Data constraints are listed under “Atom" and “Atom Pair" later in this section.

Distance

You can define a distance constraint between two reference positions (atoms, centroids, or points), from a reference position to a line or normal, or from a reference position to a plane:

The distance constraint is a range of values. Both values in the range must be greater than zero and equal or less than 1,000. The following query has a distance constraint of 2 to 10 Angstroms between the center of a phenol ring and the center of a phenyl ring:

The following are examples of the 3D structures that you retrieve:

Angle

You can define an angle constraint with three points, centroids, or atoms; or with two planes, lines, or normals:

The vertex of the angle for two planes, lines, or normals that do not intersect is an imaginary point. An angle drawn with two lines that do not intersect is equivalent to a dihedral angle through an imaginary line that connects the two lines with the shortest distance.

The angular range that you specify depends on the way that you defined the angle:

*	If you used lines or planes to define the angle, the range must lie between 0 and 90 degrees.

*	If you used three points to define the angle, the range must lie between 0 and 180 degrees.

The following query has a constraint of 30- 65 degrees on the angle between the line between two phenyl centers and a phenol oxygen:

The following are examples of the 3D structures that you retrieve:

Exclusion sphere

Use an exclusion sphere to exclude atoms within a sphere surrounding a reference position. You define the radius of the exclusion sphere. You can ignore unconnected atoms within the radius of the sphere or specify exactly which atoms that you want to be included. The radius of the sphere must be between 0 and 20 Angstroms.

Note: You cannot use a CFS/Biopoly query that consists solely of exclusion spheres. A CFS/Biopoly query must contain at least one of the following 3D query components: distance, angle, dihedral angle, linearity constraint, planarity constraint, or two or more fixed atoms.

For example, the exclusion spheres in the following query ensure that you select compounds that have no atoms within the circled areas of 1.0-Angstrom radius:

The following is an example of the 3D structures that you retrieve (For clarity, the measured values of the four distance constraints are not displayed):

You can specify that atoms that are part of the query can lie within the exclusion sphere. In the following query, for example, you might want to allow atoms from the carboxyl group within the exclusion spheres, but exclude all other atoms:

To allow other atoms in the query within the exclusion sphere, you must include these atoms in the basis of the exclusion sphere. (The basis of a 3D object or constraint is the set of atoms or 3D objects that comprise the object.) For an exclusion sphere, the basis always includes the reference position at the center of the sphere. To include additional atoms, you edit the basis to include these atoms. For example, you can edit the basis of the exclusion spheres in the previous query to include the carboxyl group. The following are examples of the 3D structures that you retrieve (For clarity, the measured value of one distance constraint is not displayed):

You can also specify that unconnected atoms that are not part of the query can lie within the volume of the exclusion spheres. For example, you might want to allow salt ions or water molecules within the volume of the exclusion sphere. To allow these atoms, you specify the following setting when you create the exclusion sphere: Allow nonquery atoms within exclusion sphere.

Note: You can use exclusion spheres to represent regions on a receptor. For examples, see Section 95.7.

Dihedral

When two planes intersect, a dihedral angle is created from the common vertex of reference positions 1 and 2 and reference positions 3 and 4:

Atoms 1 and 2 are adjacent reference points for the phenol structure, and atoms 3 and 4 are adjacent reference points for the phenyl structure. Reference points 1, 2, and 3 lie along the first plane, and reference points 2, 3, and 4 lie along the second plane. Reference points 2 and 3 share both planes and form the vertex of the dihedral angle.

The angular range that you specify must be between -180 and +180 degrees.

The following query specifies a dihedral angle between two atoms on a phenyl ring and two atoms on a phenol ring:

The following are examples of the 3D structures that you retrieve:

Linearity

You can specify that three or more reference positions (atoms, points, or ring centroids) must lie along the same line. To do this, you specify the maximum average distance (RMS deviation) of the reference positions from the best-fit line derived from the reference positions. The following shows a linearity constraint for all atoms in a trialkene:

The value that you specify must lie between 0 and 1,000.

Planarity

You can specify that four or more reference positions (atoms, points, or ring centroids) must lie along the same plane. To do this, you specify the maximum average distance (RMS deviation) of the reference positions from the best-fit plane derived from the reference positions. The following shows a planarity constraint for all atoms in a benzaldehyde:

The value that you specify must lie between 0 and 1,000.

Atom

Use atom data to specify a data constraint for selected atoms in your query, such as spectroscopic and quantum mechanical data or partial charges. For example:

The atom data constraint specifies the partial charge on the oxygen. Rn specifies that the oxygen must appear in a ring. For more information on Rgroups, see Section 95.2.

Atom-Pair

Use atom-pair data to specify a data constraint between two atoms in your query. For example, you can specify bond order, lower/upper distance constraints, and spectroscopic and quantum mechanical data. The following query specifies values for the ring proton spin-spin couplings of methyl 2-furoate:

95.7 Using Receptor Information

The previous sections showed how to use information about active compounds (that is, information about the pharmacophore) to specify query constraints. This section shows how you can use information about the receptor to specify geometric constraints in your query. Use these examples as a starting point for creating your own queries.

Note: For simplicity, the queries in this section use a simple definition of a basic nitrogen. For more refined definitions of basic nitrogen, see Section 95.4.2.

95.7.1 Specifying Hydrogen-Bond Interactions

You can use projected points and exclusion spheres to represent hydrogen bond donors and acceptors on the receptor.

Note: There are two different conventions for defining hydrogen-bond donors and acceptors. This help file uses the definition of a hydrogen-bond donor that is generally used by medicinal chemists. By this convention, the donor of a hydrogen bond is the group to which the hydrogen atom is attached:

An alternative definition of hydrogen-bond donors and acceptors defines a hydrogen-bond donor as the group that provides the lone-pair electrons (LP) to the hydrogen bond.

Hydrogen Bond Donor on Receptor

The following example shows how to construct an exclusion sphere that represents a hydrogen-bond donor on the receptor. You construct the exclusion sphere around a point that you construct from two atoms of the corresponding hydrogen-bond acceptor on the ligand.

Hydrogen Bond Acceptor on Receptor

The following example shows how to construct an exclusion sphere that represents a hydrogen-bond acceptor on the receptor. You construct the exclusion sphere around a point that you construct from two atoms of the corresponding hydrogen-bond donor on the ligand.

Distance Constraint Between Features on the Receptor

Specifying distance constraints between points on the receptor rather than the ligand can produce highly specific queries. For example, suppose you know that the receptor contains a hydrogen-bond donor that is 10 - 11.5 Angstroms from a hydrogen-bond acceptor. The following figure schematically shows two topologically different drugs bound to the same receptor site.

If you use a query that uses information about the pharmacophore (ligand-based query), you must specify a large distance range (4 - 10 Angstroms) to retrieve both classes of compounds. The ligand-based query retrieves the compounds that you want, but also retrieves many false hits (that is, false positives). If you use a query that uses information about the receptor (receptor-based query), you can specify a much narrower distance range. For example:

The greater specificity in the receptor-based query allows you to retrieve the compounds that you want while eliminating many of the false hits that the ligand-based query might produce.

95.7.2 Specifying Pi-Pi Interactions

You can use projected points and exclusion spheres to represent pi-pi interactions with aromatic groups on the receptor.

Pi-Pi Interactions Alone

Use exclusion spheres above and below aromatic rings that interact with aromatic groups on the receptor. The exclusion spheres eliminate 3D structures with atoms that intrude into the excluded area. Consequently, all 3D structures that you retrieve can contain phenyl rings that can interact freely with the receptor.

To create the exclusion spheres, you create a normal to the plane of the phenyl ring. On that normal, you place a point that is 3.0 Angstroms above (+ 3.0 Angstroms) the plane of the ring, and another point that is 3.0 Angstroms below (- 3.0 Angstroms) the plane of the ring. Around each point, you create exclusion spheres that are 1.5 Angstroms in diameter.

The following query uses exclusion spheres and a distance constraint:

Pi-Pi Interactions With a Distance Constraint

To specify a distance constraint between a lipophilic site and another site on the receptor, use a projected point on one side of an aromatic ring. Use exclusion spheres to eliminate 3D structures that do not permit the aromatic ring to interact freely with the receptor.

To construct the exclusion spheres and projected points, create a normal to the plane of the phenyl ring. On that normal, you place a point that is 2.0 Angstroms above (+ 2.0 Angstroms) the plane of the ring, and another point that is 2.0 Angstroms below (- 2.0 Angstroms) the plane of the ring. On the normal, you place another point that is 3.5 Angstroms from the plane of the ring. Around the two points at 2.0 Angstroms from the aromatic ring, you create exclusion spheres that are 1.5 Angstroms in diameter.

The following query specifies a distance constraint of 6 - 10 Angstroms between a lipophilic site on the receptor and a hydrogen-bond donor on the receptor (for clarity, the query uses a simple definition of a basic nitrogen):

(Continued in Part 2)


Remote CFS/Biopoly: Searching Concepts/Examples Part 2

Click [image] to print Part 2.    Click [image] to return to Part 1.    Click [image] to close this Request-A-Document.

To print Part 2 of this Request-A-Document, click the Printer icon at the top of the screen.

To return to Part 1, click the Part 1 icon at the top of the screen.

---------------------------------------------------------------------------------------------------------------------

95.8 The CFS/Biopoly Search Process and Its Options

This section contains information that allows you to make meaningful choices when you want to use CFS/Biopoly options that are different from the defaults.

95.8.1 Understanding the CFS/Biopoly Search Process

During both the initial and bump-checking CFS/Biopoly searches, ISIS subjects each 3D structure in the search domain to the following three-step process:

The following sections describe each step of this process in detail.

Step 1: 2D Key Screening

Every structure in a database is associated with a set of binary representations of its structural entities, called keys. The 2D key screening step retrieves all the static 3D models in the database that contain the structural fragments of your query embedded in them. The presence of structural fragments and their combinations can be represented by one or more of 960 key codes.

Step 2: Upper/Lower Distance Screening

The upper/lower distance screening step tests the fit of certain geometric constraints for those conformations from the 2D key screening step. ISIS tests the fit solely of distance and angle constraints that are defined by atoms and ring centroids. The process rotates single bonds between two atoms to find the maximum and minimum separation possible. At this stage of the process, ISIS tests the fit of each distance and angle constraint independently of the other constraints.

Step 3: Conformational Fitting

If your 3D query contains more than one distance constraint, ISIS uses a torsional fitter to retrieve those conformations from the upper or lower distance screening that can be suitably rotated about their rotatable single bonds. The torsional fitter attempts to minimize the deviations between measured values of 3D constraints and the values that are specified in your search query.

ISIS omits conformational fitting if the query contains only one distance or angle constraint.

The conformational fitting step is optional. If you do not perform conformational fitting during the search, ISIS performs conformational fitting on each 3D structure as you view it (view-time fitting).

95.8.2 Using the Default CFS/Biopoly Options

CFS/Biopoly searching provides many options that allow you to control how ISIS fits 3D structures to your query. The default CFS/Biopoly options generally provide the best balance between accuracy and speed for most CFS/Biopoly searches. This section explains how the default options affect the CFS/Biopoly search results.

Caution: The CFS options subtly interact with each other and can produce undesirable results if improperly used. If you are not sure how to use the CFS options, we strongly recommend that you use the default CFS options.

When you perform a CFS/Biopoly search, you want to balance the following factors:

*	Quality of fitted 3D structures. You want to retrieve 3D structures that are realistic. That is, you want the fitted 3D structures to be as close as possible to minimum-energy conformations.

*	Quantity of fitted 3D structures. You want to retrieve as many 3D structures as possible that can be fitted to the constraints in your query.

*	Speed of searching.

To achieve the best balance among these three factors, you generally perform a CFS/Biopoly search in two distinct passes:

1.	An initial CFS/Biopoly search. This CFS/Biopoly search ignores non-bonded (van der Waals) interactions between parts of the molecule that are rotated to fit the query, because calculating nonbonded interactions can slow search speeds. You generally use the default CFS/Biopoly options for this search.

2.	An optional bump-checking CFS/Biopoly search over the set of records that you retrieved in the initial CFS/Biopoly search. Bump checking eliminates fitted conformations that have unfavorable nonbonded interactions (that is, conformations in which atoms bump into one another) by calculating nonbonded interactions between parts of the molecule that are rotated to fit the query. The slow search speeds caused by calculating nonbonded interactions are less important, because you perform the search over a smaller set of records.

If you want, you can eliminate the bump-checking CFS/Biopoly search and perform bump checking as you view your search results (view-time bump checking). If any structures on your list have unfavorable nonbonded interactions, ISIS displays these structures without overlaying the query.

When you specify the default CFS options, ISIS does the following during the CFS/Biopoly search:

*	Automatically chooses the more appropriate torsional fitting algorithm (simplex or derivative) for your query.

*	Rotates solely acyclic single bonds that contain at least one atom that is sp3-hybridized. An exception is made for amide bonds, which are not rotated. This definition of a rotatable bond produces a high proportion of fitted structures with low-energy conformations.

*	Ignores nonbonded (van der Waals) interactions between atoms during the search and calculates nonbonded interactions for each fitted structure as you view it (that is, performs bump checking at view time only). This produces faster search speeds, yet allows you to find structures that contain unfavorable nonbonded interactions.

*	Avoids calculating derived data on van der Waals energy difference, torsional degrees of freedom (TDF), and RMS deviation for sorting, viewing, or search cutoffs. These calculations can slow search speeds. For more information on derived data, see Section 95.8.4.

*	Makes at least five attempts to fit (map) the query to each 3D structure in the search domain. This generally produces the maximum number of hits without sacrificing search speed.

If you want to experiment with the CFS options, we strongly recommend that you study Section 95.8.3 so that you can make meaningful choices.

95.8.3 Options for CFS/Biopoly Searching

This section describes each option for the conformational fitting step of CFS/Biopoly searches and explains how that option affects the search.

Fitter Selection

You can use either the simplex or derivative torsional fitter:

*	The simplex torsional fitter was originally developed in conjunction with Molecular Simulations, Inc. and uses the Nelder-Mead sequential simplex minimizer. The fitter uses variable rotation increments to approach a minimum in the objective function. You can use the simplex fitter with any 3D query components, including fixed atoms.

*	The derivative torsional fitter was developed at Zeneca Pharmaceuticals Group and attempts to minimize a differentiable objective function with a combination of first- and second-order optimization techniques. 3D query components are restricted to the following: atoms, ring centroids, angles that are defined by three atoms or ring centroids, and distances that are defined by two atoms or ring centroids.

*	If you do not specify either of these fitters, you can specify [image] Automatic to allow ISIS to choose the fitter automatically. If the query contains solely distances and angles, the automatic setting chooses the derivative fitter. If the query contains 3D constraints other than solely distances and angles, the automatic setting chooses the simplex fitter. Automatic is the default.

The following table shows the components of the 3D query that you can use with the simplex and derivative fitters:

Note: Both the simplex and derivative fitters attempt to optimize the conformation over the range of the distance or angle constraint. For the derivative fitter alone, you can also optimize the fit to the midpoint of the distance or angle constraint. That is, the derivative fitter can not only find a conformation that fits the query, but can also find the conformation that fits the query as closely as possible. If you want ISIS to optimize to the midpoint, however, you must either specify a search cutoff for RMS deviation, or specify that ISIS calculate RMS deviation for sorting and viewing. For more information on derived data and RMS deviation, see Section 95.8.4.

Fitting at Search Time

You can specify that conformational fitting either take place during the search (search-time fitting) or during viewing (view-time fitting). If your query contains solely atoms, centroids, distances, and angles defined by three atoms or ring centroids, you can omit conformational fitting at search time. If you omit conformational fitting at search time, ISIS performs only 2D key screening and upper/lower bounds checking during the CFS/Biopoly search. Consequently, your search speed will increase, but your search results might contain some false hits.

You must perform conformational fitting at search time if you want ISIS to calculate certain types of derived data such as RMS deviation and van der Waals energy difference. For more information on derived data, see Section 95.8.4

Note: You can specify conformational fitting at view time only if your query consists solely of the following 3D query components: atoms, ring centroids, distances, and angles that are defined by three atoms or ring centroids. If your query contains any other 3D query features, you must perform fitting at search time.

By default, conformational fitting occurs at search time.

Maximum Number of Attempted Fittings

The torsional fitter can attempt up to 1000 unique mappings that match the conformation to your query specifications.

In general, the higher the number of attempted fittings, the longer the search, and the more 3D structures you potentially retrieve. If your database has many large, complex 3D structures, you might want to use a low value to maximize your search speed. For typical queries that use interatomic distances, the time that the search requires increases linearly with the value of the distance constraint. However, ISIS generally retrieves very few extra hits when you specify a number greater than 5. Also, a value of 1000 might not assure that ISIS attempts all possible mappings for each 3D model.

You can specify any value from 1 to 1000. The default value is 5. However, if you activate ring flexing, we recommend that you increase this number to at least 25.

Ring Flexing

You can specify that rings of 4 to 24 atoms in size be considered flexible. ISIS considers only rings that are nonaromatic and that contain some rotatable single bonds. For example, a setting of 4 atoms for the minimum ring size and 8 atoms for the maximum ring size allows rotations about all single bonds in 4- to 8-membered rings. The suggested range is between 6 and 24 ring atoms.

When you activate ring flexing with a suitable number of attempted fittings (25 or more), you generally obtain more hits. However, ring flexing also decreases search speed.

If you activate ring flexing, we recommend that you increase the maximum number of attempted fittings to at least 25.

Ring flexing is off by default.

Rotating Single Bonds Between Unsaturated Atoms

You can specify that single bonds between unsaturated centers (for example, biphenyl) be considered flexible. When this option is inactive (the default), ISIS rotates only acyclic single bonds with the following hybridizations:

sp3 - sp3
sp3 - sp2 (except amides and similar bonds)
sp3 - sp

The definition of amides includes the following:

When you activate bond rotation between unsaturated centers, ISIS extends the definition of an acyclic single bond so that bonds with the following hybridizations can rotate:

sp3 - sp3
sp3 - sp2 (except amides and similar bonds)
sp3 - sp
sp2 - sp2
sp2 - sp
sp - sp

If you activate bond rotation between unsaturated centers, you retrieve more hits. However, some of the fitted structures might have higher-energy conformations. Single bond rotation also requires additional calculations that produce slower search speeds.

This option is off by default.

Bump Checking

You can specify that nonbonded atoms within a conformation do not bump into one another. Bump checking calculations use the van der Waals radii of atoms. If you activate bump checking, ISIS takes nonbonded interactions into account during the conformational fitting step.

Note: The additional calculations for bump checking during conformational fitting produce slower search speeds than conformational fitting without bump checking. Consequently, we strongly recommend that you not activate bump checking when you search medium or large databases. Instead, we recommend that you perform the CFS/Biopoly search in two phases. First, perform an initial CFS/Biopoly search without bump checking. Then, set the search domain to the results of the initial CFS/Biopoly search and perform a bump-checking CFS/Biopoly search to remove the invalid hits.

You must perform bump checking during the search when you want to:

*	Specify a search cutoff for van der Waals energy difference.

*	Sort your search results by van der Waals energy difference.

Also we strongly recommend that you perform bump checking during the search when you want to export fitted 3D structures to a CFS SDfile for use in a modeling software program.

For more information on calculations for van der Waals energy difference, see Section 95.8.4.

You can specify bump checking at search time, at view time, at search and view time, or no bump checking at all. The following table shows the four bump checking scenarios that you can specify. The default setting is bump checking at view time (Scenario 1).

We recommend that you use the following guidelines for bump checking:

Scenario 1: This is the default scenario, and is especially useful in improving the speed of your searches over medium or large databases. We recommend that you use this scenario for the initial phase of CFS/Biopoly searching. You retrieve approximately 10 to 15 percent additional false hits in your search results. The bump-checking CFS/Biopoly search removes these false hits.

Scenario 2: You can use this scenario if you want to view the false hits and unacceptable conformations in your search results. You might want to use this information as a way of gathering ideas for creating better search queries, or as a way of determining the contents of your database.

Scenarios 3 and 4: Use either scenario during the bump-checking CFS/Biopoly search, after you have set your search domain to the results of the initial CFS/Biopoly search. We strongly recommend that you do not use this scenario when you search over the entire database.

Note: To sort your search results by van der Waals energy difference (vdW), or to specify a vdW search cutoff, you must perform bump checking at search time. If you want to specify a vdW search cutoff or sort by vdW, you must do so during the bump-checking CFS/Biopoly search.

Global Relaxation

You can specify that ISIS rotate single bonds in other parts of the structure to reduce nonbonded interactions throughout the molecule. When global relaxation is active during bump checking, ISIS finds structures that might be eliminated if ISIS rotated single bonds solely in the region that matched the query. Global relaxation increases the size of your hit list and produces more realistic 3D structures. However, global relaxation also requires additional calculations that can slow search speeds.

To activate global relaxation, bump checking must also be active.

Global relaxation is off by default.

95.8.4 Derived Data for Search Cutoffs, Display, and Sorting

ISIS can derive specific kinds of data from the 3D structures that it retrieves during a CFS/Biopoly search. This derived data is stored in fields that you see in the database definition. You can display this data in a form and use it for sorting, just like data in an actual database field. You can also specify search cutoffs that use the derived data. When you specify a search cutoff, ISIS eliminates any fitted 3D structure for which the calculated value is greater than the value that you specify.

The data in derived fields disappears when you perform another search. Therefore, if you want to sort your search results by derived data, you must perform the sort immediately after the search. The best way to ensure this is to define your sorting instructions before the search and sort your search results automatically after the search. For more information on sorting, see the 3D Sorting Examples Request-A-Document.

ISIS can calculate three types of derived data during the search: torsional degrees of freedom (CFS_TDF field), root mean square deviation (CFS_RMS field), and van der Waals energy difference (CFS_VDW field). A fourth derived data field, CFS_FITTER, stores the name of the fitter (Simplex or Derivative) that ISIS used in the search.

Torsional Degrees of Freedom (TDF)

The number of rotatable bonds on the paths that connect the mapped atoms (Mapped atoms are the atoms in the hit that correspond to atoms in the query). The higher the TDF value, the more flexible is the portion of the 3D structure that maps to your query.

If you specify a search cutoff value, ISIS excludes fitted structures that have more than the value that you specify. We suggest a search cutoff value of 10 rotatable bonds.

To view TDF in a form, connect a form box or table column to MODEL>CFS_TDF.

RMS Deviation

The root mean square value for the goodness-of-fit of the fitted 3D structure to the 3D features that you specified in your query. This is a composite measure of the goodness-of-fit to the query. RMS deviation appears in Angstrom deviations for distances, lines, planes, and fixed atoms and in cosine deviations for angles and dihedrals.

If you specify a search cutoff, ISIS excludes fitted structures that have more than the value that you specify. If you do not specify a search cutoff value, the RMS values that ISIS calculates during the search can range from 0.0 to 1e20 RMS units.

We suggest a search cutoff value of 0.7 RMS units.

You can calculate RMS deviation data for both the simplex and derivative fitters and can view this data in your form. However, we recommend that you not use RMS deviation data to sort your search results unless you also specify the derivative fitter for the CFS/Biopoly search. The RMS deviation values that the simplex fitter calculates are not suitable for sorting because they are not optimized to the midpoint of the distance or angle constraint. Both the simplex and derivative fitters attempt to optimize the conformation over the range of the distance or angle constraint. However, only the derivative fitter optimizes the fit to the midpoint of the distance or angle constraint. That is, the derivative fitter can not only find a conformation that fits the query, but can also find the conformation that fits the query as closely as possible.

Note: If you want the derivative fitter to optimize to the midpoints of the distance and angle constraints, you must specify a search cutoff for RMS deviation and/or specify that ISIS calculate derived data on RMS deviation. If you do not calculate RMS deviation, the derivative fitter optimizes the fitted structure only to the ranges of the distance or angle constraints.

The RMS deviation is expressed as follows:

That is, the RMS deviation is the sum of the RMS deviations of the individual 3D query features. The RMS deviations from each of the individual 3D query features are computed in the following way:

where RMS(p) is the p-th constraint, n is the number of type p constraints in the query, vi is the measured value of constraint i, vu is the upper bound of constraint i, and vl is the lower bound of constraint i.

Note: To calculate RMS deviation, you must specify fitting at search time, and specify a maximum number of attempted fittings that is greater than zero. (If you do not set these CFS options, ISIS sets them for you.)

To view RMS deviation on your form, connect a form box or table column to MODEL>CFS_RMS.

Van der Waals Energy Difference (vdW)

The difference in van der Waals (vdW) nonbonded interaction energy between the fitted conformation and the conformation that is stored in the database. The values of vdW can fall within the range of -10,000 to 1e20 Kcals. If you specify a search cutoff value, ISIS excludes fitted structures that have more than the value that you specify. If you do not specify a search cutoff value, the vdW values that ISIS calculates during the search can range from  -10,000 to 1e20 Kcals. We suggest a search cutoff value of 5 Kcals.

The vdW energy is expressed as the following Lennard-Jones 6-12 potential:

Where Ri and Rj are the van der Waals radii of atoms i and j, respectively, and rij is the measured distance between atoms i and j. Atoms i and j must be at least four bonds apart.

The calculated vdW energy difference can be compared to nonbonded interaction energy in molecular mechanics solely if the fitted 3D structures contain hydrogens. If the stored 3D models in your database do not contain explicit hydrogens, then you must sprout hydrogens at all sites on the fitted 3D structures. For more information on hydrogen sprouting, see Section 95.9.

Note: To calculate data on van der Waals energy difference, you need to specify fitting at search time, bump checking at search time, and a maximum number of attempted fitting that is greater than zero (If you do not set these CFS options, ISIS sets them for you.).

To view van der Waals energy difference on a form, connect a form box or table column to MODEL>CFS_VDW.

Fitter

The type of fitter (Simplex or Derivative) that ISIS used in the CFS/Biopoly search. This data is the same for all records from a CFS/Biopoly search, so it is not suitable for sorting. To view the fitter information on a form, connect a form box or table column to MODEL>CFS_FITTER. For more information on fitters, see Section 95.8.3.

95.8.5 Requirements of CFS/Biopoly Search Options

Some CFS options require specific settings for other CFS/Biopoly search options. If you do not specify the correct values, ISIS changes them automatically. These requirements are listed as follows:

For Bump Checking

To specify bump checking at search time, you must use a value that is greater than zero for the Maximum number of attempted fittings (5 is the suggested value).

You must specify bump checking during the CFS/Biopoly search if you want to:

*	Use van der Waals energy difference to sort your search results or as a search cutoff.

*	Specify global relaxation during the CFS/Biopoly search.

Derived Data For Search Cutoffs, Viewing, and Sorting

To sort your search results by RMS deviation, you must use the derivative fitter. Also, you must specify a value that is greater than zero for the Maximum number of attempted fittings (5 is the suggested value).

To calculate van der Waals energy difference for viewing, for sorting, or as a search cutoff, you must specify the fitter of your choice, enter a value that is greater than zero for the maximum number of attempted fittings (5 is the suggested value). You must also specify bump checking at search time.

95.8.6 Limitations of CFS/Biopoly Searches

In a CFS/Biopoly search, 3D models are filtered out of the results through the three-step searching process. However, the CFS/Biopoly search might overlook 3D structures in the following ways:

Conformational Fitting Limitations

The number of iterations of attempted unique mappings required to retrieve all of the important 3D models might not be enough. Iterations depend on such factors as the number and type of query constraints, the number and mapping locale of atoms in the stored 3D models (especially for 3D models with highly symmetric or many aromatic rings), and the sizes of the 3D models. In addition, the fitter might converge to a false minimum (or local minimum) and reject a valid hit.

You can mitigate this limitation by increasing the maximum number of attempted fittings, allowing ring flexing, and by turning off bump checking. This increases the number of hits but can also produce false hits.

Bump Checking Limitations

During conformational fitting, ISIS rotates solely bonds in the region that matches the query. Therefore, atoms that are outside this region might interfere during the bond rotations and result in the exclusion of a valid hit. You can, however, remove this limitation by activating global relaxation.

95.9 Sprouting Hydrogens and Lone Pairs

3D structures in a molecule database generally don not contain explicit representations of hydrogen atoms. You can, however, create explicit hydrogen atoms on the structures that you retrieve by sprouting hydrogen atoms on 3D structures. You must sprout hydrogen atoms in the following situations:

*	During bump checking. This produces more realistic 3D structures and allows ISIS to correctly calculate data on van der Waals energy difference.

*	To export 3D structures to modeling software programs that cannot sprout hydrogens.

Note: If your query contains lone pairs, sprouting hydrogen atoms also sprouts lone pairs at sites that correspond to lone pairs on the query.

You have three options for displaying hydrogen atoms and lone pairs on the structures that you retrieve:

Off

Prevents sprouting of hydrogens and lone pairs on retrieved 3D structures. Use this setting when the 3D structures in your database already contain sufficient explicit hydrogens and lone pairs, or when your query does not contain explicit hydrogens and lone pairs.

Query Atoms Only

Sprouts hydrogens and lone pairs on retrieved 3D structures, but solely at sites where hydrogens and lone pairs appear on the query. Use this setting during the initial CFS/Biopoly search, for faster searching.

All

Sprouts hydrogens at all sites on retrieved 3D structures, and sprouts lone pairs on retrieved structures at sites where lone pairs appear on the query. In a bump-checking CFS/Biopoly search, use this setting to produce fitted structures that are more realistic. You must use this setting if you want to export 3D structures to a modeling software program that does not sprout hydrogens.

95.10 Guidelines for Revising a CFS/Biopoly Search

If your CFS/Biopoly search did not produce the results that you wanted, use the guidelines in this section to:

*	Increase or decrease the number of 3D structures that you retrieve.

*	Increase and maintain high search speeds.

*	Use multistep search strategies to refine your query.

95.10.1 Increasing or Decreasing the Number of Retrieved Structures

If your CFS/Biopoly search retrieved no records or too few records, you might want to:

*	Conduct a CFS/Biopoly search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, or increase the range of distance, angle, and other 3D constraints. If your query contains a submodel, you can increase the fixed-atom tolerances.

Note: If you make your query more general, search speed can slow significantly. For more information on maintaining high search speeds when refining your query, see Section 95.10.3.

If your CFS/Biopoly search retrieved too many records, you might want to:

*	Refine your query, and then search the same set of records. For example, you can restrict atom or bond variation with explicit atoms or bonds, add additional substructures to the query, narrow the ranges of distance, angle, and other 3D constraints. If your query contains a submodel, you can decrease fixed-atom tolerances.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, then save the list. Next, conduct an additional search for compounds that you want to exclude, and save that list. Then, subtract the second list (the one that contains compounds that you want to exclude) from the first list.

*	Set the search domain to the list of the records retrieved, then conduct another search to reduce the number of records. For example, you could conduct a Search By Form to exclude molecules above a specific molecular weight.

95.10.2 Increasing and Maintaining High Search Speeds

Each of the three steps of a CFS/Biopoly search eliminates false hits in different ways. In addition, the three-step CFS/Biopoly searching process allows you to choose whether you want to perform conformational fitting or bump checking during the search. If you perform the search without these options, your search speed increases, but your hit list will contain additional hits that would otherwise be eliminated.

2D Key Screening

Every structure in a database has a set of binary representations of its structural entities, called keys. The 2D key screening step eliminates all the 3D models in the database that do not contain the structural fragments of your query embedded in them. The presence of structural fragments and their combinations can be represented by one or more of 960 key codes.

To improve search speed, you want your query to contain as many different structural features (that is, to set as many keys) as possible. This eliminates many compounds at the 2D key screening step of CFS/Biopoly searching and thereby reduces the calculations during the slower steps that follow. The following characteristics increase the number of keys in a query:

*	Different atom types

*	Different bond types and connectivity

*	Different types of functional groups

*	Different types and sizes of rings

For example, if you are searching for carbohydrate structures, your query might contain solely carbon and oxygen atoms. You can increase the number of keys by including rings and functional groups that you know are present in the structures that you want, even if they are not part of the pharmacophore.

2D Key Screening and Upper/Lower Bounds Checking

To increase and maintain high search speeds during both the 2D key screening and upper or lower distance screening steps of a CFS/Biopoly search:

*	Use as many 2D query features as possible, and use as many specific 2D query features as possible if they can replace 3D constraints. For example, to define two atoms that are bonded, always draw the bond explicitly instead of using a distance constraint.

*	Draw as precise a query as you can, but use the fewest possible points to define lines and planes. ISIS calculates a best-fit line for three or more points and a best-fit plane for four or more points. Calculations require time.

*	Avoid using fixed atom positions in the query. This query feature slows both the upper or lower distance screening and conformational fitting steps. You might consider replacing fixed-atom positions with a few well-placed distance constraints.

*	Avoid using unconnected atoms in the query. (The slowest atoms are C and A.).

*	Avoid highly symmetrical queries. Highly symmetrical queries cause ISIS to perform the same mappings multiple times, with no increase in the number of hits. You can reduce the symmetry of a query by adding atoms or functional groups that are not part of the pharmacophore, but which you know are present in the molecules that you want.

*	Avoid multiple atom and atom-pair data constraints.

*	When you combine a CFS/Biopoly search and a data search, always conduct the data search before the CFS/Biopoly search. This applies both to text and numeric data in Search By Form (for example, molecular weight < 500 or activity LIKE "%Phosphodiesterase IV%") and to graphical queries that contain 3D atom and atom-pair data (for example, coupling constant >2.0 or charge <-0.31).

*	If your query contains a submodel, turning off the RMS deviation constraint can increase search speed.

Conformational Fitting

To increase and maintain high CFS/Biopoly search speeds in the conformational fitting step:

*	Avoid conformational fitting during the search (search-time fitting). Your results will contain 10 to 15% additional 3D models that are false hits (false positives). To prevent conformational fitting, set the maximum number of attempted fittings to zero.

*	If you need to use the conformational fitter during the search (search time), minimize the number of attempted fittings, and minimize the number of dependent constraints. (One strategy for a first pass of searching is to enter a value of 1 for the maximum number of attempted fittings.)

Note: This procedure might result in missed hits.

*	Avoid bump checking during the search (search-time bump checking). However, this can produce results that contain additional conformations with unfavorable nonbonded interactions (that is, conformations that contain atoms that bump into one another).

*	Use the derivative fitter when possible, especially if you activate ring flexing and bump checking. The derivative fitter is faster for these options.

Note: You can use the derivative fitter if your query contains solely the following 3D query components: atoms, ring centroids, distances, and angles defined by three atoms or ring centroids.

95.10.3 Using Multistep Search Strategies to Refine Your Query

To find the query that best describes the geometry of active compounds, you generally do several CFS/Biopoly searches with increasingly refined queries. You can maintain high CFS/Biopoly search speeds by using query features and CFS options that slow down searches at later stages of query refinement. Then, you search the entire database with your final query.

This approach increases search speed for individual CFS/Biopoly searches during query refinement. Conducting the final search over the entire database allows you to find hits that earlier searches might have missed.

Use the following during the initial stages of multistep search strategies:

*	If your multistep search strategy includes a 2D structural or 3D data search, perform these searches first. For example, you can conduct a Search By Form for a specific therapeutic activity and then conduct a CFS/Biopoly search for topological differences among the models retrieved from the Search By Form.

*	Avoid using exclusion spheres, lines, and planes. These constraints require calculation time that can slow search speeds.

For example, you might consider conducting a CFS/Biopoly search with a query that contains exclusion spheres after a CFS/Biopoly search with a query that does not contain exclusion spheres. You might also consider replacing a planarity constraint with an angle constraint. In the examples below, the query with the angle constraint requires much less search time than the query with the planarity constraint:

*	Avoid using unnecessary explicit hydrogens and lone pairs in the query. ISIS requires sprouting time.

*	Omit the bump-checking CFS/Biopoly search. This increases search speed but increases the number of false hits by as much as 10 - 15%.

*	If you perform a bump-checking CFS/Biopoly search over an extremely large list of structures, first conduct the search without sprouting hydrogens at all sites. Then, set the search domain to the hit list from the first bump-checking CFS/Biopoly search and conduct a second bump-checking CFS/Biopoly search with hydrogens sprouted at all sites. Sprouting hydrogens on retrieved 3D structures can require a long time.

Note: If you want to export your fitted structures to modeling software programs that cannot sprout hydrogens, you must sprout hydrogens during the bump-checking CFS/Biopoly search.

*	Avoid using Rgroups.

*	Avoid ring flexing. Ring flexing calculations can require a long time. Also, you must increase the maximum number of attempted fittings for ring flexing, which also slows search speed.

*	Avoid rotating bonds between unsaturated atoms. Rotating bonds between unsaturated atoms increases the calculation time during conformational fitting.

*	Use a small value for the maximum number of attempted fittings. This avoids spending time to fit flexible and highly functional compounds (for example, peptides) that might not interest you.

*	If you want to use a TDF search cutoff to eliminate highly flexible molecules, use it in the early stages of query development. The TDF cutoff eliminates flexible molecules before conformational fitting begins.

In the later stages of multistep search strategies:

*	During bump checking, sprout hydrogens at all sites on the fitted 3D structure and lone pairs at sites that match the query. This produces fitted structures that are more realistic.

*	Activate global relaxation during bump checking to avoid excluding valid hits. Global relaxation prevents atoms in other parts of the molecule from interfering with bond rotation in the region that fits the query.

*	Create highly specific queries. You can use Rgroups and other query features to create highly specific chemical environments. For examples of how to use Rgroups to create specific chemical environments, see Section 95.4.

95.11 Searching Example 1: Match Residues Within Fitted Biopolymers

This example shows you how to find biopolymers in your 3D database with functional groups whose single bonds are rotated to match the 3D constraints in your query.

95.11.1 Problem

You are interested in potential disulfide bonds. You to want to retrieve all biopolymers from the 3D database that contain sulfur bonds that are between 1 and 4 Angstroms apart. The stored biopolymers contain residues whose single bonds can be rotated to fit your 3D-query constraints.

95.11.2 Approach

Draw two sulfur atoms. Add an explicit hydrogen to each atom, and then specify a distance constraint of 1-4 Angstroms between the sulfur atoms. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MODELSTRUCTURE.

Conduct an CFS/Biopoly search in the remote 3D database of your choice, such as the 3D demo database ISISPDB.

95.11.3 Query

95.11.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for CFS/Biopoly, how to/examples.

95.11.5 Results

You retrieve several biopolymers from the ISISPDB 3D database that contain sulfur atoms that are between 1 and 4 Angstroms apart. The biopolymer Endothelin contains four sulfur atoms: Two of the atoms are 2.024 Angstroms apart and the other two atoms are 2.046 Angstroms apart.

In ISIS/Draw, you can measure the distances and also rotate the biopolymer (either two-dimensionally or three-dimensionally) for a better view.


SSS3D/Biopoly: Searching Concepts/Examples

Click [image] to print Part 1.    Click [image] to go to Part 2.    Click [image] to close this Request-A-Document.

This Request-A-Document contains:

Part 1:

*	Definition of SSS3D/Biopoly Search	98.1

*	Specifying Query Features on Atoms and Bonds	98.2

*	Specifying Rgroup Query Features	98.3

*	Specifying Chemical Environments	98.4

*	Specifying Submodel Components	98.5

*	Specifying 3D Objects and Constraints	98.6

*	Using Receptor Information	98.7

---------------------------------------------------------------------------------------------------------------------

Part 2:

*	Sprouting Hydrogens and Lone Pairs	98.8

*	Removing Flexible Structures	98.9

*	Guidelines for Revising an SSS3D/Biopoly Search	98.10

*	Searching Example 1: Searching For Residues
Within Rigid Biopolymers	98.11

We recommend that you print this Request-A-Document, and then browse through it. For technical reasons, this 45-page Request-A-Document has been divided into two parts. To print Part 1, click the Printer icon at the top of the screen. To print Part 2, first click the Part 2 icon, and then click the Printer icon at the top of the screen.

For step-by-step instructions on conducting an SSS3D/Biopoly search, click here.

98.1 Definition of SSS3D/Biopoly Search

A remote 3D Substructure for Biopolymers (SSS3D/Biopoly) search finds biopolymers that contain your query as a sub-sequence wholly within a larger sequence. (Conduct an SSS3D/Biopoly search rather than an SSS/Biopoly search if you need to specify 3D geometric or 3D data constraints in your query.)

An SSS3D/Biopoly search retrieves solely biopolymers that are stored in the database and does not change the conformations of the biopolymers that you retrieve.

In contrast, a CFS/Biopoly search derives additional conformations by rotating single bonds within the residues of biopolymers that you retrieve. Consequently, CFS/Biopoly can find structures that SSS3D might miss. Use SSS3D/Biopoly when fast search speed is more important than retrieving all possible structures or you want to find biopolymers that are rigid in the region that matches your query.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

98.1.1 What is a Biopolymer?

A biopolymer sequence is a linear chain of connected repeating structures that are called residues. In the following example, you see the residue codes for one of the protein Bovine Insulin, which contains 21 amino acid residues:

H2N-G I V E Q C C A S V C S L Y Q L E N Y C N-COOH

In ISIS, the list of residue codes that you can use are defined in a Residue Map file that uses the structures from a Residue Template file. In this example, the Residue Map file contains the list of 1-letter residue codes for the amino acid residues. MDL provides you with Residue Map files for 1- and 3-letter residue codes for amino acids and for the nucleic acids DNA and RNA. The sequence bond between each residue is formed by the connection of atoms that are specified within the Residue Template file.

If the list of residue codes or their underlying structures are not sufficient for your specific needs, you can edit an existing Residue Map file or Residue Template file or create your own.

To improve the readability of a sequence, you can group residues into suitably sized blocks, limit the number of residues per line, or change the spacing between blocks or residues:

98.1.2 SSS3D/Biopoly Search Queries

An SSS3D/Biopoly search query can contain any of the following 3D query features:

*	Submodel. A submodel is a three-dimensional (3D) representation of a portion of a molecule. A submodel contains two or more atoms in a fixed spatial arrangement (F). You construct a submodel from an existing 3D structure. For example:

For more information on submodels, see Section 98.5.

*	3D geometric constraints. You construct geometric constraints from atoms or from 3D objects such as points, lines, and centroids. For example, you can specify that the centers (centroids) of two rings must be separated by a distance of 2 to 10 Angstroms:

For more information on 3D geometric constraints, see Section 98.6.

*	3D data constraints that you apply to individual atoms or to pairs of atoms. The following example shows calculated values (in Hz) for the ring proton spin-spin couplings of methyl 2-furoate:

For more information on 3D data constraints, see Section 98.6.

An SSS3D/Biopoly search query can also contain 2D query features. A 2D query feature is a restriction on an atom or bond that specifies solely the number, type, and connectivity of atoms in a molecule, without any information on spatial arrangement. 2D query features can include:

*	Query features on atoms and bonds. You can allow or exclude specific atoms at certain locations, allow or exclude specific types of bonds, and so on. For example, the following query specifies that only carbon, nitrogen, or oxygen can be present at a specific position on the ring:

For more information on atom and bond query features, see Section 98.2.

*	Rgroups. An Rgroup query contains a root structure with defined Rgroup substituents attached to it at specific positions. An Rgroup consists of the molecule fragments (substituents) that can attach to the corresponding Rgroup sites on the root. That is, any Rgroup substituents that are members of the Rgroup R1 can attach to any position with the Rgroup label R1.

For example, you can specify that the Rgroup label R1 on the root structure allows a carboxyl group at its position and that R2 allows either a chloride atom or a sulfonic acid group at its position:

For more information on Rgroups, see Section 98.3.

You can combine 2D and 3D query features to specify:

*	Chemical environments. You can use 2D query features to specify chemical environments such as basic nitrogens, acidic centers, hydrogen-bond donors, or hydrogen-bond acceptors on the molecules that you retrieve. For example, the following can be considered a hydrogen-bond donor:

For more information on chemical environments, see Section 98.4.

*	Information on the receptor with which active structures interact. For example, you can specify a distance constraint between a hydrogen-bond donor and a hydrogen-bond acceptor on the receptor:

For more information on queries that use information on the receptor, see Section 98.7.

98.1.3 Choosing Between CFS/Biopoly and SSS3D/Biopoly Searches

An SSS3D/Biopoly search retrieves solely 3D structures that are actually stored in the database. ISIS makes no attempt to make stored 3D structures fit the query by rotating single bonds to create additional conformations.

In contrast, a Conformationally Flexible Substructure (CFS/Biopoly) search finds 3D structures that can be made to fit the query by rotation about single bonds. Consequently, a CFS/Biopoly search might produce conformations that are different from the conformations that are stored in the database. For example:

Your choice of CFS/Biopoly or SSS3D/Biopoly search depends on your 3D searching strategy:

*	Use CFS/Biopoly when your database does not necessarily contain all possible conformations of each 3D structure, and you want to find additional conformations that fit the query. By deriving additional conformations during the search, CFS/Biopoly can find structures that SSS3D/Biopoly might miss.

*	Use SSS3D/Biopoly when your database already contains 3D structures with the desired conformations, and you want to find solely those conformations.

*	Use SSS3D/Biopoly when fast search speed is more important than retrieving all possible conformations. SSS3D/Biopoly is faster than a CFS/Biopoly search. In a preliminary study, for example, you might want to use a series of SSS3D/Biopoly searches to obtain a representative series of compounds and use this information to refine your query. After you have refined your query, you can perform a CFS/Biopoly search that retrieves as many structures as possible.

*	Use SSS3D/Biopoly when you want to find 3D structures that are rigid in the region that matches the query. For example, you might want to export rigid structures to a modeling software program so that you can use them in structure-activity studies. The SSS3D/Biopoly finds both rigid and flexible structures. However, you can remove the flexible structures by conducting a CFS/Biopoly search over the set of records that you retrieve from the SSS3D/Biopoly search. For more information on removing flexible structures, see Section 98.9.

98.2 Specifying Query Features on Atoms and Bonds

A query feature on an atom and/or a bond in a molecule is a restriction that specifies the retrieval of certain types of molecule records from an ISIS/Base database. If you do not use query features, the molecules retrieved contain solely your exact substructure query embedded wholly within them. For example:

You can also define Rgroups that specify a root structure with defined Rgroup substituents attached to it at specific positions. For more information on Rgroups, see Section 98.3.

Caution: Atom and bond query features are 2D query features. 2D query features specify solely the number, type, and connectivity of atoms in a molecule. An SSS3D/Biopoly query should contain at least one component that specifies the spatial distribution of atoms in a 3D structure; otherwise, the query will fail. To specify the spatial distribution of atoms, you can use a submodel with two or more fixed atoms, and/or use 3D geometric constraints such as distances and angles. For more information on submodels, see Section 98.5. For more information on 3D geometric constraints, see Section 98.6.

98.2.1 Definition of Aromaticity

For remote databases: ISIS interprets the following ring systems as aromatic:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:

Note: The bonds of six-membered aromatic ring systems and the perimeter bonds of azulenes are stored as aromatic bonds in the database. The bonds of five-membered aromatic rings, however, are stored as single and double bonds and interpreted as aromatic during a search. The differences between five-membered rings and other types of aromatic rings can cause different search results for five- and six-membered rings/azulenes when you use the following bonds in queries: Single, Double, and Single/Double query bonds. For more information on the Single/Double query bond, see Section 98.2.8.

98.2.2 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except implicit or explicit hydrogens:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

98.2.3 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature: H0

Prohibits the attachment of implicit hydrogens. For example:

98.2.4 Allowing an Unsaturated Atom

Use an atom query feature to specify that an atom is unsaturated, or attached to at least one multiple bond: double, triple, or aromatic.

Atom Query Feature: Unsaturated Atom (u)

Specifies that the atom of your choice is unsaturated. For example, the following query specifies both an unsaturated atom and single or double bonds (the double dashed lines).

98.2.5 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

Use explicit hydrogens to block non-hydrogen attachments on atoms. For example:

Atom Query Feature: Substitution Count of Zero, s0

Specifies that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of an isolated atom.

Atom Query Feature: Substitution Count of One, s1

Specifies that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Two, s2

Specifies that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Three, s3

Specifies that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Four, s4

Specifies that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Five, s5

Specifies that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of at Least Six, s6

Specifies that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count as Drawn, s*

Specifies that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:

98.2.6 Allowing a Specific Number of Ring Bond Attachments

Use atom query features to specify the number of ring bond attachments.

Atom Query Feature: Ring Bond Count of Zero, r0

Specifies that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:

Atom Query Feature: Ring Bond Count of Two, r2

Specifies that the records retrieved have solely two ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of Three, r3

Specifies that the records retrieved have solely three ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of at Least Four, r4

Specifies that the records retrieved have at least four ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count as Drawn, r*

Specifies that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:

98.2.7 Allowing Additional Atoms and/or Bonds in a Chain or a Ring

Use a query feature that is for either atoms or bonds to specify the addition of atoms and/or bonds in a chain or a ring.

Atom or Bond Query Feature: Link Node

Use a link node to specify the addition of variable numbers repeating units (atoms and/or bonds) to a ring or chain. A repeating unit must be attached to two adjacent bonds. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the link node [L1-3]:

Or, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the link node [L1-3]:

98.2.8 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Note: An aromatic query bond hits any bond in all types of aromatic rings: 6-membered ring bonds, 5-membered ring bonds, and azulene perimeter bonds. For more information on the structures that ISIS interprets as aromatic, see Section 98.2.1.

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

Note: A Single/Double query bond does not hit bonds in 6-membered aromatic rings, or perimeter bonds of azulenes, because bonds in these structures are stored in the database as aromatic bonds. However, a Single/Double query bond does hit bonds in 5-membered rings that ISIS interprets as aromatic. For more information on the structures that ISIS interprets as aromatic, see Section 98.2.1.

Bond Query Feature: Single/Aromatic Bond

Specifies either a single or an aromatic bond at that position:

Bond Query Feature: Double/Aromatic Bond

Specifies either a double or an aromatic bond at that position:

98.2.9 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is attached to a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

98.2.10 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is attached to a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

98.3 Specifying Rgroup Query Features

An Rgroup query finds structures that contain your query as a root structure with defined Rgroup substituents attached to it at specific positions. Your query can contain restrictions on the Rgroup substituents, called Rgroup conditions: You can specify the number of Rgroup sites that must be occupied in the records retrieved, specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site, or specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

Your Rgroup query can also contain restrictions on atoms and bonds of the root structure and Rgroup substituents. For example, you can use the atom query feature H(0) to prohibit the attachment of implicit hydrogens on a specific atom in the structures retrieved.

An example of an Rgroup query is as follows:

You can use Rgroups and atom and bond query features to specify chemical environments such as basic nitrogens and acidic centers. For more information on chemical environments, see Section 98.4.

Note: Like atom and bond query features, Rgroup queries contain no information about the spatial distribution of atoms in a 3D structure. An SSS3D/Biopoly query should contain at least one component that specifies the spatial distribution of atoms in a 3D structure; otherwise, the query will fail. To specify the spatial distribution of atoms, you can use a submodel with two or more fixed atoms, and/or use 3D constraints such as distances and angles. For more information on submodels, see Section 98.5. For more information on 3D constraints, see Section 98.6.

98.3.1 The Root Structure

The root structure contains the portion of the structure that does not vary among the structures retrieved. For example, if you want to find 2, 5-Dihydroxypyridine in which the substituent at position 2 can be COOH, CN, or Ph, and the substituent at position 5 can be OH or CH3, the root structure is 2, 5-Dihydroxypyridine with Rgroups (such as R1 and R2):

Rgroups

On the root structure, Rgroups (R1 through R32) are placeholders that designate where the lists of functional groups and atoms that can attach to the root structure. In the example above, the Rgroup R1 designates that the members of the list R1 (the Rgroup substituents) are allowed at position 5 on the root structure. The Rgroup R2 designates that the members of the list R2 (the Rgroup substituents) are allowed at position 2 on the root structure.

Multiple Rgroups at One Position

You can specify multiple Rgroups at a single site on the root structure. For example:

One Rgroup at Multiple Positions

You can specify a single Rgroup (such as R1) at multiple positions on the root structure. For example:

Note: See the section 98.3.3 Rgroup Conditions to restrict the number of Rgroups that must be occupied in the records retrieved. A molecule might not have to satisfy all the Rgroup sites on the root structure to be retrieved. For example, the Rgroup condition R1 > 0 specifies that any molecule in which at least one of the R1 sites is filled by an R1 member will be retrieved. In addition, the Rgroup condition RestH determines whether the unsatisfied sites must be filled with hydrogen atoms or if other molecule fragments are allowed to be attached if they are not on the list.

98.3.2 Rgroup Substituents

Rgroup substituents are the members of the list of Rgroups. You define the Rgroup substituents that you will allow to be found at specified positions in the molecules retrieved. Rgroup substituents can be any structural fragment, including functional groups and single atoms.

In the example below, the Rgroup substituents COOH, CN, or Ph are allowed at position 5 (R1) on the root structure and the Rgroup substituents OH or CH3 are allowed at position 2 (R2) on the root structure:

Attachment Points

An attachment point (marked with an arrow and an asterisk) designates the atom on the Rgroup substituent that is attached to the root structure:

You must designate an attachment point on an Rgroup substituent for each bond that is attached to the substituent. If an Rgroup is attached to two bonds on the root structure, you must designate two attachment points. The bond on the root structure that is marked with double quotes corresponds to the attachment point on the Rgroup substituent that is marked with double quotes. The other attachment point on the Rgroup substituent is marked with a single quote:

Nested Rgroups

A nested Rgroup is an Rgroup that is a placeholder within another Rgroup rather than within the root structure. (You cannot nest an Rgroup any lower than this level.) In the following example, Rgroup R2 is nested within the Rgroup R1:

Nested Rgroups are equivalent to the following structures:

98.3.3 Rgroup Conditions

You can apply restrictions to each Rgroup in your query after you assemble all the Rgroups. The set of restrictions is called the Rgroup conditions.

If you do not apply Rgroup conditions, ISIS assigns the default conditions: Occurrence > 0 and RestH off for each Rgroup.

Occurrence

With the Rgroup condition Occurrence, you can specify the number of Rgroup sites that must be occupied in the records retrieved. For example, the occurrence designation R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved. Type one of the following values in the Occurrence range text box:

Value	Explanation

0	All members of the Rgroup are excluded from the Rgroup site (such as R1). To allow any other Rgroup substituent at the Rgroup site, set RestH to off.

> 0	At least one Rgroup must be satisfied. If RestH is off, any other substituent can attach to unsatisfied sites. If RestH is on, unsatisfied sites must be filled solely by hydrogens.

n	Exactly n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

< n	Less than n number of sites (including zero) must be satisfied. RestH controls substitution at unsatisfied sites.

m - n	Any number of sites falling within the range of m to n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

m,n,...	Any combination of the above expressions, separated by commas. For example: 1, 3-5, 9, >12.

For example, the Rgroup condition R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved.

In another example, the Rgroup condition R1 > 0 and R2 > 0 specifies that an Rgroup substituent from the R1 list AND an Rgroup substituent from the R2 list must occupy at least one site on the root structure in the records retrieved.

Finally, the Rgroup conditions R1 = 1, 3-5, 9, >12 specify that either 1, 3, 4, 5, 9, or more than 12 sites must be satisfied:

RestH

With the Rgroup condition RestH, you can specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site.

An unsatisfied Rgroup site is an Rgroup site on the root structure that does not have an Rgroup member attached: If RestH is off, any functional group or atom may be attached at unsatisfied Rgroup sites on the root structure. If RestH is on, solely hydrogens are allowed to be attached at unsatisfied Rgroup sites on the root structure.

If/Then

With the Rgroup condition If/then, you can specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

For example, If R1 then R2 specifies that if the conditions for R1 are satisfied, then the conditions for R2 must also be satisfied. (If the conditions for R1 are not satisfied, then the conditions for R2 are ignored.) The If/then condition implies that a molecule may be retrieved even though R1 is not satisfied.

In the following query, R1 contains a nitro group and a sulfonic acid group. R2 contains a chlorine atom. The condition If R1 then R2 specifies that if a nitro group or a sulfonic acid group is attached at R1 on the root structure, then a chlorine must also be attached at R2. However, if the R1 site on the root structure does not have either the nitro or the sulfonic acid group (R1 is unsatisfied), then R2 can have any substituent (R2 is ignored):

98.4 Specifying Chemical Environments

You can incorporate specific chemical environments into your SSS3D/Biopoly query. This section contains examples of several chemical environments that you can create with 2D query features and Rgroups. MDL supplies ISIS/Draw sketch files that contain specific types of chemical environments. You can incorporate these structures into your own queries and modify them if desired.

Note: There are two different conventions for defining hydrogen-bond donors and acceptors. This help file uses the definition of a hydrogen-bond donor that is generally used by medicinal chemists. By this convention, the donor of a hydrogen bond is the group to which the hydrogen atom is attached:

An alternative definition of hydrogen-bond donors and acceptors defines a hydrogen-bond donor as the group that provides the lone-pair electrons (LP) to the hydrogen bond.

98.4.1 Acidic Center

The file ACID_CTR.SKC contains the following definition of an acidic center:

This query defines an acidic center as either an oxygen of a carboxylic acid or any nitrogen of an unsubstituted tetrazole.

98.4.2 Basic Nitrogen

BSC_N_1.SKC File

The file BSC_N_1.SKC contains a definition of a basic nitrogen that includes alkyl amines (nsp3), amidines (nsp2), and guanidines (nsp2). This definition excludes other nitrogens such as aromatic nitrogens, aniline-type nitrogens, N=O, NHC=O, and NHC=C:

You can change this definition to fit your needs. For example, if you want to include aromatic nitrogens, delete R2 from the definition.

BSC_N_2.SKC File

The definition of basic nitrogen in the file BSC_N_2.SKC excludes all amides or anilines, and other conjugated systems that reduce the accessibility of the electron pair on the nitrogen atom:

Simple Definition

The following is a simple definition of a basic nitrogen:

98.4.3 Hydrogen-Bond Acceptor

The definition of a hydrogen bond acceptor in the file H_ACCEPT.SKC extends the definition of a basic nitrogen to include oxygen and sulfur:

Note: There are two different conventions for defining hydrogen-bond donors and acceptors. This help file uses the definition of a hydrogen-bond donor that is generally used by medicinal chemists. By this convention, the donor of a hydrogen bond is the group to which the hydrogen atom is attached:

An alternative definition of hydrogen-bond donors and acceptors defines a hydrogen-bond donor as the group that provides the lone-pair electrons (LP) to the hydrogen bond.

98.4.4 Hydrogen-Bond Donor

The following is an example of a hydrogen bond donor:

98.5 Specifying Submodel Components

A submodel is a three-dimensional (3D) representation of a portion of a molecule. A submodel search retrieves all models that contain the same spatial arrangement of atoms as those specified in your submodel query, within specified deviations of the individual and overall atoms.

You specify the spatial arrangement of atoms in a submodel query by fixing the 3D coordinates of two or more atoms in the structure. To create a submodel, you eliminate parts of an existing 3D structure until you have the submodel that you want to find in other 3D structures. Then, you fix the positions of the atoms of your choice. The figure below shows how you create a submodel query from the 3D structure of Trandolapril. Circles mark the atoms in Trandolapril that are fixed (F) in the query:

When you conduct a search with a submodel query, you must specify how closely the 3D structures that you retrieve must match the spatial arrangement of the fixed atoms in the submodel query. Two fixed-atom tolerances specify how closely the structures must match the query:

*	Maximum atomic displacement specifies the maximum allowed deviation of individual fixed atoms in the query from those in the structures that you retrieve.

*	Maximum RMS deviation specifies the maximum allowed deviation of all fixed atoms in the query from fixed atoms in the structures that you retrieve. During the search, ISIS superimposes the fixed atoms in the 3D structure on those of the query and performs a least-squares calculation.

When your query contains fixed atoms, you must specify at least one fixed-atom tolerance for the SSS3D search. You can specify:

*	Maximum atomic displacement only (structures with 2 or 3 fixed atoms)

*	Maximum RMS deviation only (structures with at least 4 fixed atoms)

*	Both fixed-atom tolerances (structures with at least 4 fixed atoms)

Your ISIS Administrator sets default fixed-atom tolerances that your site uses to register 3D structures to the database. These tolerances are specified in the Session Settings file that your ISIS Administrator supplies you. To change fixed-atom tolerances for searching, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for fixed-atom tolerances, changing.

Caution: If you change the default fixed-atom tolerances for searching, you must restore the default fixed-atom tolerances before you register 3D structures.

The following are examples of the 3D structures that you retrieve from a search with the query that you derive from Trandolapril, with both fixed-atom tolerances set to 0.5:

Note: Queries that contain fixed atoms produce slower search speeds than queries that do not contain fixed atoms. As an alternative to the fixed-atom query shown previously, you can use a query with distance constraints that incorporate the fixed-atom tolerances:

You can also use other 3D query features to specify the spatial distribution of atoms within a 3D structure. For more information on distance constraints and other 3D constraints, see Section 98.6.

98.6 3D Objects and Constraints

To specify the spatial relationships between atoms, you can construct 3D objects and create 3D constraints that use atoms and/or constructed 3D objects.

98.6.1 Specifying 3D Objects

You can set geometric constraints on various molecular or constructed geometric 3D objects. These objects can be points, lines, planes, centroids, and normal vectors. Lines, planes, and normal vectors actually extend infinitely, but are represented in ISIS as shown below:

Centroid

Use a centroid to define the geometric center of a set of reference points or atoms of your choice. For example, the centroids in the structures below (depicted by the triangles) are the geometric centers of selected atoms. The centroid on the left is created when all six ring atoms are selected. The centroid on the right is created when the atoms in the box are selected (the box is used here to indicate atoms selected, and does not appear in the query):

Line

Use a line to define a path through two or more reference positions, such as points, atoms, or centroids:

ISIS derives a best-fit line if you use at least three reference positions to define the line. You can specify a linearity constraint for a best-fit line. For more information, see 98.6.2.

Normal

Use a normal to specify a line (with an arrowhead) that is perpendicular to a plane and that passes through a reference position (a point, atom, or centroid):

In ISIS, the direction of the normal arrow is defined by the sequence in which you selected the first three components of the plane. To reverse the direction of the arrow, simply reverse the order in which you define the components of a plane.

Note: If you define a normal through a point that lies in the same plane, the direction of the normal is undefined.

Plane

Use a plane to define a surface that consists of three or more reference positions (points, atoms, or centroids). A plane actually extends infinitely in all directions, but is depicted in ISIS as a small rectangular surface. In the following figure, the entire molecule specifies the plane:

ISIS derives a best-fit plane if you use at least four reference positions to define the line. You can specify a planarity constraint for a best-fit plane. For more information, see Section 98.6.2.

Point

A point is a reference position. You specify a point at a defined distance and direction from a distance reference position (another point, atom or centroid). To specify the direction, you can use either another reference position (called the direction reference position) or a normal.

You can specify the distance from the distance reference position to the direction reference position in Angstroms or as a percentage. Angstrom distances must lie between -100 and +100 Angstroms. Percentage distances must lie between -1,000% and +1,000%, and must include the % sign.

The following example defines a point at a distance of 1.4 Angstroms from a ring nitrogen (the distance reference position) to a ring oxygen (the direction reference position):

The point that you specify need not lie between the two reference positions. The following example shows a point projected 2.8 Angstroms along a line between the nitrogen atom (the distance reference position) and the hydrogen (the direction reference position):

When you use a normal to specify the direction of the point from the distance reference position, you must specify the distance from the distance reference position in Angstroms.

The following example uses a normal to create points that lie 2.8 Angstroms above and below the center of a phenyl ring. The normal is perpendicular to the plane of the ring and passes through the ring centroid. The direction of the normal is undefined, because the point that defines it lies in the plane. To define points on both sides of the plane, use plus (+) and minus (-) signs with Angstrom values to specify the distances:

To create a point on only one side of the plane, specify a distance of 2.8 Angstroms without the plus (+) or minus (-) sign:

Note: You can use points to represent features on a receptor. For examples, see Section 98.7.

98.6.2 Specifying 3D Constraints

You can apply 3D geometric constraints to 3D objects. 3D geometric constraints include distances, angles, dihedral angles, exclusion spheres, linearity constraints, and planarity constraints:

You can also apply 3D data constraints to atoms and atom pairs. Data constraints are listed under “Atom" and “Atom Pair" later in this section.

Distance

You can define a distance constraint between two reference positions (atoms, centroids, or points), from a reference position to a line or normal, or from a reference position to a plane:

The distance constraint is a range of values. Both values in the range must be greater than zero and equal or less than 1,000. The following query has a distance constraint of 2 to 10 Angstroms between the center of a phenol ring and the center of a phenyl ring:

The following are examples of the 3D structures that you retrieve:

Angle

You can define an angle constraint with three points, centroids, or atoms; or with two planes, lines, or normals:

The vertex of the angle for two planes, lines, or normals that do not intersect is an imaginary point. An angle drawn with two lines that do not intersect is equivalent to a dihedral angle through an imaginary line that connects the two lines with the shortest distance.

The angular range that you specify depends on the way that you defined the angle:

*	If you used lines or planes to define the angle, the range must lie between 0 and 90 degrees.

*	If you used three points to define the angle, the range must lie between 0 and 180 degrees.

The following query has a constraint of 30- 65 degrees on the angle between the line between two phenyl centers and a phenol oxygen:

The following are examples of the 3D structures that you retrieve:

Exclusion sphere

Use an exclusion sphere to exclude atoms within a sphere surrounding a reference position (atom, point, or centroid). You specify the radius of the exclusion sphere in Angstroms. The radius of the sphere must be between 0.1 and 20 Angstroms.

Note: You cannot use an SSS3D/Biopoly query that consists solely of exclusion spheres. An SSS3D/Biopoly query must contain at least one of the following 3D query components: distance, angle, dihedral angle, linearity constraint, planarity constraint, or two or more fixed atoms.

For example, the exclusion spheres in the following query ensure that you select compounds that have no atoms within the circled areas of 1.0-Angstrom radius:

The following is an example of the 3D structures that you retrieve (For clarity, the measured values of the four distance constraints are not displayed):

You can specify that other atoms in the query can lie within the exclusion sphere. In the following query, for example, you might want to allow atoms from the carboxyl group within the exclusion spheres, but exclude all other atoms:

To allow other atoms in the query within the exclusion sphere, you must include these atoms in the basis of the exclusion sphere. (The basis of a 3D object or constraint is the set of atoms or 3D objects that comprise the object.) For an exclusion sphere, the basis always includes the reference position at the center of the sphere. To include additional atoms, you edit the basis to include these atoms. For example, you can edit the basis of the exclusion spheres in the previous query to include the carboxyl group. The following are examples of the 3D structures that you retrieve (For clarity, the measured value of one distance constraint is not displayed):

You can also specify that unconnected atoms that are not part of the query can lie within the volume of the exclusion spheres. For example, you might want to allow salt ions or water molecules within the volume of the exclusion sphere. To allow these atoms, you specify the following setting when you create the exclusion sphere: Allow nonquery atoms within exclusion sphere.

Note: You can use exclusion spheres to represent regions on a receptor. For examples, see Section 98.7.

Dihedral

When two planes intersect, a dihedral angle is created from the common vertex of reference positions 1 and 2 and reference positions 3 and 4:

Atoms 1 and 2 are adjacent reference points for the phenol structure, and atoms 3 and 4 are adjacent reference points for the phenyl structure. Reference points 1, 2, and 3 lie along the first plane, and reference points 2, 3, and 4 lie along the second plane. Reference points 2 and 3 share both planes and form the vertex of the dihedral angle.

The angular range that you specify must be between -180 and +180 degrees.

The following query specifies a dihedral angle between two atoms on a phenyl ring and two atoms on a phenol ring:

The following are examples of the 3D structures that you retrieve:

Linearity

You can specify that three or more reference positions (atoms, points, or ring centroids) must lie along the same line. To do this, you specify the maximum average distance (RMS deviation) of the reference positions from the best-fit line derived from the reference positions. The following shows a linearity constraint for all atoms in a trialkene:

The value that you specify must lie between 0 and 1,000.

Planarity

You can specify that four or more reference positions (atoms, points, or ring centroids) must lie along the same plane. To do this, you specify the maximum average distance (RMS deviation) of the reference positions from the best-fit plane derived from the reference positions. The following shows a planarity constraint for all atoms in a benzaldehyde:

The value that you specify must lie between 0 and 1,000.

Atom

Use atom data to specify a data constraint for selected atoms in your query, such as spectroscopic and quantum mechanical data or partial charges. For example:

The atom data constraint specifies the partial charge on the oxygen. Rn specifies that the oxygen must appear in a ring. For more information on Rgroups, see Section 98.2.

Atom-Pair

Use atom-pair data to specify a data constraint between two atoms in your query. For example, you can specify bond order, lower/upper distance constraints, and spectroscopic and quantum mechanical data. The following query specifies values for the ring proton spin-spin couplings of methyl 2-furoate:

98.7 Using Receptor Information

The previous sections showed how to use information about active compounds (that is, information about the pharmacophore) to specify query constraints. This section shows how you can use information about the receptor to specify geometric constraints in your query. Use these examples as a starting point for creating your own queries.

Note: For simplicity, the queries in this section use a simple definition of a basic nitrogen. For more refined definitions of basic nitrogen, see Section 98.4.2.

98.7.1 Specifying Hydrogen-Bond Interactions

You can use projected points and exclusion spheres to represent hydrogen bond donors and acceptors on the receptor.

Note: There are two different conventions for defining hydrogen-bond donors and acceptors. This help file uses the definition of a hydrogen-bond donor that is generally used by medicinal chemists. By this convention, the donor of a hydrogen bond is the group to which the hydrogen atom is attached:

An alternative definition of hydrogen-bond donors and acceptors defines a hydrogen-bond donor as the group that provides the lone-pair electrons (LP) to the hydrogen bond.

Hydrogen-Bond Donor on Receptor

The following example shows how to construct an exclusion sphere that represents a hydrogen-bond donor on the receptor. The hydrogen-bond donor on the receptor forms a hydrogen bond with a complementary hydrogen-bond acceptor on the ligand. You construct the exclusion sphere around a point that you construct from two atoms of the hydrogen-bond acceptor on the ligand.

Hydrogen-Bond Acceptor on Receptor

The following example shows how to construct an exclusion sphere that represents a hydrogen-bond acceptor on the receptor. The hydrogen-bond acceptor on the receptor forms a hydrogen bond with a complementary hydrogen-bond donor on the ligand. You construct the exclusion sphere around a point that you construct from two atoms of the hydrogen-bond donor on the ligand.

Distance Constraint Between Features on the Receptor

Specifying distance constraints between points on the receptor rather than the ligand can produce highly specific queries. For example, suppose you know that the receptor contains a hydrogen bond donor that is 10 - 11.5 Angstroms from a basic nitrogen. The following figure schematically shows how two topologically different drugs can bind to the same receptor site:

If you use a query that uses information about the pharmacophore (ligand-based query), you must specify a large distance range (4 - 10 Angstroms) to retrieve both classes of compounds. The ligand-based query retrieves the compounds that you want, but also retrieves many false hits. If you use a query that uses information about the receptor (receptor-based query), you can specify a much narrower distance range. For example:

The greater specificity in the receptor-based query allows you to retrieve the compounds that you want while eliminating many of the false hits that the ligand-based query might produce.

98.7.2 Specifying Pi-Pi Interactions

You can use projected points and exclusion spheres to represent pi-pi interactions with aromatic groups on the receptor.

Pi-Pi Interactions Alone

Use exclusion spheres above and below aromatic rings that interact with aromatic groups on the receptor. The exclusion spheres eliminate 3D structures with atoms that intrude into the excluded area. Consequently, all 3D structures that you retrieve can contain phenyl rings that can interact freely with the receptor.

To create the exclusion spheres, you create a normal to the plane of the phenyl ring. On that normal, you place a point that is 3.0 Angstroms above (+ 3.0 Angstroms) the plane of the ring, and another point that is 3.0 Angstroms below (- 3.0 Angstroms) the plane of the ring. Around each point, you create exclusion spheres that are 1.5 Angstroms in diameter.

The following query uses exclusion spheres and a distance constraint:

Pi-Pi Interactions With a Distance Constraint

To specify a distance constraint between a lipophilic site and another site on the receptor, use a projected point on one side of an aromatic ring. Use exclusion spheres to eliminate 3D structures that do not permit the aromatic ring to interact freely with the receptor.

To construct the exclusion spheres and projected points, create a normal to the plane of the phenyl ring. On that normal, you place a point that is 2.0 Angstroms above (+ 2.0 Angstroms) the plane of the ring, and another point that is 2.0 Angstroms below (- 2.0 Angstroms) the plane of the ring. On the normal, you place another point that is 3.5 Angstroms from the plane of the ring. Around the two points at 2.0 Angstroms from the aromatic ring, you create exclusion spheres that are 1.5 Angstroms in diameter.

The following query specifies a distance constraint of 6 - 10 Angstroms between a lipophilic site on the receptor and a hydrogen-bond donor on the receptor (for clarity, the query uses a simple definition of a basic nitrogen):

(Continued in Part 2)


Remote SSS3D: Searching Concepts/Examples Part 2

Click [image] to print Part 2.    Click [image] to return to Part 1.    Click [image] to close this Request-A-Document.

To print Part 2 of this Request-A-Document, click the Printer icon at the top of the screen.

To return to Part 1, click the Part 1 icon at the top of the screen.

---------------------------------------------------------------------------------------------------------------------

98.8 Sprouting Hydrogens and Lone Pairs

3D structures in a molecule database generally do not contain explicit representations of hydrogen atoms. You can, however, create explicit hydrogen atoms on the structures that you retrieve by sprouting hydrogen atoms on 3D structures. You must sprout hydrogen atoms when you export 3D structures to modeling software programs that cannot sprout hydrogens.

Note: If your query contains lone pairs, sprouting hydrogen atoms also sprouts lone pairs at sites that correspond to lone pairs on the query.

You have three options for displaying hydrogen atoms and lone pairs on the structures that you retrieve:

Off

Prevents sprouting of hydrogens and lone pairs on retrieved 3D structures. Use this setting when the 3D structures in your database already contain sufficient explicit hydrogens and lone pairs, or when your query does not contain explicit hydrogens and lone pairs.

Query Atoms Only

Sprouts hydrogens and lone pairs on retrieved 3D structures, but solely at sites where hydrogens and lone pairs appear on the query.

All

Sprouts hydrogens at all sites on retrieved 3D structures, and sprouts lone pairs on retrieved structures at sites where lone pairs appear on the query. Use this setting when you want to export 3D structures to a modeling software program that does not sprout hydrogens.

98.9 Removing Flexible Molecules

If you want to use the results of your SSS3D/Biopoly search in structure-activity studies, you might want only structures that are rigid in the region that matches the query. For example:

However, an SSS3D/Biopoly search retrieves both rigid and flexible 3D structures from the database. That is, some structures that you retrieve might be flexible, but have a conformation that fits the query. To remove these flexible structures, you can conduct a Conformationally Flexible Substructure (CFS) search with the following CFS options:

*	Search cutoff for Torsional Degrees of Freedom (TDF) = 1

*	Default values for all other CFS options.

Allowing only one torsional degree of freedom ensures that the region of the structure that matches the query can contain only one rotatable single bond. Rotatable single bonds must meet the following requirements:

*	At least one atom in the bond must be saturated, that is, sp3-hybridized.

*	Amide and similar bonds are not rotatable. The following types of bonds are considered amides:

*	Ring bonds are not rotatable.

98.10 Guidelines for Revising an SSS3D/Biopoly Search

If your SSS3D/Biopoly search did not produce the results that you wanted, use the guidelines in this section to:

*	Increase or decrease the number of 3D structures that you retrieve.

*	Optimize your query for fast search speeds.

*	Use multistep search strategies to refine your query.

98.10.1 Increasing or Decreasing the Number of Retrieved Structures

If your SSS3D/Biopoly search retrieved no records or too few records, you might want to:

*	Conduct an SSS3D/Biopoly search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, or increase the range of distance, angle, and other 3D constraints. If your query contains a submodel, you can increase the fixed-atom tolerances.

Note: If you make your query more general, search speed can decrease significantly. For more information on maintaining high search speeds when refining your query, see Section 98.10.3.

If your SSS3D/Biopoly search retrieved too many records, you might want to:

*	Refine your query, and then search the same set of records. For example, you can restrict atom or bond variation with explicit atoms or bonds, add additional substructures to the query, narrow the ranges of distance, angle, and other 3D constraints. If your query contains a submodel, you can decrease fixed-atom tolerances.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, then save the list. Next, conduct an additional search for compounds that you want to exclude, and save that list. Then, subtract the second list (the one that contains compounds that you want to exclude) from the first list.

*	Set the search domain to the list of the records retrieved, then conduct another search to reduce the number of records. For example, you could conduct a Search By Form to exclude molecules above a specific molecular weight.

If you used a CFS/Biopoly search to remove flexible structures, and that CFS/Biopoly search retrieved no records or too few records, try increasing the TDF to 2, 3, or 4.

If you used a CFS/Biopoly search to remove flexible structures, and that CFS/Biopoly search retrieved too many records, try decreasing the TDF to 0.

98.10.2 Optimizing the Query for Fast Search Speeds

ISIS performs an SSS3D/Biopoly search in two stages:

*	2D and 3D key screening. At this stage, ISIS rapidly eliminates compounds that cannot fit the query constraints. You want ISIS to eliminate as many structures as possible at this stage, before the slower atom-atom mapping process begins.

*	Atom-atom mapping. At this phase, ISIS attempts to match the atoms and constraints in the query to each 3D structure that remains after key screening. ISIS might need to map the query to a potential hit structure many times before it can eliminate it. Therefore, you want to design your query so that ISIS performs as few mappings as possible.

2D and 3D key screening

Every structure in a database has a set of binary representations of its structural entities, called keys. 2D keys code for 2D structural features, while 3D keys code for 3D features such as distances and angles. To improve search speed, you want your query to contain as many different structural features (that is, to set as many keys) as possible. This reduces number of structures that must be processed by atom-atom mapping.

The following characteristics increase the number of 2D keys in a query:

*	Different atom types

*	Different bond types and connectivity

*	Different types of functional groups

*	Different types and sizes of rings

For example, if you are searching for carbohydrate structures, your query might contain solely carbon and oxygen atoms. You can increase the number of keys by including rings and functional groups that you know are present in the structures that you want, even if they are not part of the pharmacophore.

The following are examples of features that increase the number of 3D keys in a query:

*	Distances between two heteroatoms

*	Distances between a heteroatom and a ring centroid, where the ring contains 3 - 7 atoms

*	Distances between two ring centroids

Key screening and atom-atom mapping

To increase and maintain high search speeds during both the key screening and atom mapping phases of an SSS3D/Biopoly search:

*	Draw as precise a query as you can, but use the fewest possible points to define lines and planes. ISIS calculates a best-fit line for three or more points and a best-fit plane for four or more points. These calculations can require a long time.

*	Use as many 2D query features as possible, and use as many specific 2D query features as possible if they can replace 3D constraints. For example, to define two atoms that are close together, draw a bond between them instead of using a distance constraint. This sets more keys an eliminates a 3D constraint.

*	Avoid using unconnected atoms in the query. (The slowest atoms are C and A.). ISIS must check all possible combinations of the specified atoms during the slower atom-atom mapping stage of the search.

*	Construct constraints with ring centroids rather than ring atoms. Ring centroids set additional keys and reduce the number of atom-atom mappings.

*	Avoid highly symmetrical queries. Highly symmetrical queries cause ISIS to perform the same mappings many times, with no increase in the number of hits. You can reduce the symmetry of a query by adding atoms or functional groups that are not part of the pharmacophore, but which you know are present in the molecules that you want.

*	Avoid multiple atom and atom-pair data constraints.

98.10.3 Using Multistep Search Strategies to Refine Your Query

You can refine a query by performing successive searches on a smaller and smaller set of retrieved molecules. You can maintain high search speeds by using query features that slow down searches at later stages of query refinement. Use the following strategies during the initial stages of multistep search strategies:

*	If your multistep search strategy includes a 2D structural or 3D data search, perform these searches first. For example, you can conduct a Search By Form for a specific therapeutic activity and then conduct a SSS3D/Biopoly search for topological differences among the models retrieved from the Search By Form.

*	Avoid using exclusion spheres. Exclusion spheres require calculation time that can decrease search speed. You might consider conducting an SSS3D/Biopoly search with a query that contains exclusion spheres after an SSS3D/Biopoly search with a query that does not contain exclusion spheres.

*	Avoid using lines and planes. ISIS must calculate the RMS deviation for each compound during the search. For example, you might want to substitute an angle constraint for a planarity constraint. In the examples below, the query with the angle constraint runs ten times faster than the query with the planarity constraint:

*	Avoid using unnecessary explicit hydrogens and lone pairs in the query. ISIS requires sprouting time.

*	Avoid using Rgroups.

*	Avoid using residues (superatoms).

98.11 Searching Example 1: Match Residues Within Rigid Biopolymers

This example shows you how to find biopolymers in your 3D database with functional groups that match the 3D constraints in your query (without any rotation of single bonds during the search).

98.11.1 Problem

You are interested in potential disulfide bonds. You to want to retrieve all biopolymers from the 3D database that contain sulfur bonds that are between 1 and 4 Angstroms apart.

98.11.2 Approach

Draw two sulfur atoms. Add an explicit hydrogen to each atom, and then specify a distance constraint of 1-4 Angstroms between the sulfur atoms. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MODELSTRUCTURE.

Conduct a SSS3D/Biopoly search in the remote 3D database of your choice, such as the 3D demo database ISISPDB.

98.11.3 Query

98.11.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS3D/Biopoly, how to/examples.

98.11.5 Results

You retrieve several biopolymers from the ISISPDB 3D database that contain sulfur atoms that are between 1 and 4 Angstroms apart. The biopolymer Endothelin contains four sulfur atoms: Two of the atoms are 2.024 Angstroms apart and the other two atoms are 2.046 Angstroms apart.

In ISIS/Draw, you can measure the distances and also rotate the biopolymer (either two-dimensionally or three-dimensionally) for a better view.


Remote 3DEXACT: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of 3DEXACT Search	25.1

*	Guidelines for Revising the Search	25.2

*	Searching Example: An Exact Match Search with
Loose Tolerance Values	25.3

We recommend that you print this 3-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a 3DEXACT search, click here.

25.1 Definition of 3DEXACT Search

An Exact 3D Search (3DEXACT) retrieves 3D structure records that are duplicates of your 3D search query. The atoms in a duplicate 3D structure have the same 3D coordinates within allowed deviations. The allowed deviations are the two fixed atom tolerances:

*	Maximum atomic displacement specifies the allowed deviation (in Angstroms) of individual atoms in a 3D structure from the corresponding atoms in the query. For example, if the maximum atomic displacement is 0.1, then the displacement between any atom in the retrieved structure and the corresponding atom in the query cannot exceed 0.1 Angstroms.

*	Maximum RMS deviation specifies allowed root-mean-square (RMS) deviation of all the atoms in a 3D structure from the atoms in the query. For example, if the maximum RMS deviation is 0.5, then the root mean square deviation of atoms in the structure from atoms in the query cannot exceed 0.5 Angstroms.

Caution: Your ISIS Administrator establishes default values for the two fixed atom tolerances. ISIS uses these default values to define duplicate 3D structures for registration. If you change the default fixed atom tolerances for searching, you must restore the default values before you register 3D structures to the database. For more information on registration at your site, see your ISIS Administrator.

To conduct an MEXACT search, you must specify at least one fixed-atom tolerance.

25.2 Guidelines for Revising the Search

If your 3DEXACT search retrieved no records or too few records, you might want to:

*	Conduct a 3DEXACT search on a different set of records with the same query.

*	Conduct a 3DEXACT search on the same set of records, and with the same query, but increase the fixed-atom tolerances.

*	Check that search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

25.3 Searching Example: An Exact Match Search with Loose Tolerance Values

The following searching example shows you how to retrieve all models that exactly match the 3D structure query within allowed deviations of their individual and overall atoms.

25.3.1 Problem

You want to retrieve models that can only differ from the following model by 0.1 Angstrom for the fit of each individual atom and by 0.5 Angstrom for the overall fit of the structure:

25.3.2 Approach

Retrieve the 3D structure to use as a query. Use any of the following information to search for the 3D structure in the ISISMX3D database:

*	Name (MOLNAME or MODELNAME): YM-09730-5

*	Model number (MODELREGNO), 97

*	ID number (CORP_ID), MUSE33300717

*	Formula, C27H29N3O6

*	Molecular weight, 491.55.

25.3.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for 3DEXACT, how to/examples.

Fixed-atom tolerances (Step 4): Specify the following fixed-atom tolerances for the search:

Maximum atomic displacement: 0.5

Maximum RMS deviation: 0.5

25.3.4 Results

Only one 3D structure in the ISISMX3D database exactly matches the 3D structure query (within your specified deviation limits for the fit of the individual and overall atoms).

Note: This search works as described if you use the ISISMX3D.DB (Mac=ISISMX3D) database. To obtain the same search results in another database, see your ISIS Administrator. Your database must be configured with the 3D structures at the top level and the 2D structures at a lower level. If your database is configured in reverse order, you will retrieve 2D structures instead of 3D structures for the exact-match search.


Local 3DEXACT: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of 3DEXACT Search	26.1

*	Revising the Search	26.2

*	Searching Example: An Exact Match Search	26.3

We recommend that you print this 2-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a 3DEXACT search, click here.

26.1 Definition of 3DEXACT Search

An Exact 3D Search (3DEXACT) retrieves 3D structure records that exactly match your 3D search query.

Note: A 3DEXACT search in a local database uses solely information on the number, type, and connectivity of atoms in a molecule (2D information), and ignores the spatial arrangement of atoms.

26.2 Guidelines for Revising the Search

If your 3DEXACT search retrieved no records or too few records, you might want to:

*	Conduct a 3DEXACT search on a different set of records with the same query.

*	Check that search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

26.3 Searching Example: An Exact Match Search

The following searching example shows you how to retrieve all 3D structures that exactly match the 3D structure query.

26.3.1 Problem

You want to retrieve 3D structures that exactly match the following 3D structure:

26.3.2 Approach

Retrieve the 3D structure to use as a query. Use any of the following information to search for the model in the LOCALMX database:

*	Name: YM-09730-5

*	Model number, 20

*	ID number, MUSE33300717

*	Formula, C27H29N3O6

*	Molecular weight, 491.55.

26.3.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for 3DEXACT, how to/examples.

26.3.4 Results

Only one model record in the LOCALMX database exactly matches the 3D structure query.

Note: This search works as described if you use the LOCALMX.DB (Mac=LOCALMX) database. To obtain the same search results in another database, see your ISIS Administrator.


Remote SSS3D: Searching Concepts/Examples

Click [image] to print Part 1.    Click [image] to go to Part 2.    Click [image] to close this Request-A-Document.

This Request-A-Document contains:

Part 1:

*	Definition of SSS3D Search	31.1

*	Specifying Query Features on Atoms and Bonds	31.2

*	Specifying Rgroup Query Features	31.3

*	Specifying Chemical Environments	31.4

*	Specifying Submodel Components	31.5

*	Specifying 3D Objects and Constraints	31.6

*	Using Receptor Information	31.7

---------------------------------------------------------------------------------------------------------------------

Part 2:

*	Sprouting Hydrogens and Lone Pairs	31.8

*	Removing Flexible Structures	31.9

*	Guidelines for Revising an SSS3D Search	31.10

*	Searching Example 1: Searching For
Pharmacophores with 3D Substructure Queries 	31.11

*	Searching Example 2: Searching For
Pharmacophores with Submodel Queries 	31.12

We recommend that you print this Request-A-Document, and then browse through it. For technical reasons, this 49-page Request-A-Document has been divided into two parts. To print Part 1, click the Printer icon at the top of the screen. To print Part 2, first click the Part 2 icon, and then click the Printer icon at the top of the screen.

For step-by-step instructions on conducting an SSS3D search, click here.

31.1 Definition of SSS3D Search

A 3D Substructure (SSS3D) search finds 3D structures that contain your query as a substructure wholly within a larger structure. An SSS3D search:

*	Retrieves solely 3D structures that are stored in the database.

*	Does not change the conformations of the 3D structures that you retrieve.

In contrast, a Conformationally Flexible Substructure (CFS) search derives additional conformations by rotating single bonds in the structures that you retrieve. Consequently, CFS can find structures that SSS3D might miss.

Use SSS3D when:

*	Fast search speed is more important than retrieving all possible structures. For example, if you conduct a series of searches to refine your query, you might want to use SSS3D in the early stages of query refinement.

*	You want to find 3D structures that are rigid in the region that matches your query.

31.1.1 SSS3D Search Queries

An SSS3D search query can contain any of the following 3D query features:

*	Submodel. A submodel is a three-dimensional (3D) representation of a portion of a molecule. A submodel contains two or more atoms in a fixed spatial arrangement (F). You construct a submodel from an existing 3D structure. For example:

For more information on submodels, see Section 31.5.

*	3D geometric constraints. You construct geometric constraints from atoms or from 3D objects such as points, lines, and centroids. For example, you can specify that the centers (centroids) of two rings must be separated by a distance of 2 to 10 Angstroms:

For more information on 3D geometric constraints, see Section 31.6.

*	3D data constraints that you apply to individual atoms or to pairs of atoms. The following example shows calculated values (in Hz) for the ring proton spin-spin couplings of methyl 2-furoate:

For more information on 3D data constraints, see Section 31.6.

An SSS3D search query can also contain 2D query features. A 2D query feature is a restriction on an atom or bond that specifies solely the number, type, and connectivity of atoms in a molecule, without any information on spatial arrangement. 2D query features can include:

*	Query features on atoms and bonds. You can allow or exclude specific atoms at certain locations, allow or exclude specific types of bonds, and so on. For example, the following query specifies that only carbon, nitrogen, or oxygen can be present at a specific position on the ring:

For more information on atom and bond query features, see Section 31.2.

*	Rgroups. An Rgroup query contains a root structure with defined Rgroup substituents attached to it at specific positions. An Rgroup consists of the molecule fragments (substituents) that can attach to the corresponding Rgroup sites on the root. That is, any Rgroup substituents that are members of the Rgroup R1 can attach to any position with the Rgroup label R1.

For example, you can specify that the Rgroup label R1 on the root structure allows a carboxyl group at its position and that R2 allows either a chloride atom or a sulfonic acid group at its position:

For more information on Rgroups, see Section 31.3.

You can combine 2D and 3D query features to specify:

*	Chemical environments. You can use 2D query features to specify chemical environments such as basic nitrogens, acidic centers, hydrogen-bond donors, or hydrogen-bond acceptors on the molecules that you retrieve. For example, the following can be considered a hydrogen-bond donor:

For more information on chemical environments, see Section 31.4.

*	Information on the receptor with which active structures interact. For example, you can specify a distance constraint between a hydrogen-bond donor and a hydrogen-bond acceptor on the receptor:

For more information on queries that use information on the receptor, see Section 31.7.

31.1.2 Choosing Between CFS and SSS3D Searches

An SSS3D search retrieves solely 3D structures that are actually stored in the database. ISIS makes no attempt to make stored 3D structures fit the query by rotating single bonds to create additional conformations.

In contrast, a Conformationally Flexible Substructure (CFS) search finds 3D structures that can be made to fit the query by rotation about single bonds. Consequently, a CFS search might produce conformations that are different from the conformations that are stored in the database. For example:

Your choice of CFS or SSS3D search depends on your 3D searching strategy:

*	Use CFS when your database does not necessarily contain all possible conformations of each 3D structure, and you want to find additional conformations that fit the query. By deriving additional conformations during the search, CFS can find structures that SSS3D might miss.

*	Use SSS3D when your database already contains 3D structures with the desired conformations, and you want to find solely those conformations.

*	Use SSS3D when fast search speed is more important than retrieving all possible conformations. SSS3D is faster than a CFS search. In a preliminary study, for example, you might want to use a series of SSS3D searches to obtain a representative series of compounds and use this information to refine your query. After you have refined your query, you can perform a CFS search that retrieves as many structures as possible.

*	Use SSS3D when you want to find 3D structures that are rigid in the region that matches the query. For example, you might want to export rigid structures to a modeling software program so that you can use them in structure-activity studies. The SSS3D finds both rigid and flexible structures. However, you can remove the flexible structures by conducting a CFS search over the set of records that you retrieve from the SSS3D search. For more information on removing flexible structures, see Section 31.9.

31.2 Specifying Query Features on Atoms and Bonds

A query feature on an atom and/or a bond in a molecule is a restriction that specifies the retrieval of certain types of molecule records from an ISIS/Base database. If you do not use query features, the molecules retrieved contain solely your exact substructure query embedded wholly within them. For example:

You can also define Rgroups that specify a root structure with defined Rgroup substituents attached to it at specific positions. For more information on Rgroups, see Section 31.3.

Caution: Atom and bond query features are 2D query features. 2D query features specify solely the number, type, and connectivity of atoms in a molecule. An SSS3D query should contain at least one component that specifies the spatial distribution of atoms in a 3D structure; otherwise, the query will fail. To specify the spatial distribution of atoms, you can use a submodel with two or more fixed atoms, and/or use 3D geometric constraints such as distances and angles. For more information on submodels, see Section 31.5. For more information on 3D geometric constraints, see Section 31.6.

31.2.1 Definition of Aromaticity

For remote databases: ISIS interprets the following ring systems as aromatic:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:

Note: The bonds of six-membered aromatic ring systems and the perimeter bonds of azulenes are stored as aromatic bonds in the database. The bonds of five-membered aromatic rings, however, are stored as single and double bonds and interpreted as aromatic during a search. The differences between five-membered rings and other types of aromatic rings can cause different search results for five- and six-membered rings/azulenes when you use the following bonds in queries: Single, Double, and Single/Double query bonds. For more information on the Single/Double query bond, see Section 31.2.8.

31.2.2 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except implicit or explicit hydrogens:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

31.2.3 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of implicit hydrogens. For example:

31.2.4 Allowing an Unsaturated Atom

Use an atom query feature to specify that an atom is unsaturated, or attached to at least one multiple bond: double, triple, or aromatic.

Atom Query Feature: Unsaturated Atom (u)

Specifies that the atom of your choice is unsaturated. For example, the following query specifies both an unsaturated atom and single or double bonds (the double dashed lines).

31.2.5 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

Use explicit hydrogens to block non-hydrogen attachments on atoms. For example:

Atom Query Feature: Substitution Count of Zero, s0

Specifies that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of an isolated atom.

Atom Query Feature: Substitution Count of One, s1

Specifies that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Two, s2

Specifies that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Three, s3

Specifies that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Four, s4

Specifies that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Five, s5

Specifies that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of at Least Six, s6

Specifies that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count as Drawn, s*

Specifies that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:

31.2.6 Allowing a Specific Number of Ring Bond Attachments

Use atom query features to specify the number of ring bond attachments.

Atom Query Feature: Ring Bond Count of Zero, r0

Specifies that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:

Atom Query Feature: Ring Bond Count of Two, r2

Specifies that the records retrieved have solely two ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of Three, r3

Specifies that the records retrieved have solely three ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of at Least Four, r4

Specifies that the records retrieved have at least four ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count as Drawn, r*

Specifies that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:

31.2.7 Allowing Additional Atoms and/or Bonds in a Chain or a Ring

Use a query feature that is for either atoms or bonds to specify the addition of atoms and/or bonds in a chain or a ring.

Atom or Bond Query Feature: Link Node

Use a link node to specify the addition of variable numbers repeating units (atoms and/or bonds) to a ring or chain. A repeating unit must be attached to two adjacent bonds. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the link node [L1-3]:

Or, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the link node [L1-3]:

31.2.8 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Note: An aromatic query bond hits any bond in all types of aromatic rings: 6-membered ring bonds, 5-membered ring bonds, and azulene perimeter bonds. For more information on the structures that ISIS interprets as aromatic, see Section 31.2.1.

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

Note: A Single/Double query bond does not hit bonds in 6-membered aromatic rings, or perimeter bonds of azulenes, because bonds in these structures are stored in the database as aromatic bonds. However, a Single/Double query bond does hit bonds in 5-membered rings that ISIS interprets as aromatic. For more information on the structures that ISIS interprets as aromatic, see Section 31.2.1.

Bond Query Feature: Single/Aromatic Bond

Specifies either a single or an aromatic bond at that position:

Bond Query Feature: Double/Aromatic Bond

Specifies either a double or an aromatic bond at that position:

31.2.9 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is attached to a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

31.2.10 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is attached to a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

31.3 Specifying Rgroup Query Features

An Rgroup query finds structures that contain your query as a root structure with defined Rgroup substituents attached to it at specific positions. Your query can contain restrictions on the Rgroup substituents, called Rgroup conditions: You can specify the number of Rgroup sites that must be occupied in the records retrieved, specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site, or specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

Your Rgroup query can also contain restrictions on atoms and bonds of the root structure and Rgroup substituents. For example, you can use the atom query feature H(0) to prohibit the attachment of implicit hydrogens on a specific atom in the structures retrieved.

An example of an Rgroup query is as follows:

You can use Rgroups and atom and bond query features to specify chemical environments such as basic nitrogens and acidic centers. For more information on chemical environments, see Section 31.4.

Note: Like atom and bond query features, Rgroup queries contain no information about the spatial distribution of atoms in a 3D structure. An SSS3D query should contain at least one component that specifies the spatial distribution of atoms in a 3D structure; otherwise, the query will fail. To specify the spatial distribution of atoms, you can use a submodel with two or more fixed atoms, and/or use 3D constraints such as distances and angles. For more information on submodels, see Section 31.5. For more information on 3D constraints, see Section 31.6.

31.3.1 The Root Structure

The root structure contains the portion of the structure that does not vary among the structures retrieved. For example, if you want to find 2, 5-Dihydroxypyridine in which the substituent at position 2 can be COOH, CN, or Ph, and the substituent at position 5 can be OH or CH3, the root structure is 2, 5-Dihydroxypyridine with Rgroups (such as R1 and R2):

Rgroups

On the root structure, Rgroups (R1 through R32) are placeholders that designate where the lists of functional groups and atoms that can attach to the root structure. In the example above, the Rgroup R1 designates that the members of the list R1 (the Rgroup substituents) are allowed at position 5 on the root structure. The Rgroup R2 designates that the members of the list R2 (the Rgroup substituents) are allowed at position 2 on the root structure.

Multiple Rgroups at One Position

You can specify multiple Rgroups at a single site on the root structure. For example:

One Rgroup at Multiple Positions

You can specify a single Rgroup (such as R1) at multiple positions on the root structure. For example:

Note: See the section 31.3.3 Rgroup Conditions to restrict the number of Rgroups that must be occupied in the records retrieved. A molecule might not have to satisfy all the Rgroup sites on the root structure to be retrieved. For example, the Rgroup condition R1 > 0 specifies that any molecule in which at least one of the R1 sites is filled by an R1 member will be retrieved. In addition, the Rgroup condition RestH determines whether the unsatisfied sites must be filled with hydrogen atoms or if other molecule fragments are allowed to be attached if they are not on the list.

31.3.2 Rgroup Substituents

Rgroup substituents are the members of the list of Rgroups. You define the Rgroup substituents that you will allow to be found at specified positions in the molecules retrieved. Rgroup substituents can be any structural fragment, including functional groups and single atoms.

In the example below, the Rgroup substituents COOH, CN, or Ph are allowed at position 5 (R1) on the root structure and the Rgroup substituents OH or CH3 are allowed at position 2 (R2) on the root structure:

Attachment Points

An attachment point (marked with an arrow and an asterisk) designates the atom on the Rgroup substituent that is attached to the root structure:

You must designate an attachment point on an Rgroup substituent for each bond that is attached to the substituent. If an Rgroup is attached to two bonds on the root structure, you must designate two attachment points. The bond on the root structure that is marked with double quotes corresponds to the attachment point on the Rgroup substituent that is marked with double quotes. The other attachment point on the Rgroup substituent is marked with a single quote:

Nested Rgroups

A nested Rgroup is an Rgroup that is a placeholder within another Rgroup rather than within the root structure. (You cannot nest an Rgroup any lower than this level.) In the following example, Rgroup R2 is nested within the Rgroup R1:

Nested Rgroups are equivalent to the following structures:

31.3.3 Rgroup Conditions

You can apply restrictions to each Rgroup in your query after you assemble all the Rgroups. The set of restrictions is called the Rgroup conditions.

If you do not apply Rgroup conditions, ISIS assigns the default conditions: Occurrence > 0 and RestH off for each Rgroup.

Occurrence

With the Rgroup condition Occurrence, you can specify the number of Rgroup sites that must be occupied in the records retrieved. For example, the occurrence designation R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved. Type one of the following values in the Occurrence range text box:

Value	Explanation

0	All members of the Rgroup are excluded from the Rgroup site (such as R1). To allow any other Rgroup substituent at the Rgroup site, set RestH to off.

> 0	At least one Rgroup must be satisfied. If RestH is off, any other substituent can attach to unsatisfied sites. If RestH is on, unsatisfied sites must be filled solely by hydrogens.

n	Exactly n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

< n	Less than n number of sites (including zero) must be satisfied. RestH controls substitution at unsatisfied sites.

m - n	Any number of sites falling within the range of m to n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

m,n,...	Any combination of the above expressions, separated by commas. For example: 1, 3-5, 9, >12.

For example, the Rgroup condition R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved.

In another example, the Rgroup condition R1 > 0 and R2 > 0 specifies that an Rgroup substituent from the R1 list AND an Rgroup substituent from the R2 list must occupy at least one site on the root structure in the records retrieved.

Finally, the Rgroup conditions R1 = 1, 3-5, 9, >12 specify that either 1, 3, 4, 5, 9, or more than 12 sites must be satisfied:

RestH

With the Rgroup condition RestH, you can specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site.

An unsatisfied Rgroup site is an Rgroup site on the root structure that does not have an Rgroup member attached: If RestH is off, any functional group or atom may be attached at unsatisfied Rgroup sites on the root structure. If RestH is on, solely hydrogens are allowed to be attached at unsatisfied Rgroup sites on the root structure.

If/Then

With the Rgroup condition If/then, you can specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

For example, If R1 then R2 specifies that if the conditions for R1 are satisfied, then the conditions for R2 must also be satisfied. (If the conditions for R1 are not satisfied, then the conditions for R2 are ignored.) The If/then condition implies that a molecule may be retrieved even though R1 is not satisfied.

In the following query, R1 contains a nitro group and a sulfonic acid group. R2 contains a chlorine atom. The condition If R1 then R2 specifies that if a nitro group or a sulfonic acid group is attached at R1 on the root structure, then a chlorine must also be attached at R2. However, if the R1 site on the root structure does not have either the nitro or the sulfonic acid group (R1 is unsatisfied), then R2 can have any substituent (R2 is ignored):

31.4 Specifying Chemical Environments

You can incorporate specific chemical environments into your SSS3D query. This section contains examples of several chemical environments that you can create with 2D query features and Rgroups. MDL supplies ISIS/Draw sketch files that contain specific types of chemical environments. You can incorporate these structures into your own queries and modify them if desired.

Note: There are two different conventions for defining hydrogen-bond donors and acceptors. This help file uses the definition of a hydrogen-bond donor that is generally used by medicinal chemists. By this convention, the donor of a hydrogen bond is the group to which the hydrogen atom is attached:

An alternative definition of hydrogen-bond donors and acceptors defines a hydrogen-bond donor as the group that provides the lone-pair electrons (LP) to the hydrogen bond.

31.4.1 Acidic Center

The file ACID_CTR.SKC contains the following definition of an acidic center:

This query defines an acidic center as either an oxygen of a carboxylic acid or any nitrogen of an unsubstituted tetrazole.

31.4.2 Basic Nitrogen

BSC_N_1.SKC File

The file BSC_N_1.SKC contains a definition of a basic nitrogen that includes alkyl amines (nsp3), amidines (nsp2), and guanidines (nsp2). This definition excludes other nitrogens such as aromatic nitrogens, aniline-type nitrogens, N=O, NHC=O, and NHC=C:

You can change this definition to fit your needs. For example, if you want to include aromatic nitrogens, delete R2 from the definition.

BSC_N_2.SKC File

The definition of basic nitrogen in the file BSC_N_2.SKC excludes all amides or anilines, and other conjugated systems that reduce the accessibility of the electron pair on the nitrogen atom:

Simple Definition

The following is a simple definition of a basic nitrogen:

31.4.3 Hydrogen-Bond Acceptor

The definition of a hydrogen bond acceptor in the file H_ACCEPT.SKC extends the definition of a basic nitrogen to include oxygen and sulfur:

31.4.4 Hydrogen-Bond Donor

The following is an example of a hydrogen bond donor:

31.5 Specifying Submodel Components

A submodel is a three-dimensional (3D) representation of a portion of a molecule. A submodel search retrieves all models that contain the same spatial arrangement of atoms as those specified in your submodel query, within specified deviations of the individual and overall atoms.

You specify the spatial arrangement of atoms in a submodel query by fixing the 3D coordinates of two or more atoms in the structure. To create a submodel, you eliminate parts of an existing 3D structure until you have the submodel that you want to find in other 3D structures. Then, you fix the positions of the atoms of your choice. The figure below shows how you create a submodel query from the 3D structure of Trandolapril. Circles mark the atoms in Trandolapril that are fixed (F) in the query:

When you conduct a search with a submodel query, you must specify how closely the 3D structures that you retrieve must match the spatial arrangement of the fixed atoms in the submodel query. Two fixed-atom tolerances specify how closely the structures must match the query:

*	Maximum atomic displacement specifies the maximum allowed deviation of individual fixed atoms in the query from those in the structures that you retrieve.

*	Maximum RMS deviation specifies the maximum allowed deviation of all fixed atoms in the query from fixed atoms in the structures that you retrieve. During the search, ISIS superimposes the fixed atoms in the 3D structure on those of the query and performs a least-squares calculation.

When your query contains fixed atoms, you must specify at least one fixed-atom tolerance for the SSS3D search. You can specify:

*	Maximum atomic displacement only (structures with 2 or 3 fixed atoms)

*	Maximum RMS deviation only (structures with at least 4 fixed atoms)

*	Both fixed-atom tolerances (structures with at least 4 fixed atoms)

Your ISIS Administrator sets default fixed-atom tolerances that your site uses to register 3D structures to the database. These tolerances are specified in the Session Settings file that your ISIS Administrator supplies you. To change fixed-atom tolerances for searching, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for fixed-atom tolerances, changing.

Caution: If you change the default fixed-atom tolerances for searching, you must restore the default fixed-atom tolerances before you register 3D structures.

The following are examples of the 3D structures that you retrieve from a search with the query that you derive from Trandolapril, with both fixed-atom tolerances set to 0.5:

Note: Queries that contain fixed atoms produce slower search speeds than queries that do not contain fixed atoms. As an alternative to the fixed-atom query shown previously, you can use a query with distance constraints that incorporate the fixed-atom tolerances:

You can also use other 3D query features to specify the spatial distribution of atoms within a 3D structure. For more information on distance constraints and other 3D constraints, see Section 31.6.

31.6 3D Objects and Constraints

To specify the spatial relationships between atoms, you can construct 3D objects and create 3D constraints that use atoms and/or constructed 3D objects.

31.6.1 Specifying 3D Objects

You can set geometric constraints on various molecular or constructed geometric 3D objects. These objects can be points, lines, planes, centroids, and normal vectors. Lines, planes, and normal vectors actually extend infinitely, but are represented in ISIS as shown below:

Centroid

Use a centroid to define the geometric center of a set of reference points or atoms of your choice. For example, the centroids in the structures below (depicted by the triangles) are the geometric centers of selected atoms. The centroid on the left is created when all six ring atoms are selected. The centroid on the right is created when the atoms in the box are selected (the box is used here to indicate atoms selected, and does not appear in the query):

Line

Use a line to define a path through two or more reference positions, such as points, atoms, or centroids:

ISIS derives a best-fit line if you use at least three reference positions to define the line. You can specify a linearity constraint for a best-fit line. For more information, see 31.6.2.

Normal

Use a normal to specify a line (with an arrowhead) that is perpendicular to a plane and that passes through a reference position (a point, atom, or centroid):

In ISIS, the direction of the normal arrow is defined by the sequence in which you selected the first three components of the plane. To reverse the direction of the arrow, simply reverse the order in which you define the components of a plane.

Note: If you define a normal through a point that lies in the same plane, the direction of the normal is undefined.

Plane

Use a plane to define a surface that consists of three or more reference positions (points, atoms, or centroids). A plane actually extends infinitely in all directions, but is depicted in ISIS as a small rectangular surface. In the following figure, the entire molecule specifies the plane:

ISIS derives a best-fit plane if you use at least four reference positions to define the line. You can specify a planarity constraint for a best-fit plane. For more information, see Section 31.6.2.

Point

A point is a reference position. You specify a point at a defined distance and direction from a distance reference position (another point, atom or centroid). To specify the direction, you can use either another reference position (called the direction reference position) or a normal.

You can specify the distance from the distance reference position to the direction reference position in Angstroms or as a percentage. Angstrom distances must lie between -100 and +100 Angstroms. Percentage distances must lie between -1,000% and +1,000%, and must include the % sign.

The following example defines a point at a distance of 1.4 Angstroms from a ring nitrogen (the distance reference position) to a ring oxygen (the direction reference position):

The point that you specify need not lie between the two reference positions. The following example shows a point projected 2.8 Angstroms along a line between the nitrogen atom (the distance reference position) and the hydrogen (the direction reference position):

When you use a normal to specify the direction of the point from the distance reference position, you must specify the distance from the distance reference position in Angstroms.

The following example uses a normal to create points that lie 2.8 Angstroms above and below the center of a phenyl ring. The normal is perpendicular to the plane of the ring and passes through the ring centroid. The direction of the normal is undefined, because the point that defines it lies in the plane. To define points on both sides of the plane, use plus (+) and minus (-) signs with Angstrom values to specify the distances:

To create a point on only one side of the plane, specify a distance of 2.8 Angstroms without the plus (+) or minus (-) sign:

Note: You can use points to represent features on a receptor. For examples, see Section 31.7.

31.6.2 Specifying 3D Constraints

You can apply 3D geometric constraints to 3D objects. 3D geometric constraints include distances, angles, dihedral angles, exclusion spheres, linearity constraints, and planarity constraints:

You can also apply 3D data constraints to atoms and atom pairs. Data constraints are listed under “Atom" and “Atom Pair" later in this section.

Distance

You can define a distance constraint between two reference positions (atoms, centroids, or points), from a reference position to a line or normal, or from a reference position to a plane:

The distance constraint is a range of values. Both values in the range must be greater than zero and equal or less than 1,000. The following query has a distance constraint of 2 to 10 Angstroms between the center of a phenol ring and the center of a phenyl ring:

The following are examples of the 3D structures that you retrieve:

Angle

You can define an angle constraint with three points, centroids, or atoms; or with two planes, lines, or normals:

The vertex of the angle for two planes, lines, or normals that do not intersect is an imaginary point. An angle drawn with two lines that do not intersect is equivalent to a dihedral angle through an imaginary line that connects the two lines with the shortest distance.

The angular range that you specify depends on the way that you defined the angle:

*	If you used lines or planes to define the angle, the range must lie between 0 and 90 degrees.

*	If you used three points to define the angle, the range must lie between 0 and 180 degrees.

The following query has a constraint of 30- 65 degrees on the angle between the line between two phenyl centers and a phenol oxygen:

The following are examples of the 3D structures that you retrieve:

Exclusion sphere

Use an exclusion sphere to exclude atoms within a sphere surrounding a reference position (atom, point, or centroid). You specify the radius of the exclusion sphere in Angstroms. The radius of the sphere must be between 0.1 and 20 Angstroms.

Note: You cannot use an SSS3D query that consists solely of exclusion spheres. An SSS3D query must contain at least one of the following 3D query components: distance, angle, dihedral angle, linearity constraint, planarity constraint, or two or more fixed atoms.

For example, the exclusion spheres in the following query ensure that you select compounds that have no atoms within the circled areas of 1.0-Angstrom radius:

The following is an example of the 3D structures that you retrieve (For clarity, the measured values of the four distance constraints are not displayed):

You can specify that other atoms in the query can lie within the exclusion sphere. In the following query, for example, you might want to allow atoms from the carboxyl group within the exclusion spheres, but exclude all other atoms:

To allow other atoms in the query within the exclusion sphere, you must include these atoms in the basis of the exclusion sphere. (The basis of a 3D object or constraint is the set of atoms or 3D objects that comprise the object.) For an exclusion sphere, the basis always includes the reference position at the center of the sphere. To include additional atoms, you edit the basis to include these atoms. For example, you can edit the basis of the exclusion spheres in the previous query to include the carboxyl group. The following are examples of the 3D structures that you retrieve (For clarity, the measured value of one distance constraint is not displayed):

You can also specify that unconnected atoms that are not part of the query can lie within the volume of the exclusion spheres. For example, you might want to allow salt ions or water molecules within the volume of the exclusion sphere. To allow these atoms, you specify the following setting when you create the exclusion sphere: Allow nonquery atoms within exclusion sphere.

Note: You can use exclusion spheres to represent regions on a receptor. For examples, see Section 31.7.

Dihedral

When two planes intersect, a dihedral angle is created from the common vertex of reference positions 1 and 2 and reference positions 3 and 4:

Atoms 1 and 2 are adjacent reference points for the phenol structure, and atoms 3 and 4 are adjacent reference points for the phenyl structure. Reference points 1, 2, and 3 lie along the first plane, and reference points 2, 3, and 4 lie along the second plane. Reference points 2 and 3 share both planes and form the vertex of the dihedral angle.

The angular range that you specify must be between -180 and +180 degrees.

The following query specifies a dihedral angle between two atoms on a phenyl ring and two atoms on a phenol ring:

The following are examples of the 3D structures that you retrieve:

Linearity

You can specify that three or more reference positions (atoms, points, or ring centroids) must lie along the same line. To do this, you specify the maximum average distance (RMS deviation) of the reference positions from the best-fit line derived from the reference positions. The following shows a linearity constraint for all atoms in a trialkene:

The value that you specify must lie between 0 and 1,000.

Planarity

You can specify that four or more reference positions (atoms, points, or ring centroids) must lie along the same plane. To do this, you specify the maximum average distance (RMS deviation) of the reference positions from the best-fit plane derived from the reference positions. The following shows a planarity constraint for all atoms in a benzaldehyde:

The value that you specify must lie between 0 and 1,000.

Atom

Use atom data to specify a data constraint for selected atoms in your query, such as spectroscopic and quantum mechanical data or partial charges. For example:

The atom data constraint specifies the partial charge on the oxygen. Rn specifies that the oxygen must appear in a ring. For more information on Rgroups, see Section 31.2.

Atom-Pair

Use atom-pair data to specify a data constraint between two atoms in your query. For example, you can specify bond order, lower/upper distance constraints, and spectroscopic and quantum mechanical data. The following query specifies values for the ring proton spin-spin couplings of methyl 2-furoate:

31.7 Using Receptor Information

The previous sections showed how to use information about active compounds (that is, information about the pharmacophore) to specify query constraints. This section shows how you can use information about the receptor to specify geometric constraints in your query. Use these examples as a starting point for creating your own queries.

Note: For simplicity, the queries in this section use a simple definition of a basic nitrogen. For more refined definitions of basic nitrogen, see Section 31.4.2.

31.7.1 Specifying Hydrogen-Bond Interactions

You can use projected points and exclusion spheres to represent hydrogen bond donors and acceptors on the receptor.

Note: There are two different conventions for defining hydrogen-bond donors and acceptors. This help file uses the definition of a hydrogen-bond donor that is generally used by medicinal chemists. By this convention, the donor of a hydrogen bond is the group to which the hydrogen atom is attached:

An alternative definition of hydrogen-bond donors and acceptors defines a hydrogen-bond donor as the group that provides the lone-pair electrons (LP) to the hydrogen bond.

Hydrogen-Bond Donor on Receptor

The following example shows how to construct an exclusion sphere that represents a hydrogen-bond donor on the receptor. The hydrogen-bond donor on the receptor forms a hydrogen bond with a complementary hydrogen-bond acceptor on the ligand. You construct the exclusion sphere around a point that you construct from two atoms of the hydrogen-bond acceptor on the ligand.

Hydrogen-Bond Acceptor on Receptor

The following example shows how to construct an exclusion sphere that represents a hydrogen-bond acceptor on the receptor. The hydrogen-bond acceptor on the receptor forms a hydrogen bond with a complementary hydrogen-bond donor on the ligand. You construct the exclusion sphere around a point that you construct from two atoms of the hydrogen-bond donor on the ligand.

Distance Constraint Between Features on the Receptor

Specifying distance constraints between points on the receptor rather than the ligand can produce highly specific queries. For example, suppose you know that the receptor contains a hydrogen bond donor that is 10 - 11.5 Angstroms from a basic nitrogen. The following figure schematically shows how two topologically different drugs can bind to the same receptor site:

If you use a query that uses information about the pharmacophore (ligand-based query), you must specify a large distance range (4 - 10 Angstroms) to retrieve both classes of compounds. The ligand-based query retrieves the compounds that you want, but also retrieves many false hits. If you use a query that uses information about the receptor (receptor-based query), you can specify a much narrower distance range. For example:

The greater specificity in the receptor-based query allows you to retrieve the compounds that you want while eliminating many of the false hits that the ligand-based query might produce.

31.7.2 Specifying Pi-Pi Interactions

You can use projected points and exclusion spheres to represent pi-pi interactions with aromatic groups on the receptor.

Pi-Pi Interactions Alone

Use exclusion spheres above and below aromatic rings that interact with aromatic groups on the receptor. The exclusion spheres eliminate 3D structures with atoms that intrude into the excluded area. Consequently, all 3D structures that you retrieve can contain phenyl rings that can interact freely with the receptor.

To create the exclusion spheres, you create a normal to the plane of the phenyl ring. On that normal, you place a point that is 3.0 Angstroms above (+ 3.0 Angstroms) the plane of the ring, and another point that is 3.0 Angstroms below (- 3.0 Angstroms) the plane of the ring. Around each point, you create exclusion spheres that are 1.5 Angstroms in diameter.

The following query uses exclusion spheres and a distance constraint:

Pi-Pi Interactions With a Distance Constraint

To specify a distance constraint between a lipophilic site and another site on the receptor, use a projected point on one side of an aromatic ring. Use exclusion spheres to eliminate 3D structures that do not permit the aromatic ring to interact freely with the receptor.

To construct the exclusion spheres and projected points, create a normal to the plane of the phenyl ring. On that normal, you place a point that is 2.0 Angstroms above (+ 2.0 Angstroms) the plane of the ring, and another point that is 2.0 Angstroms below (- 2.0 Angstroms) the plane of the ring. On the normal, you place another point that is 3.5 Angstroms from the plane of the ring. Around the two points at 2.0 Angstroms from the aromatic ring, you create exclusion spheres that are 1.5 Angstroms in diameter.

The following query specifies a distance constraint of 6 - 10 Angstroms between a lipophilic site on the receptor and a hydrogen-bond donor on the receptor (for clarity, the query uses a simple definition of a basic nitrogen):

(Continued in Part 2)


Remote SSS3D: Searching Concepts/Examples Part 2

Click [image] to print Part 2.    Click [image] to return to Part 1.    Click [image] to close this Request-A-Document.

To print Part 2 of this Request-A-Document, click the Printer icon at the top of the screen.

To return to Part 1, click the Part 1 icon at the top of the screen.

---------------------------------------------------------------------------------------------------------------------

31.8 Sprouting Hydrogens and Lone Pairs

3D structures in a molecule database generally do not contain explicit representations of hydrogen atoms. You can, however, create explicit hydrogen atoms on the structures that you retrieve by sprouting hydrogen atoms on 3D structures. You must sprout hydrogen atoms when you export 3D structures to modeling software programs that cannot sprout hydrogens.

Note: If your query contains lone pairs, sprouting hydrogen atoms also sprouts lone pairs at sites that correspond to lone pairs on the query.

You have three options for displaying hydrogen atoms and lone pairs on the structures that you retrieve:

Off

Prevents sprouting of hydrogens and lone pairs on retrieved 3D structures. Use this setting when the 3D structures in your database already contain sufficient explicit hydrogens and lone pairs, or when your query does not contain explicit hydrogens and lone pairs.

Query Atoms Only

Sprouts hydrogens and lone pairs on retrieved 3D structures, but solely at sites where hydrogens and lone pairs appear on the query.

All

Sprouts hydrogens at all sites on retrieved 3D structures, and sprouts lone pairs on retrieved structures at sites where lone pairs appear on the query. Use this setting when you want to export 3D structures to a modeling software program that does not sprout hydrogens.

31.9 Removing Flexible Molecules

If you want to use the results of your SSS3D search in structure-activity studies, you might want only structures that are rigid in the region that matches the query. For example:

However, an SSS3D search retrieves both rigid and flexible 3D structures from the database. That is, some structures that you retrieve might be flexible, but have a conformation that fits the query. To remove these flexible structures, you can conduct a Conformationally Flexible Substructure (CFS) search with the following CFS options:

*	Search cutoff for Torsional Degrees of Freedom (TDF) = 1

*	Default values for all other CFS options.

Allowing only one torsional degree of freedom ensures that the region of the structure that matches the query can contain only one rotatable single bond. Rotatable single bonds must meet the following requirements:

*	At least one atom in the bond must be saturated, that is, sp3-hybridized.

*	Amide and similar bonds are not rotatable. The following types of bonds are considered amides:

*	Ring bonds are not rotatable.

31.10 Guidelines for Revising an SSS3D Search

If your SSS3D search did not produce the results that you wanted, use the guidelines in this section to:

*	Increase or decrease the number of 3D structures that you retrieve.

*	Optimize your query for fast search speeds.

*	Use multistep search strategies to refine your query.

31.10.1 Increasing or Decreasing the Number of Retrieved Structures

If your SSS3D search retrieved no records or too few records, you might want to:

*	Conduct an SSS3D search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, or increase the range of distance, angle, and other 3D constraints. If your query contains a submodel, you can increase the fixed-atom tolerances.

Note: If you make your query more general, search speed can decrease significantly. For more information on maintaining high search speeds when refining your query, see Section 31.10.3.

If your SSS3D search retrieved too many records, you might want to:

*	Refine your query, and then search the same set of records. For example, you can restrict atom or bond variation with explicit atoms or bonds, add additional substructures to the query, narrow the ranges of distance, angle, and other 3D constraints. If your query contains a submodel, you can decrease fixed-atom tolerances.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, then save the list. Next, conduct an additional search for compounds that you want to exclude, and save that list. Then, subtract the second list (the one that contains compounds that you want to exclude) from the first list.

*	Set the search domain to the list of the records retrieved, then conduct another search to reduce the number of records. For example, you could conduct a Search By Form to exclude molecules above a specific molecular weight.

If you used a CFS search to remove flexible structures, and that CFS search retrieved no records or too few records, try increasing the TDF to 2, 3, or 4.

If you used a CFS search to remove flexible structures, and that CFS search retrieved too many records, try decreasing the TDF to 0.

31.10.2 Optimizing the Query for Fast Search Speeds

ISIS performs an SSS3D search in two stages:

*	2D and 3D key screening. At this stage, ISIS rapidly eliminates compounds that cannot fit the query constraints. You want ISIS to eliminate as many structures as possible at this stage, before the slower atom-atom mapping process begins.

*	Atom-atom mapping. At this phase, ISIS attempts to match the atoms and constraints in the query to each 3D structure that remains after key screening. ISIS might need to map the query to a potential hit structure many times before it can eliminate it. Therefore, you want to design your query so that ISIS performs as few mappings as possible.

2D and 3D key screening

Every structure in a database has a set of binary representations of its structural entities, called keys. 2D keys code for 2D structural features, while 3D keys code for 3D features such as distances and angles. To improve search speed, you want your query to contain as many different structural features (that is, to set as many keys) as possible. This reduces number of structures that must be processed by atom-atom mapping.

The following characteristics increase the number of 2D keys in a query:

*	Different atom types

*	Different bond types and connectivity

*	Different types of functional groups

*	Different types and sizes of rings

For example, if you are searching for carbohydrate structures, your query might contain solely carbon and oxygen atoms. You can increase the number of keys by including rings and functional groups that you know are present in the structures that you want, even if they are not part of the pharmacophore.

The following are examples of features that increase the number of 3D keys in a query:

*	Distances between two heteroatoms

*	Distances between a heteroatom and a ring centroid, where the ring contains 3 - 7 atoms

*	Distances between two ring centroids

Key screening and atom-atom mapping

To increase and maintain high search speeds during both the key screening and atom mapping phases of an SSS3D search:

*	Draw as precise a query as you can, but use the fewest possible points to define lines and planes. ISIS calculates a best-fit line for three or more points and a best-fit plane for four or more points. These calculations can require a long time.

*	Use as many 2D query features as possible, and use as many specific 2D query features as possible if they can replace 3D constraints. For example, to define two atoms that are close together, draw a bond between them instead of using a distance constraint. This sets more keys an eliminates a 3D constraint.

*	Avoid using unconnected atoms in the query. (The slowest atoms are C and A.). ISIS must check all possible combinations of the specified atoms during the slower atom-atom mapping stage of the search.

*	Construct constraints with ring centroids rather than ring atoms. Ring centroids set additional keys and reduce the number of atom-atom mappings.

*	Avoid highly symmetrical queries. Highly symmetrical queries cause ISIS to perform the same mappings many times, with no increase in the number of hits. You can reduce the symmetry of a query by adding atoms or functional groups that are not part of the pharmacophore, but which you know are present in the molecules that you want.

*	Avoid multiple atom and atom-pair data constraints.

31.10.3 Using Multistep Search Strategies to Refine Your Query

You can refine a query by performing successive searches on a smaller and smaller set of retrieved molecules. You can maintain high search speeds by using query features that slow down searches at later stages of query refinement. Use the following strategies during the initial stages of multistep search strategies:

*	If your multistep search strategy includes a 2D structural or 3D data search, perform these searches first. For example, you can conduct a Search By Form for a specific therapeutic activity and then conduct a SSS3D search for topological differences among the models retrieved from the Search By Form.

*	Avoid using exclusion spheres. Exclusion spheres require calculation time that can decrease search speed. You might consider conducting an SSS3D search with a query that contains exclusion spheres after an SSS3D search with a query that does not contain exclusion spheres.

*	Avoid using lines and planes. ISIS must calculate the RMS deviation for each compound during the search. For example, you might want to substitute an angle constraint for a planarity constraint. In the examples below, the query with the angle constraint runs ten times faster than the query with the planarity constraint:

*	Avoid using unnecessary explicit hydrogens and lone pairs in the query. ISIS requires sprouting time.

*	Avoid using Rgroups.

*	Avoid using residues (superatoms).

31.11 Searching Example 1: Searching For Pharmacophores with 3D Substructure Queries

This example uses the 3D query that is based on a pharmacophore hypothesis proposed by Kato and coworkers (Kato, K., et al., J. Med. Chem. 1985, 28, 287-294). The 3D query contains a 3D substructure.

This example uses the ISISMX3D database.

Note: We provide the ISISMX3D database for demonstration purposes alone. ISISMX3D contains a small number of 3D structures. You generally want to conduct 3D searches in medium to large databases such as MDDR-3D.

31.11.1 Problem

Find compounds that inhibit thromboxane synthetase and have the following characteristics:

*	1-imidazolyl or 3-pyridyl on one end

*	Carboxylic acid at the other end

*	A distance of 8.5 to 10.0 Angstroms between the oxygen of the carboxylic acid and the nitrogen of the imidazole or pyridine ring

31.11.2 Approach

Draw a query that contains two fragments: one to represent the carboxylic acid and the other to represent the aromatic nitrogen. Add a distance constraint between the oxygen of the carboxylic acid and the nitrogen of the ring.

31.11.3 Query

31.11.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for SSS3D, how to/examples.

Search domain (Step 1)

Set the search domain to the entire database.

31.11.5 Results

In this searching example, the SSS3D search retrieves Model Regnos 80 and 95:

31.11 Searching Example 2: Searching for Pharmacophores With Submodel Queries

This example uses the 3D query by Petrillo and coworkers (Petrillo, E. W., and Ondetti, M. A. Med. Res. Rev. 1982, 2, 1-41) to retrieve compounds with the SSS3D search. The 3D query contains both a 3D substructure and a submodel.

This example uses the ISISMX3D database.

Note: We provide the ISISMX3D database for demonstration purposes alone. ISISMX3D contains a small number of 3D structures. You generally want to conduct 3D searches in medium to large databases such as MDDR-3D.

31.12.1 Problem

Find compounds that inhibit angiotensin-converting enzyme (ACE) and have the following features in common with Spirapril:

*	A fixed spatial arrangement of the alpha carboxylic acid group with respect to the ring nitrogen.

*	Similar distance constraints among two oxygens and a nitrogen in the aliphatic group.

31.12.2 Approach

To create the submodel query, retrieve Spirapril from the database, and then eliminate all but two portions of the 3D structure. Fix the three atom positions, and then add the three distance constraints. The following figure shows how to construct the query (atoms in boldface in the structure of Spirapril are also present in the query):

31.12.3 Query

31.12.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for SSS3D, how to/examples.

Search domain (Step 1)

Set the search domain to the entire database.

Fixed-atom tolerances (Step 4)

You require the following settings:

*	Maximum atomic displacement: 0.5. The individual atoms in the 3D models that correspond to the three fixed atom positions in the query will be checked for deviations that are within 0.5 Angstroms.

*	Maximum RMS deviation: 0.5. The overall spatial arrangement of atoms in the 3D models that correspond atoms in the submodel in the query will be checked for deviations that are within 0.5 Angstroms.

31.12.5 Results

The SSS3D search retrieves four 3D models in ascending order by Model Regno. The first three 3D models are known ACE inhibitors. Therefore, the last 3D model might a be valid conformation and can be tested for activity.

The fixed atom positions, (F), shown here are for illustrative purposes and do not appear when the query is overlaid onto the 3D model.

Note: If you conduct a search to remove flexible molecules, you obtain only one 3D structure (Model Regno 95). This structure contains only one flexible bond in the region that matches the query:


Remote CFS: Searching Concepts/Examples, Part 1

Click [image] to print Part 1.    Click [image] to go to Part 2.    Click [image] to close this Request-A-Document.

This Request-A-Document contains:

Part 1:

*	Definition of CFS Search	32.1

*	Specifying Query Features on Atoms and Bonds	32.2

*	Specifying Rgroup Query Features	32.3

*	Specifying Chemical Environments	32.4

*	Specifying Submodel Components	32.5

*	Specifying 3D Objects and Constraints	32.6

*	Using Receptor Information	32.7

---------------------------------------------------------------------------------------------------------------------

Part 2:

*	The CFS Search Process and Its Options	32.8

*	Sprouting Hydrogens and Lone Pairs	32.9

*	Guidelines for Revising a CFS Search	32.10

*	Searching Example 1: Searching For Pharmacophores
with 3D Substructure Queries 	32.11

*	Searching Example 2: Searching For Pharmacophores
with Submodel Queries 	32.12

We recommend that you print this Request-A-Document, and then browse through it. For technical reasons, this 58-page Request-A-Document has been divided into two parts. To print Part 1, click the Printer icon at the top of the screen. To print Part 2, first click the Part 2 icon, and then click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a CFS search, click here.

32.1 Definition of CFS Search

Conformationally Flexible Substructure (CFS) searching finds 3D structures in the database that contain the query structure embedded within them and that can be made to fit the query by rotating single bonds in the structure. For example:

32.1.1 CFS Search Queries

A CFS search query must contain at least one of the following 3D query features:

*	Submodel. A submodel is a three-dimensional (3D) representation of a portion of a molecule. A submodel contains two or more atoms in a fixed spatial arrangement (F). You construct a submodel from an existing 3D structure. For example:

For more information on submodels, see Section 32.5.

*	3D geometric constraints. You construct geometric constraints from atoms or from 3D objects such as points, lines, and centroids. For example, you can specify that the centers (centroids) of two rings must be separated by a distance of 2 to 10 Angstroms:

For more information on 3D geometric constraints, see Section 32.6.

*	3D data constraints that you apply to individual atoms or to pairs of atoms. The following example shows calculated values (in Hz) for the ring proton spin-spin couplings of methyl 2-furoate:

For more information on 3D data constraints, see Section 32.6.

A CFS search query can also contain 2D query features. A 2D query feature is a restriction on an atom or bond that specifies solely the number, type, and connectivity of atoms in a molecule, without any information on spatial arrangement. 2D query features can include:

*	Query features on atoms and bonds. You can allow or exclude specific atoms at certain locations, allow or exclude specific types of bonds, and so on. For example, the following query specifies that only carbon, nitrogen, or oxygen can be present at a specific position on the ring:

For more information on atom and bond query features, see Section 32.2.

*	Rgroups. An Rgroup query contains a root structure with defined Rgroup substituents attached to it at specific positions. An Rgroup consists of the molecule fragments (substituents) that can attach to the corresponding Rgroup sites on the root. That is, any Rgroup substituents that are members of the Rgroup R1 can attach to any position with the Rgroup label R1.

For example, you can specify that the Rgroup label R1 on the root structure allows a carboxyl group at its position and that R2 allows either a chloride atom or a sulfonic acid group at its position:

For more information on Rgroups, see Section 32.3.

You can combine 2D and 3D query features to specify:

*	Chemical environments. You can use 2D query features to specify chemical environments such as basic nitrogens, acidic centers, hydrogen-bond donors, or hydrogen-bond acceptors on the molecules that you retrieve. For example, the following can be considered a hydrogen-bond donor:

For more information on chemical environments, see Section 32.4.

*	Information on the receptor with which active structures interact. For example, you can specify a distance constraint between a hydrogen-bond donor and a hydrogen-bond acceptor on the receptor:

For more information on queries that use information on the receptor, see Section 32.7.

32.1.2 CFS Search Options

CFS searching provides many options that allow you to control how ISIS fits 3D structures to your query. For example, you can specify:

*	The algorithm (simplex or derivative) that ISIS uses to fit 3D structures to the query.

*	The number of times that ISIS attempts to fit (map) the query to each 3D structure.

*	The types of single bonds that ISIS can rotate when fitting 3D structures to the query. For example, you can specify whether single bonds in rings can be rotated, or whether to include single bonds between unsaturated centers (for example, biphenyls).

*	Whether to ignore nonbonded (van der Waals) interactions when fitting 3D structures to the query (bump checking). For example, you can ignore van der Waals interactions during the CFS search, then calculate van der Waals interactions on individual 3D structures as you view them.

*	Whether to rotate single bonds in other regions of a 3D structure so that the 3D structure can be fitted to the query (global relaxation).

*	Whether to calculate specific types of data that are derived from the fitted 3D structures. For example, you can calculate the difference in van der Waals interaction energy between the fitted 3D structure and the conformation that is stored in the database.

Caution: the CFS options subtly interact with each other and can produce undesirable results if improperly used. Therefore, we strongly recommend that you use the default CFS options, except for specific situations that are specified in the step-by-step instructions. For step-by-step instructions on conducting a CFS search, click here. Alternatively, choose Help > Index, and choose CFS, how-to/examples.

After you have more experience with CFS searching, you might want to experiment with CFS options. For information on the default CFS options, and on how to specify meaningful combinations of CFS options, see Section 32.8.

32.1.3 Choosing Between CFS and SSS3D Searches

A CFS search produces a set of 3D structures (hit list) whose fitted conformations might be different from the 3D conformations that are stored in the database. In contrast, an SSS3D search retrieves solely 3D conformations that are actually stored in the database.

Note: The 3D structures that you obtain from a CFS search (hits) are not necessarily low-energy conformations. You can, however, export the fitted structures to a modeling program for further processing.

Your choice of CFS or SSS3D search depends on your 3D searching strategy:

*	Use CFS when your database does not necessarily contain all possible conformations of each 3D structure, and you want to find additional conformations that fit the query. By deriving additional conformations during the search, CFS can find structures that SSS3D might miss.

*	Use SSS3D when your database already contains 3D structures with the desired conformations, and you want to find solely those conformations.

*	Use SSS3D when fast search speed is more important than retrieving all possible conformations. SSS3D is faster than a CFS search. In a preliminary study, for example, you might want to use a series of SSS3D searches to obtain a representative series of compounds and use this information to refine your query. After you have refined your query, you can perform a CFS search that retrieves as many structures as possible.

*	Use SSS3D when you want to find 3D structures that are rigid in the region that matches the query. For example, you might want to export rigid structures to a modeling software program so that you can use them in structure-activity studies. The SSS3D finds both rigid and flexible structures. However, you can remove the flexible structures by conducting a CFS search over the set of records that you retrieve from the SSS3D search. For more information on removing flexible structures, see Section 32.9.

32.2 Specifying Query Features on Atoms and Bonds

A query feature on an atom and/or a bond in a molecule is a restriction that specifies the retrieval of certain types of molecule records from an ISIS/Base database. If you do not use query features, the molecules retrieved contain solely your exact substructure query embedded wholly within them. For example:

You can also define Rgroups that specify a root structure with defined Rgroup substituents attached to it at specific positions. For more information on Rgroups, see Section 32.3.

Caution: Atom and bond query features are 2D query features. 2D query features specify solely the number, type, and connectivity of atoms in a molecule. A CFS query must contain at least one component that specifies the spatial distribution of atoms in a 3D structure; otherwise, the query will fail. To specify the spatial distribution of atoms, you can use a submodel with two or more fixed atoms, and/or use 3D geometric constraints such as distances and angles. For more information on submodels, see Section 32.5. For more information on 3D geometric constraints, see Section 32.6.

32.2.1 Definition of Aromaticity

For remote databases: ISIS interprets the following ring systems as aromatic:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:

Note: The bonds of six-membered aromatic ring systems and the perimeter bonds of azulenes are stored as aromatic bonds in the database. The bonds of five-membered aromatic rings, however, are stored as single and double bonds and interpreted as aromatic during a search. The differences between five-membered rings and other types of aromatic rings can cause different search results for five- and six-membered rings/azulenes when you use the following bonds in queries: Single, Double, and Single/Double query bonds. For more information on the Single/Double query bond, see Section 32.2.8.

32.2.2 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except implicit or explicit hydrogens:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

32.2.3 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of implicit hydrogens. For example:

32.2.4 Allowing an Unsaturated Atom

Use an atom query feature to specify that an atom is unsaturated, or attached to at least one multiple bond: double, triple, or aromatic.

Atom Query Feature: Unsaturated Atom (u)

Specifies that the atom of your choice is unsaturated. For example, the following query specifies both an unsaturated atom and single or double bonds (the double dashed lines).

32.2.5 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

Use explicit hydrogens to block non-hydrogen attachments on atoms. For example:

Atom Query Feature: Substitution Count of Zero, s0

Specifies that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of an isolated atom.

Atom Query Feature: Substitution Count of One, s1

Specifies that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Two, s2

Specifies that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Three, s3

Specifies that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Four, s4

Specifies that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Five, s5

Specifies that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of at Least Six, s6

Specifies that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count as Drawn, s*

Specifies that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:

32.2.6 Allowing a Specific Number of Ring Bond Attachments

Use atom query features to specify the number of ring bond attachments.

Atom Query Feature: Ring Bond Count of Zero, r0

Specifies that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:

Atom Query Feature: Ring Bond Count of Two, r2

Specifies that the records retrieved have solely two ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of Three, r3

Specifies that the records retrieved have solely three ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of at Least Four, r4

Specifies that the records retrieved have at least four ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count as Drawn, r*

Specifies that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:

32.2.7 Allowing Additional Atoms and/or Bonds in a Chain or a Ring

Use a query feature that is for either atoms or bonds to specify the addition of atoms and/or bonds in a chain or a ring.

Atom or Bond Query Feature: Link Node

Use a link node to specify the addition of variable numbers repeating units (atoms and/or bonds) to a ring or chain. A repeating unit must be attached to two adjacent bonds. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the link node [L1-3]:

Or, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the link node [L1-3]:

32.2.8 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Note: An aromatic query bond hits any bond in all types of aromatic rings: 6-membered ring bonds, 5-membered ring bonds, and azulene perimeter bonds. For more information on the structures that ISIS interprets as aromatic, see Section 32.2.1.

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

Note: A Single/Double query bond does not hit bonds in 6-membered aromatic rings, or perimeter bonds of azulenes, because bonds in these structures are stored in the database as aromatic bonds. However, a Single/Double query bond does hit bonds in 5-membered rings that ISIS interprets as aromatic. For more information on the structures that ISIS interprets as aromatic, see Section 32.2.1.

Bond Query Feature: Single/Aromatic Bond

Specifies either a single or an aromatic bond at that position:

Bond Query Feature: Double/Aromatic Bond

Specifies either a double or an aromatic bond at that position:

32.2.9 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is attached to a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

32.2.10 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is attached to a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

32.3 Specifying Rgroup Query Features

An Rgroup query finds structures that contain your query as a root structure with defined Rgroup substituents attached to it at specific positions. Your query can contain restrictions on the Rgroup substituents, called Rgroup conditions: You can specify the number of Rgroup sites that must be occupied in the records retrieved, specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site, or specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

Your Rgroup query can also contain restrictions on atoms and bonds of the root structure and Rgroup substituents. For example, you can use the atom query feature H(0) to prohibit the attachment of implicit hydrogens on a specific atom in the structures retrieved.

An example of an Rgroup query is as follows:

You can use Rgroups and atom and bond query features to specify chemical environments such as basic nitrogens and acidic centers. For more information on chemical environments, see Section 32.4.

Caution: Like atom and bond query features, Rgroup queries contain no information about the spatial distribution of atoms in a 3D structure. A CFS query must contain at least one component that specifies the spatial distribution of atoms in a 3D structure; otherwise, the query will fail. To specify the spatial distribution of atoms, you can use a submodel with two or more fixed atoms, and/or use 3D constraints such as distances and angles. For more information on submodels, see Section 32.5. For more information on 3D constraints, see Section 32.6.

32.3.1 The Root Structure

The root structure contains the portion of the structure that does not vary among the structures retrieved. For example, if you want to find 2, 5-Dihydroxypyridine in which the substituent at position 2 can be COOH, CN, or Ph, and the substituent at position 5 can be OH or CH3, the root structure is 2, 5-Dihydroxypyridine with Rgroups (such as R1 and R2):

Rgroups

On the root structure, Rgroups (R1 through R32) are placeholders that designate where the lists of functional groups and atoms that can attach to the root structure. In the example above, the Rgroup R1 designates that the members of the list R1 (the Rgroup substituents) are allowed at position 5 on the root structure. The Rgroup R2 designates that the members of the list R2 (the Rgroup substituents) are allowed at position 2 on the root structure.

Multiple Rgroups at One Position

You can specify multiple Rgroups at a single site on the root structure. For example:

One Rgroup at Multiple Positions

You can specify a single Rgroup (such as R1) at multiple positions on the root structure. For example:

Note: For information on how to restrict the number of Rgroups that must be occupied in the records retrieved, See Section 32.2.3, "Rgroup Conditions." A molecule need not satisfy all the Rgroup sites on the root structure to be retrieved. For example, the Rgroup condition R1 > 0 specifies that any molecule in which at least one of the R1 sites is filled by an R1 member will be retrieved. In addition, the Rgroup condition RestH determines whether the unsatisfied sites must be filled with hydrogen atoms or if other molecule fragments are allowed to be attached if they are not on the list.

32.3.2 Rgroup Substituents

Rgroup substituents are the members of the list of Rgroups. You define the Rgroup substituents that you will allow to be found at specified positions in the molecules retrieved. Rgroup substituents can be any structural fragment, including functional groups and single atoms.

In the example below, the Rgroup substituents COOH, CN, or Ph are allowed at position 5 (R1) on the root structure and the Rgroup substituents OH or CH3 are allowed at position 2 (R2) on the root structure:

Attachment Points

An attachment point (marked with an arrow and an asterisk) designates the atom on the Rgroup substituent that is attached to the root structure:

You must designate an attachment point on an Rgroup substituent for each bond that is attached to the substituent. If an Rgroup is attached to two bonds on the root structure, you must designate two attachment points. The bond on the root structure that is marked with double quotes corresponds to the attachment point on the Rgroup substituent that is marked with double quotes. The other attachment point on the Rgroup substituent is marked with a single quote:

Nested Rgroups

A nested Rgroup is an Rgroup that is a placeholder within another Rgroup rather than within the root structure. (You cannot nest an Rgroup any lower than this level.) In the following example, Rgroup R2 is nested within the Rgroup R1:

Nested Rgroups are equivalent to the following structures:

32.3.3 Rgroup Conditions

You can apply restrictions to each Rgroup in your query after you assemble all the Rgroups. The set of restrictions is called the Rgroup conditions.

If you do not apply Rgroup conditions, ISIS assigns the default conditions: Occurrence > 0 and RestH off for each Rgroup.

Occurrence

With the Rgroup condition Occurrence, you can specify the number of Rgroup sites that must be occupied in the records retrieved. For example, the occurrence designation R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved. Type one of the following values in the Occurrence range text box:

Value	Explanation

0	All members of the Rgroup are excluded from the Rgroup site (such as R1). To allow any other Rgroup substituent at the Rgroup site, set RestH to off.

> 0	At least one Rgroup must be satisfied. If RestH is off, any other substituent can attach to unsatisfied sites. If RestH is on, unsatisfied sites must be filled solely by hydrogens.

n	Exactly n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

< n	Less than n number of sites (including zero) must be satisfied. RestH controls substitution at unsatisfied sites.

m - n	Any number of sites falling within the range of m to n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

m,n,...	Any combination of the above expressions, separated by commas. For example: 1, 3-5, 9, >12.

For example, the Rgroup condition R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved.

In another example, the Rgroup condition R1 > 0 and R2 > 0 specifies that an Rgroup substituent from the R1 list AND an Rgroup substituent from the R2 list must occupy at least one site on the root structure in the records retrieved.

Finally, the Rgroup conditions R1 = 1, 3-5, 9, >12 specify that either 1, 3, 4, 5, 9, or more than 12 sites must be satisfied:

RestH

With the Rgroup condition RestH, you can specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site.

An unsatisfied Rgroup site is an Rgroup site on the root structure that does not have an Rgroup member attached: If RestH is off, any functional group or atom may be attached at unsatisfied Rgroup sites on the root structure. If RestH is on, solely hydrogens are allowed to be attached at unsatisfied Rgroup sites on the root structure.

If/Then

With the Rgroup condition If/then, you can specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

For example, If R1 then R2 specifies that if the conditions for R1 are satisfied, then the conditions for R2 must also be satisfied. (If the conditions for R1 are not satisfied, then the conditions for R2 are ignored.) The If/then condition implies that a molecule may be retrieved even though R1 is not satisfied.

In the following query, R1 contains a nitro group and a sulfonic acid group. R2 contains a chlorine atom. The condition If R1 then R2 specifies that if a nitro group or a sulfonic acid group is attached at R1 on the root structure, then a chlorine must also be attached at R2. However, if the R1 site on the root structure does not have either the nitro or the sulfonic acid group (R1 is unsatisfied), then R2 can have any substituent (R2 is ignored):

32.4 Specifying Chemical Environments

You can incorporate specific chemical environments into your CFS query. This section contains examples of several chemical environments that you can create with 2D query features and Rgroups. MDL supplies ISIS/Draw sketch files that contain specific types of chemical environments. You can incorporate these structures into your own queries and modify them if desired.

32.4.1 Acidic Center

The file ACID_CTR.SKC contains the following definition of an acidic center:

This query defines an acidic center as either an oxygen of a carboxylic acid or any nitrogen of an unsubstituted tetrazole.

32.4.2 Basic Nitrogen

BSC_N_1.SKC File

The file BSC_N_1.SKC contains a definition of a basic nitrogen that includes alkyl amines (nsp3), amidines (nsp2), and guanidines (nsp2). This definition excludes other nitrogens such as aromatic nitrogens, aniline-type nitrogens, N=O, NHC=O, and NHC=C:

You can change this definition to fit your needs. For example, if you want to include aromatic nitrogens, delete R2 from the definition.

BSC_N_2.SKC File

The definition of basic nitrogen in the file BSC_N_2.SKC excludes all amides or anilines, and other conjugated systems that reduce the accessibility of the electron pair on the nitrogen atom:

Simple Definition

The following is a simple definition of a basic nitrogen:

32.4.3 Hydrogen-Bond Acceptor

The definition of a hydrogen bond acceptor in the file H_ACCEPT.SKC extends the definition of a basic nitrogen to include oxygen and sulfur:

Note: There are two different conventions for defining hydrogen-bond donors and acceptors. This help file uses the definition of a hydrogen-bond donor that is generally used by medicinal chemists. By this convention, the donor of a hydrogen bond is the group to which the hydrogen atom is attached:

An alternative definition of hydrogen-bond donors and acceptors defines a hydrogen-bond donor as the group that provides the lone-pair electrons (LP) to the hydrogen bond.

32.4.4 Hydrogen-Bond Donor

The following is an example of a hydrogen bond donor:

32.5 Specifying Submodel Components

A submodel is a three-dimensional (3D) representation of a portion of a molecule. A submodel search retrieves all models that contain the same spatial arrangement of atoms as those specified in your submodel query, within specified deviations of the individual and overall atoms.

You specify the spatial arrangement of atoms in a submodel query by fixing the 3D coordinates of two or more atoms in the structure. To create a submodel, you eliminate parts of an existing 3D structure until you have the submodel that you want to find in other 3D structures. Then, you fix the positions of the atoms of your choice. The figure below shows how you create a submodel query from the 3D structure of Trandolapril. Circles mark the atoms in Trandolapril that are fixed (F) in the query:

When you conduct a search with a submodel query, you must specify how closely the 3D structures that you retrieve must match the spatial arrangement of the fixed atoms in the submodel query. Two fixed-atom tolerances specify how closely the structures must match the query:

*	Maximum atomic displacement specifies the maximum allowed deviation of individual fixed atoms in the query from those in the structures that you retrieve.

*	Maximum RMS deviation specifies the maximum allowed deviation of all fixed atoms in the query from fixed atoms in the structures that you retrieve. During the search, ISIS superimposes the fixed atoms in the 3D structure on those of the query and performs a least-squares calculation.

When your query contains fixed atoms, you must specify at least one fixed-atom tolerance for the SSS3D search. You can specify:

*	Maximum atomic displacement only (structures with 2 or 3 fixed atoms)

*	Maximum RMS deviation only (structures with at least 4 fixed atoms)

*	Both fixed-atom tolerances (structures with at least 4 fixed atoms)

Your ISIS Administrator sets default fixed-atom tolerances that your site uses to register 3D structures to the database. These tolerances are specified in the Session Settings file that your ISIS Administrator supplies you. To change fixed-atom tolerances for searching, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for fixed-atom tolerances, changing.

Caution: If you change the default fixed-atom tolerances for searching, you must restore the default fixed-atom tolerances before you register 3D structures.

The following are examples of the 3D structures that you retrieve from a search with the query that you derive from Trandolapril, with both fixed-atom tolerances set to 0.5:

Note: Queries that contain fixed atoms produce slower search speeds than queries that do not contain fixed atoms. As an alternative to the fixed-atom query shown previously, you can use a query with distance constraints that incorporate the fixed-atom tolerances:

You can also use other 3D query features to specify the spatial distribution of atoms within a 3D structure. For more information on distance constraints and other 3D constraints, see Section 32.6.

32.6 3D Objects and Constraints

To specify the spatial relationships between atoms, you can construct 3D objects and create 3D constraints that use atoms and/or constructed 3D objects.

32.6.1 Specifying 3D Objects

You can set geometric constraints on various molecular or constructed geometric 3D objects. These objects can be points, lines, planes, centroids, and normal vectors. Lines, planes, and normal vectors actually extend infinitely, but are represented in ISIS as shown below:

Centroid

Use a centroid to define the geometric center of a set of reference points or atoms of your choice. For example, the centroids in the structures below (depicted by the triangles) are the geometric centers of selected atoms. The centroid on the left is created when all six ring atoms are selected. The centroid on the right is created when the atoms in the box are selected (the box is used here to indicate atoms selected, and does not appear in the query):

Line

Use a line to define a path through two or more reference positions, such as points, atoms, or centroids:

ISIS derives a best-fit line if you use at least three reference positions to define the line. You can specify a linearity constraint for a best-fit line. For more information, see 32.6.2.

Normal

Use a normal to specify a line (with an arrowhead) that is perpendicular to a plane and that passes through a reference position (a point, atom, or centroid):

In ISIS, the direction of the normal arrow is defined by the sequence in which you selected the first three components of the plane. To reverse the direction of the arrow, simply reverse the order in which you define the components of a plane.

Note: If you define a normal through a point that lies in the same plane, the direction of the normal is undefined.

Plane

Use a plane to define a surface that consists of three or more reference positions (points, atoms, or centroids). A plane actually extends infinitely in all directions, but is depicted in ISIS as a small rectangular surface. In the following figure, the entire molecule specifies the plane:

ISIS derives a best-fit plane if you use at least four reference positions to define the line. You can specify a planarity constraint for a best-fit plane. For more information, see Section 32.6.2.

Point

A point is a reference position. You specify a point at a defined distance and direction from a distance reference position (another point, atom or centroid). To specify the direction, you can use either another reference position (called the direction reference position) or a normal.

You can specify the distance from the distance reference position to the direction reference position in Angstroms or as a percentage. Angstrom distances must lie between -100 and +100 Angstroms. Percentage distances must lie between -1,000% and +1,000%, and must include the % sign.

The following example defines a point at a distance of 1.4 Angstroms from a ring nitrogen (the distance reference position) to a ring oxygen (the direction reference position):

The point that you specify need not lie between the two reference positions. The following example shows a point projected 2.8 Angstroms along a line between the nitrogen atom (the distance reference position) and the hydrogen (the direction reference position):

When you use a normal to specify the direction of the point from the distance reference position, you must specify the distance from the distance reference position in Angstroms.

The following example uses a normal to create points that lie 2.8 Angstroms above and below the center of a phenyl ring. The normal is perpendicular to the plane of the ring and passes through the ring centroid. The direction of the normal is undefined, because the point that defines it lies in the plane. To define points on both sides of the plane, use plus (+) and minus (-) signs with Angstrom values to specify the distances:

To create a point on only one side of the plane, specify a distance of 2.8 Angstroms without the plus (+) or minus (-) sign:

Note: You can use points to represent features on a receptor. For examples, see Section 32.7.

32.6.2 Specifying 3D Constraints

You can apply 3D geometric constraints to 3D objects. 3D geometric constraints include distances, angles, dihedral angles, exclusion spheres, linearity constraints, and planarity constraints:

You can also apply 3D data constraints to atoms and atom pairs. Data constraints are listed under “Atom" and “Atom Pair" later in this section.

Distance

You can define a distance constraint between two reference positions (atoms, centroids, or points), from a reference position to a line or normal, or from a reference position to a plane:

The distance constraint is a range of values. Both values in the range must be greater than zero and equal or less than 1,000. The following query has a distance constraint of 2 to 10 Angstroms between the center of a phenol ring and the center of a phenyl ring:

The following are examples of the 3D structures that you retrieve:

Angle

You can define an angle constraint with three points, centroids, or atoms; or with two planes, lines, or normals:

The vertex of the angle for two planes, lines, or normals that do not intersect is an imaginary point. An angle drawn with two lines that do not intersect is equivalent to a dihedral angle through an imaginary line that connects the two lines with the shortest distance.

The angular range that you specify depends on the way that you defined the angle:

*	If you used lines or planes to define the angle, the range must lie between 0 and 90 degrees.

*	If you used three points to define the angle, the range must lie between 0 and 180 degrees.

The following query has a constraint of 30- 65 degrees on the angle between the line between two phenyl centers and a phenol oxygen:

The following are examples of the 3D structures that you retrieve:

Exclusion sphere

Use an exclusion sphere to exclude atoms within a sphere surrounding a reference position. You define the radius of the exclusion sphere. You can ignore unconnected atoms within the radius of the sphere or specify exactly which atoms that you want to be included. The radius of the sphere must be between 0.1 and 20 Angstroms.

Note: You cannot use a CFS query that consists solely of exclusion spheres. A CFS query must contain at least one of the following 3D query components: distance, angle, dihedral angle, linearity constraint, planarity constraint, or two or more fixed atoms.

For example, the exclusion spheres in the following query ensure that you select compounds that have no atoms within the circled areas of 1.0-Angstrom radius:

The following is an example of the 3D structures that you retrieve (For clarity, the measured values of the four distance constraints are not displayed):

You can specify that atoms that are part of the query can lie within the exclusion sphere. In the following query, for example, you might want to allow atoms from the carboxyl group within the exclusion spheres, but exclude all other atoms:

To allow other atoms in the query within the exclusion sphere, you must include these atoms in the basis of the exclusion sphere. (The basis of a 3D object or constraint is the set of atoms or 3D objects that comprise the object.) For an exclusion sphere, the basis always includes the reference position at the center of the sphere. To include additional atoms, you edit the basis to include these atoms. For example, you can edit the basis of the exclusion spheres in the previous query to include the carboxyl group. The following are examples of the 3D structures that you retrieve (For clarity, the measured value of one distance constraint is not displayed):

You can also specify that unconnected atoms that are not part of the query can lie within the volume of the exclusion spheres. For example, you might want to allow salt ions or water molecules within the volume of the exclusion sphere. To allow these atoms, you specify the following setting when you create the exclusion sphere: Allow nonquery atoms within exclusion sphere.

Note: You can use exclusion spheres to represent regions on a receptor. For examples, see Section 32.7.

Dihedral

When two planes intersect, a dihedral angle is created from the common vertex of reference positions 1 and 2 and reference positions 3 and 4:

Atoms 1 and 2 are adjacent reference points for the phenol structure, and atoms 3 and 4 are adjacent reference points for the phenyl structure. Reference points 1, 2, and 3 lie along the first plane, and reference points 2, 3, and 4 lie along the second plane. Reference points 2 and 3 share both planes and form the vertex of the dihedral angle.

The angular range that you specify must be between -180 and +180 degrees.

The following query specifies a dihedral angle between two atoms on a phenyl ring and two atoms on a phenol ring:

The following are examples of the 3D structures that you retrieve:

Linearity

You can specify that three or more reference positions (atoms, points, or ring centroids) must lie along the same line. To do this, you specify the maximum average distance (RMS deviation) of the reference positions from the best-fit line derived from the reference positions. The following shows a linearity constraint for all atoms in a trialkene:

The value that you specify must lie between 0 and 1,000.

Planarity

You can specify that four or more reference positions (atoms, points, or ring centroids) must lie along the same plane. To do this, you specify the maximum average distance (RMS deviation) of the reference positions from the best-fit plane derived from the reference positions. The following shows a planarity constraint for all atoms in a benzaldehyde:

The value that you specify must lie between 0 and 1,000.

Atom

Use atom data to specify a data constraint for selected atoms in your query, such as spectroscopic and quantum mechanical data or partial charges. For example:

The atom data constraint specifies the partial charge on the oxygen. Rn specifies that the oxygen must appear in a ring. For more information on Rgroups, see Section 32.2.

Atom-Pair

Use atom-pair data to specify a data constraint between two atoms in your query. For example, you can specify bond order, lower/upper distance constraints, and spectroscopic and quantum mechanical data. The following query specifies values for the ring proton spin-spin couplings of methyl 2-furoate:

32.7 Using Receptor Information

The previous sections showed how to use information about active compounds (that is, information about the pharmacophore) to specify query constraints. This section shows how you can use information about the receptor to specify geometric constraints in your query. Use these examples as a starting point for creating your own queries.

Note: For simplicity, the queries in this section use a simple definition of a basic nitrogen. For more refined definitions of basic nitrogen, see Section 32.4.2.

32.7.1 Specifying Hydrogen-Bond Interactions

You can use projected points and exclusion spheres to represent hydrogen bond donors and acceptors on the receptor.

Note: There are two different conventions for defining hydrogen-bond donors and acceptors. This help file uses the definition of a hydrogen-bond donor that is generally used by medicinal chemists. By this convention, the donor of a hydrogen bond is the group to which the hydrogen atom is attached:

An alternative definition of hydrogen-bond donors and acceptors defines a hydrogen-bond donor as the group that provides the lone-pair electrons (LP) to the hydrogen bond.

Hydrogen-Bond Donor on Receptor

The following example shows how to construct an exclusion sphere that represents a hydrogen-bond donor on the receptor. The hydrogen-bond donor on the receptor forms a hydrogen bond with a complementary hydrogen-bond acceptor on the ligand. You construct the exclusion sphere around a point that you construct from two atoms of the hydrogen-bond acceptor on the ligand.

Hydrogen-Bond Acceptor on Receptor

The following example shows how to construct an exclusion sphere that represents a hydrogen-bond acceptor on the receptor. The hydrogen-bond acceptor on the receptor forms a hydrogen bond with a complementary hydrogen-bond donor on the ligand. You construct the exclusion sphere around a point that you construct from two atoms of the hydrogen-bond donor on the ligand.

Distance Constraint Between Features on the Receptor

Specifying distance constraints between points on the receptor rather than the ligand can produce highly specific queries. For example, suppose you know that the receptor contains a hydrogen bond donor that is 10 - 11.5 Angstroms from a basic nitrogen. The following figure schematically shows how two topologically different drugs that can bind to the same receptor site.

If you use a query that uses information about the pharmacophore (ligand-based query), you must specify a large distance range (4 - 10 Angstroms) to retrieve both classes of compounds. The ligand-based query retrieves the compounds that you want, but also retrieves many false hits. If you use a query that uses information about the receptor (receptor-based query), you can specify a much narrower distance range. For example:

The greater specificity in the receptor-based query allows you to retrieve the compounds that you want while eliminating many of the false hits that the ligand-based query might produce.

32.7.2 Specifying Pi-Pi Interactions

You can use projected points and exclusion spheres to represent pi-pi interactions with aromatic groups on the receptor.

Pi-Pi Interactions Alone

Use exclusion spheres above and below aromatic rings that interact with aromatic groups on the receptor. The exclusion spheres eliminate 3D structures with atoms that intrude into the excluded area. Consequently, all 3D structures that you retrieve can contain phenyl rings that can interact freely with the receptor.

To create the exclusion spheres, you create a normal to the plane of the phenyl ring. On that normal, you place a point that is 3.0 Angstroms above (+ 3.0 Angstroms) the plane of the ring, and another point that is 3.0 Angstroms below (- 3.0 Angstroms) the plane of the ring. Around each point, you create exclusion spheres that are 1.5 Angstroms in diameter.

The following query uses exclusion spheres and a distance constraint:

Pi-Pi Interactions With a Distance Constraint

To specify a distance constraint between a lipophilic site and another site on the receptor, use a projected point on one side of an aromatic ring. Use exclusion spheres to eliminate 3D structures that do not permit the aromatic ring to interact freely with the receptor.

To construct the exclusion spheres and projected points, create a normal to the plane of the phenyl ring. On that normal, you place a point that is 2.0 Angstroms above (+ 2.0 Angstroms) the plane of the ring, and another point that is 2.0 Angstroms below (- 2.0 Angstroms) the plane of the ring. On the normal, you place another point that is 3.5 Angstroms from the plane of the ring. Around the two points at 2.0 Angstroms from the aromatic ring, you create exclusion spheres that are 1.5 Angstroms in diameter.

The following query specifies a distance constraint of 6 - 10 Angstroms between a lipophilic site on the receptor and a hydrogen-bond donor on the receptor (for clarity, the query uses a simple definition of a basic nitrogen):

(Continued in Part 2)


Remote CFS: Searching Concepts/Examples Part 2
Remote CFS: Searching Concepts/Examples, Part 2

Click [image] to print Part 2.    Click [image] to return to Part 1.    Click [image] to close this Request-A-Document.

To print Part 2 of this Request-A-Document, click the Printer icon at the top of the screen.

To return to Part 1, click the Part 1 icon at the top of the screen.

---------------------------------------------------------------------------------------------------------------------

32.8 The CFS Search Process and Its Options

This section contains information that allows you to make meaningful choices when you want to use CFS options that are different from the defaults.

32.8.1 Understanding the CFS Search Process

During both the initial and bump-checking CFS searches, ISIS subjects each 3D structure in the search domain to the following three-step process:

The following sections describe each step of this process in detail.

Step 1: 2D Key Screening

Every structure in a database is associated with a set of binary representations of its structural entities, called keys. The 2D key screening step retrieves all the static 3D models in the database that contain the structural fragments of your query embedded in them. The presence of structural fragments and their combinations can be represented by one or more of 960 key codes.

Step 2: Upper/Lower Distance Screening

The upper/lower distance screening step tests the fit of certain geometric constraints for those conformations from the 2D key screening step. ISIS tests the fit solely of distance and angle constraints that are defined by atoms and ring centroids. The process rotates single bonds between two atoms to find the maximum and minimum separation possible. At this stage of the process, ISIS tests the fit of each distance and angle constraint independently of the other constraints.

Step 3: Conformational Fitting

If your 3D query contains more than one distance constraint, ISIS uses a torsional fitter to retrieve those conformations from the upper or lower distance screening that can be suitably rotated about their rotatable single bonds. The torsional fitter attempts to minimize the deviations between measured values of 3D constraints and the values that are specified in your search query.

ISIS omits conformational fitting if the query contains only one distance or angle constraint.

The conformational fitting step is optional. If you do not perform conformational fitting during the search, ISIS performs conformational fitting on each 3D structure as you view it (view-time fitting).

32.8.2 Using the Default CFS Options

CFS searching provides many options that allow you to control how ISIS fits 3D structures to your query. The default CFS options generally provide the best balance between accuracy and speed for most CFS searches. This section explains how the default options affect the CFS search results.

Caution: The CFS options subtly interact with each other and can produce undesirable results if improperly used. If you are not sure how to use the CFS options, we strongly recommend that you use the default CFS options.

When you perform a CFS search, you want to balance the following factors:

*	Quality of fitted 3D structures. You want to retrieve 3D structures that are realistic. That is, you want the fitted 3D structures to be as close as possible to minimum-energy conformations.

*	Quantity of fitted 3D structures. You want to retrieve as many 3D structures as possible that can be fitted to the constraints in your query.

*	Speed of searching.

To achieve the best balance among these three factors, you generally perform a CFS search in two distinct passes:

1.	An initial CFS search. This CFS search ignores non-bonded (van der Waals) interactions between parts of the molecule that are rotated to fit the query, because calculating nonbonded interactions can slow search speeds. You generally use the default CFS options for this search.

2.	An optional bump-checking CFS search over the set of records that you retrieved in the initial CFS search. Bump checking eliminates fitted conformations that have unfavorable nonbonded interactions (that is, conformations in which atoms bump into one another) by calculating nonbonded interactions between parts of the molecule that are rotated to fit the query. The slow search speeds caused by calculating nonbonded interactions are less important, because you perform the search over a smaller set of records.

If you want, you can eliminate the bump-checking CFS search and perform bump checking as you view your search results (view-time bump checking). If any structures on your list have unfavorable nonbonded interactions, ISIS displays these structures without overlaying the query.

When you specify the default CFS options, ISIS does the following during the CFS search:

*	Automatically chooses the more appropriate torsional fitting algorithm (simplex or derivative) for your query.

*	Rotates solely acyclic single bonds that contain at least one atom that is sp3-hybridized. An exception is made for amide bonds, which are not rotated. This definition of a rotatable bond produces a high proportion of fitted structures with low-energy conformations.

*	Ignores nonbonded (van der Waals) interactions between atoms during the search and calculates nonbonded interactions for each fitted structure as you view it (that is, performs bump checking at view time only). This produces faster search speeds, yet allows you to find structures that contain unfavorable nonbonded interactions.

*	Avoids calculating derived data on van der Waals energy difference, torsional degrees of freedom (TDF), and RMS deviation for sorting, viewing, or search cutoffs. These calculations can slow search speeds. For more information on derived data, see Section 32.8.4.

*	Makes at least five attempts to fit (map) the query to each 3D structure in the search domain. This generally produces the maximum number of hits without sacrificing search speed.

If you want to experiment with the CFS options, we strongly recommend that you study Section 32.8.3 so that you can make meaningful choices.

32.8.3 Options for CFS Searching

This section describes each option for the conformational fitting step of CFS searches and explains how that option affects the search.

Fitter Selection

You can use either the simplex or derivative torsional fitter:

*	The simplex torsional fitter was originally developed in conjunction with Molecular Simulations, Inc. and uses the Nelder-Mead sequential simplex minimizer. The fitter uses variable rotation increments to approach a minimum in the objective function. You can use the simplex fitter with any 3D query components, including fixed atoms.

*	The derivative torsional fitter was developed at Zeneca Pharmaceuticals Group and attempts to minimize a differentiable objective function with a combination of first- and second-order optimization techniques. 3D query components are restricted to the following: atoms, ring centroids, angles that are defined by three atoms or ring centroids, and distances that are defined by two atoms or ring centroids.

*	If you do not specify either of these fitters, you can specify [image] Automatic to allow ISIS to choose the fitter automatically. If the query contains solely distances and angles, the automatic setting chooses the derivative fitter. If the query contains 3D constraints other than solely distances and angles, the automatic setting chooses the simplex fitter. Automatic is the default.

The following table shows the components of the 3D query that you can use with the simplex and derivative fitters:

Note: Both the simplex and derivative fitters attempt to optimize the conformation over the range of the distance or angle constraint. For the derivative fitter alone, you can also optimize the fit to the midpoint of the distance or angle constraint. That is, the derivative fitter can not only find a conformation that fits the query, but can also find the conformation that fits the query as closely as possible. If you want ISIS to optimize to the midpoint, however, you must either specify a search cutoff for RMS deviation, or specify that ISIS calculate RMS deviation for sorting and viewing. For more information on derived data and RMS deviation, see Section 32.8.4.

Fitting at Search Time

You can specify that conformational fitting either take place during the search (search-time fitting) or during viewing (view-time fitting). If your query contains solely atoms, centroids, distances, and angles defined by three atoms or ring centroids, you can omit conformational fitting at search time. If you omit conformational fitting at search time, ISIS performs only 2D key screening and upper/lower bounds checking during the CFS search. Consequently, your search speed will increase, but your search results might contain some false hits.

You must perform conformational fitting at search time if you want ISIS to calculate certain types of derived data such as RMS deviation and van der Waals energy difference. For more information on derived data, see Section 32.8.4

Note: You can specify conformational fitting at view time only if your query consists solely of the following 3D query components: atoms, ring centroids, distances, and angles that are defined by three atoms or ring centroids. If your query contains any other 3D query features, you must perform fitting at search time.

By default, conformational fitting occurs at search time.

Maximum Number of Attempted Fittings

The torsional fitter can attempt up to 1000 unique mappings that match the conformation to your query specifications.

In general, the higher the number of attempted fittings, the longer the search, and the more 3D structures you potentially retrieve. If your database has many large, complex 3D structures, you might want to use a low value to maximize your search speed. For typical queries that use interatomic distances, the time that the search requires increases linearly with the value of the distance constraint. However, ISIS generally retrieves very few extra hits when you specify a number greater than 5. Also, a value of 1000 might not assure that ISIS attempts all possible mappings for each 3D model.

You can specify any value from 1 to 1000. The default value is 5. However, if you activate ring flexing, we recommend that you increase this number to at least 25.

Ring Flexing

You can specify that rings of 4 to 24 atoms in size be considered flexible. ISIS considers only rings that are nonaromatic and that contain some rotatable single bonds. For example, a setting of 4 atoms for the minimum ring size and 8 atoms for the maximum ring size allows rotations about all single bonds in 4- to 8-membered rings. The suggested range is between 6 and 24 ring atoms.

When you activate ring flexing with a suitable number of attempted fittings (25 or more), you generally obtain more hits. However, ring flexing also decreases search speed.

If you activate ring flexing, we recommend that you increase the maximum number of attempted fittings to at least 25.

Ring flexing is off by default.

Rotating Single Bonds Between Unsaturated Atoms

You can specify that single bonds between unsaturated centers (for example, biphenyl) be considered flexible. When this option is inactive (the default), ISIS rotates only acyclic single bonds with the following hybridizations:

sp3 - sp3
sp3 - sp2 (except amides and similar bonds)
sp3 - sp

The definition of amides includes the following:

When you activate bond rotation between unsaturated centers, ISIS extends the definition of an acyclic single bond so that bonds with the following hybridzations can rotate:

sp3 - sp3
sp3 - sp2 (except amides and similar bonds)
sp3 - sp
sp2 - sp2
sp2 - sp
sp - sp

If you activate bond rotation between unsaturated centers, you retrieve more hits. However, some of the fitted structures might have higher-energy conformations. Single bond rotation also requires additional calculations that produce slower search speeds.

This option is off by default.

Bump Checking

You can specify that nonbonded atoms within a conformation do not bump into one another. Bump checking calculations use the van der Waals radii of atoms. If you activate bump checking, ISIS takes nonbonded interactions into account during the conformational fitting step.

Note: The additional calculations for bump checking during conformational fitting produce slower search speeds than conformational fitting without bump checking. Consequently, we strongly recommend that you not activate bump checking when you search medium or large databases. Instead, we recommend that you perform the CFS search in two phases. First, perform an initial CFS search without bump checking. Then, set the search domain to the results of the initial CFS search and perform a bump-checking CFS search to remove the invalid hits.

You must perform bump checking during the search when you want to:

*	Specify a search cutoff for van der Waals energy difference.

*	Sort your search results by van der Waals energy difference.

Also we strongly recommend that you perform bump checking during the search when you want to export fitted 3D structures to a CFS SDfile for use in a modeling software program.

For more information on calculations for van der Waals energy difference, see Section 32.8.4.

You can specify bump checking at search time, at view time, at search and view time, or no bump checking at all. The following table shows the four bump checking scenarios that you can specify. The default setting is bump checking at view time (Scenario 1).

We recommend that you use the following guidelines for bump checking:

Scenario 1: This is the default scenario, and is especially useful in improving the speed of your searches over medium or large databases. We recommend that you use this scenario for the initial phase of CFS searching. You retrieve approximately 10 to 15 percent additional false hits in your search results. The bump-checking CFS search removes these false hits.

Scenario 2: You can use this scenario if you want to view the false hits and unacceptable conformations in your search results. You might want to use this information as a way of gathering ideas for creating better search queries, or as a way of determining the contents of your database.

Scenarios 3 and 4: Use either scenario during the bump-checking CFS search, after you have set your search domain to the results of the initial CFS search. We strongly recommend that you do not use this scenario when you search over the entire database.

Note: To sort your search results by van der Waals energy difference (vdW), or to specify a vdW search cutoff, you must perform bump checking at search time. If you want to specify a vdW search cutoff or sort by vdW, you must do so during the bump-checking CFS search.

Global Relaxation

You can specify that ISIS rotate single bonds in other parts of the structure to reduce nonbonded interactions throughout the molecule. When global relaxation is active during bump checking, ISIS finds structures that might be eliminated if ISIS rotated single bonds solely in the region that matched the query. Global relaxation increases the size of your hit list and produces more realistic 3D structures. However, global relaxation also requires additional calculations that can slow search speeds.

To activate global relaxation, bump checking must also be active.

Global relaxation is off by default.

32.8.4 Derived Data for Search Cutoffs, Display, and Sorting

ISIS can derive specific kinds of data from the 3D structures that it retrieves during a CFS search. This derived data is stored in fields that you see in the database definition. You can display this data in a form and use it for sorting, just like data in an actual database field. You can also specify search cutoffs that use the derived data. When you specify a search cutoff, ISIS eliminates any fitted 3D structure for which the calculated value is greater than the value that you specify.

If you want to sort your search results by derived data, we strongly recommend that you define sorting instructions before the search, and sort search results automatically after the search. If you sort search results manually after the search ISIS must repeat the search to calculate derived data. For more information on sorting, see the 3D Sorting Examples Request-A-Document.

ISIS can calculate three types of derived data during the search: torsional degrees of freedom (CFS_TDF field), root mean square deviation (CFS_RMS field), and van der Waals energy difference (CFS_VDW field). A fourth derived data field, CFS_FITTER, stores the name of the fitter (Simplex or Derivative) that ISIS used in the search.

Torsional Degrees of Freedom (TDF)

The number of rotatable bonds on the paths that connect the mapped atoms (Mapped atoms are the atoms in the hit that correspond to atoms in the query). The higher the TDF value, the more flexible is the portion of the 3D structure that maps to your query.

If you specify a search cutoff value, ISIS excludes fitted structures that have more than the value that you specify. We suggest a search cutoff value of 10 rotatable bonds.

To view TDF in a form, connect a form box or table column to MODEL>CFS_TDF.

RMS Deviation

The root mean square value for the goodness-of-fit of the fitted 3D structure to the 3D features that you specified in your query. This is a composite measure of the goodness-of-fit to the query. RMS deviation appears in Angstrom deviations for distances, lines, planes, and fixed atoms and in cosine deviations for angles and dihedrals.

If you specify a search cutoff, ISIS excludes fitted structures that have more than the value that you specify. If you do not specify a search cutoff value, the RMS values that ISIS calculates during the search can range from 0.0 to 1e20 RMS units.

We suggest a search cutoff value of 0.7 RMS units.

You can calculate RMS deviation data for both the simplex and derivative fitters and can view this data in your form. However, we recommend that you not use RMS deviation data to sort your search results unless you also specify the derivative fitter for the CFS search. The RMS deviation values that the simplex fitter calculates are not suitable for sorting because they are not optimized to the midpoint of the distance or angle constraint. Both the simplex and derivative fitters attempt to optimize the conformation over the range of the distance or angle constraint. However, only the derivative fitter optimizes the fit to the midpoint of the distance or angle constraint. That is, the derivative fitter can not only find a conformation that fits the query, but can also find the conformation that fits the query as closely as possible.

Note: If you want the derivative fitter to optimize to the midpoints of the distance and angle constraints, you must specify a search cutoff for RMS deviation and/or specify that ISIS calculate derived data on RMS deviation. If you do not calculate RMS deviation, the derivative fitter optimizes the fitted structure only to the ranges of the distance or angle constraints.

The RMS deviation is expressed as follows:

That is, the RMS deviation is the sum of the RMS deviations of the individual 3D query features. The RMS deviations from each of the individual 3D query features are computed in the following way:

where RMS(p) is the p-th constraint, n is the number of type p constraints in the query, vi is the measured value of constraint i, vu is the upper bound of constraint i, and vl is the lower bound of constraint i.

Note: To calculate RMS deviation, you must specify fitting at search time, and specify a maximum number of attempted fittings that is greater than zero. (If you do not set these CFS options, ISIS sets them for you.)

To view RMS deviation on your form, connect a form box or table column to MODEL>CFS_RMS.

Van der Waals Energy Difference (vdW)

The difference in van der Waals (vdW) nonbonded interaction energy between the fitted conformation and the conformation that is stored in the database. The values of vdW can fall within the range of -10,000 to 1e20 Kcals. If you specify a search cutoff value, ISIS excludes fitted structures that have more than the value that you specify. If you do not specify a search cutoff value, the vdW values that ISIS calculates during the search can range from  -10,000 to 1e20 Kcals. We suggest a search cutoff value of 5 Kcals.

The vdW energy is expressed as the following Lennard-Jones 6-12 potential:

Where Ri and Rj are the van der Waals radii of atoms i and j, respectively, and rij is the measured distance between atoms i and j. Atoms i and j must be at least four bonds apart.

The calculated vdW energy difference can be compared to nonbonded interaction energy in molecular mechanics solely if the fitted 3D structures contain hydrogens. If the stored 3D models in your database do not contain explicit hydrogens, then you must sprout hydrogens at all sites on the fitted 3D structures. For more information on hydrogen sprouting, see Section 32.9.

Note: To calculate data on van der Waals energy difference, you need to specify fitting at search time, bump checking at search time, and a maximum number of attempted fitting that is greater than zero (If you do not set these CFS options, ISIS sets them for you.).

To view van der Waals energy difference on a form, connect a form box or table column to MODEL>CFS_VDW.

Fitter

The type of fitter (Simplex or Derivative) that ISIS used in the CFS search. This data is the same for all records from a CFS search, so it is not suitable for sorting. To view the fitter information on a form, connect a form box or table column to MODEL>CFS_FITTER. For more information on fitters, see Section 32.8.3.

32.8.5 Requirements of CFS Search Options

Some CFS options require specific settings for other CFS search options. If you do not specify the correct values, ISIS changes them automatically. These requirements are listed as follows:

For Bump Checking

To specify bump checking at search time, you must use a value that is greater than zero for the Maximum number of attempted fittings (5 is the suggested value).

You must specify bump checking during the CFS search if you want to:

*	Use van der Waals energy difference to sort your search results or as a search cutoff.

*	Specify global relaxation during the CFS search.

Derived Data For Search Cutoffs, Viewing, and Sorting

To sort your search results by RMS deviation, you must use the derivative fitter. Also, you must specify a value that is greater than zero for the Maximum number of attempted fittings (5 is the suggested value).

To calculate van der Waals energy difference for viewing, for sorting, or as a search cutoff, you must specify the fitter of your choice, enter a value that is greater than zero for the maximum number of attempted fittings (5 is the suggested value). You must also specify bump checking at search time.

32.8.6 Limitations of CFS Searches

In a CFS search, 3D models are filtered out of the results through the three-step searching process. However, the CFS search might overlook 3D structures in the following ways:

Conformational Fitting Limitations

The number of iterations of attempted unique mappings required to retrieve all of the important 3D models might not be enough. Iterations depend on such factors as the number and type of query constraints, the number and mapping locale of atoms in the stored 3D models (especially for 3D models with highly symmetric or many aromatic rings), and the sizes of the 3D models. In addition, the fitter might converge to a false minimum (or local minimum) and reject a valid hit.

You can mitigate this limitation by increasing the maximum number of attempted fittings, allowing ring flexing, and by turning off bump checking. This increases the number of hits but can also produce false hits.

Bump Checking Limitations

During conformational fitting, ISIS rotates solely bonds in the region that matches the query. Therefore, atoms that are outside this region might interfere during the bond rotations and result in the exclusion of a valid hit. You can, however, remove this limitation by activating global relaxation.

32.9 Sprouting Hydrogens and Lone Pairs

3D structures in a molecule database generally don not contain explicit representations of hydrogen atoms. You can, however, create explicit hydrogen atoms on the structures that you retrieve by sprouting hydrogen atoms on 3D structures. You must sprout hydrogen atoms in the following situations:

*	During bump checking. This produces more realistic 3D structures and allows ISIS to correctly calculate data on van der Waals energy difference.

*	To export 3D structures to modeling software programs that cannot sprout hydrogens.

Note: If your query contains lone pairs, sprouting hydrogen atoms also sprouts lone pairs at sites that correspond to lone pairs on the query.

You have three options for displaying hydrogen atoms and lone pairs on the structures that you retrieve:

Off

Prevents sprouting of hydrogens and lone pairs on retrieved 3D structures. Use this setting when the 3D structures in your database already contain sufficient explicit hydrogens and lone pairs, or when your query does not contain explicit hydrogens and lone pairs.

Query Atoms Only

Sprouts hydrogens and lone pairs on retrieved 3D structures, but solely at sites where hydrogens and lone pairs appear on the query. Use this setting during the initial CFS search, for faster searching.

All

Sprouts hydrogens at all sites on retrieved 3D structures, and sprouts lone pairs on retrieved structures at sites where lone pairs appear on the query. In a bump-checking CFS search, use this setting to produce fitted structures that are more realistic. You must use this setting if you want to export 3D structures to a modeling software program that does not sprout hydrogens.

32.10 Guidelines for Revising a CFS Search

If your CFS search did not produce the results that you wanted, use the guidelines in this section to:

*	Increase or decrease the number of 3D structures that you retrieve.

*	Increase and maintain high search speeds.

*	Use multistep search strategies to refine your query.

32.10.1 Increasing or Decreasing the Number of Retrieved Structures

If your CFS search retrieved no records or too few records, you might want to:

*	Conduct a CFS search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, or increase the range of distance, angle, and other 3D constraints. If your query contains a submodel, you can increase the fixed-atom tolerances.

Note: If you make your query more general, search speed can slow significantly. For more information on maintaining high search speeds when refining your query, see Section 32.10.3.

If your CFS search retrieved too many records, you might want to:

*	Refine your query, and then search the same set of records. For example, you can restrict atom or bond variation with explicit atoms or bonds, add additional substructures to the query, narrow the ranges of distance, angle, and other 3D constraints. If your query contains a submodel, you can decrease fixed-atom tolerances.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, then save the list. Next, conduct an additional search for compounds that you want to exclude, and save that list. Then, subtract the second list (the one that contains compounds that you want to exclude) from the first list.

*	Set the search domain to the list of the records retrieved, then conduct another search to reduce the number of records. For example, you could conduct a Search By Form to exclude molecules above a specific molecular weight.

32.10.2 Increasing and Maintaining High Search Speeds

Each of the three steps of a CFS search eliminates false hits in different ways. In addition, the three-step CFS searching process allows you to choose whether you want to perform conformational fitting or bump checking during the search. If you perform the search without these options, your search speed increases, but your hit list will contain additional hits that would otherwise be eliminated.

2D Key Screening

Every structure in a database has a set of binary representations of its structural entities, called keys. The 2D key screening step eliminates all the 3D models in the database that do not contain the structural fragments of your query embedded in them. The presence of structural fragments and their combinations can be represented by one or more of 960 key codes.

To improve search speed, you want your query to contain as many different structural features (that is, to set as many keys) as possible. This eliminates many compounds at the 2D key screening step of CFS searching and thereby reduces the calculations during the slower steps that follow. The following characteristics increase the number of keys in a query:

*	Different atom types

*	Different bond types and connectivity

*	Different types of functional groups

*	Different types and sizes of rings

For example, if you are searching for carbohydrate structures, your query might contain solely carbon and oxygen atoms. You can increase the number of keys by including rings and functional groups that you know are present in the structures that you want, even if they are not part of the pharmacophore.

2D Key Screening and Upper/Lower Bounds Checking

To increase and maintain high search speeds during both the 2D key screening and upper or lower distance screening steps of a CFS search:

*	Use as many 2D query features as possible, and use as many specific 2D query features as possible if they can replace 3D constraints. For example, to define two atoms that are bonded, always draw the bond explicitly instead of using a distance constraint.

*	Draw as precise a query as you can, but use the fewest possible points to define lines and planes. ISIS calculates a best-fit line for three or more points and a best-fit plane for four or more points. Calculations require time.

*	Avoid using fixed-atom positions in the query. This query feature slows both the upper or lower distance screening and conformational fitting steps. You might consider replacing fixed-atom positions with a few well-placed distance constraints.

*	Avoid using unconnected atoms in the query. (The slowest atoms are C and A.).

*	Avoid highly symmetrical queries. Highly symmetrical queries cause ISIS to perform the same mappings multiple times, with no increase in the number of hits. You can reduce the symmetry of a query by adding atoms or functional groups that are not part of the pharmacophore, but which you know are present in the molecules that you want.

*	Avoid multiple atom and atom-pair data constraints.

*	When you combine a CFS search and a data search, always conduct the data search before the CFS search. This applies both to text and numeric data in Search By Form (for example, molecular weight < 500 or activity LIKE "%Phosphodiesterase IV%") and to graphical queries that contain 3D atom and atom-pair data (for example, coupling constant >2.0 or charge <-0.31).

*	If your query contains a submodel, turning off the RMS deviation constraint can increase search speed.

Conformational Fitting

To increase and maintain high CFS search speeds in the conformational fitting step:

*	Avoid conformational fitting during the search (search-time fitting). Your results will contain 10 to 15% additional 3D models that are false hits (false positives). To prevent conformational fitting, set the maximum number of attempted fittings to zero.

*	If you need to use the conformational fitter during the search (search time), minimize the number of attempted fittings, and minimize the number of dependent constraints. (One strategy for a first pass of searching is to enter a value of 1 for the maximum number of attempted fittings.)

Note: This procedure might result in missed hits.

*	Avoid bump checking during the search (search-time bump checking). However, this can produce results that contain additional conformations with unfavorable nonbonded interactions (that is, conformations that contain atoms that bump into one another).

*	Use the derivative fitter when possible, especially if you activate ring flexing and bump checking. The derivative fitter is faster for these options.

Note: You can use the derivative fitter if your query contains solely the following 3D query components: atoms, ring centroids, distances, and angles defined by three atoms or ring centroids.

32.10.3 Using Multistep Search Strategies to Refine Your Query

To find the query that best describes the geometry of active compounds, you generally do several CFS searches with increasingly refined queries. You can maintain high CFS search speeds by using query features and CFS options that slow down searches at later stages of query refinement. Then, you search the entire database with your final query.

This approach increases search speed for individual CFS searches during query refinement. Conducting the final search over the entire database allows you to find hits that earlier searches might have missed.

Use the following during the initial stages of multistep search strategies:

*	If your multistep search strategy includes a 2D structural or 3D data search, perform these searches first. For example, you can conduct a Search By Form for a specific therapeutic activity and then conduct a CFS search for topological differences among the models retrieved from the Search By Form.

*	Avoid using exclusion spheres, lines, and planes. These constraints require calculation time that can slow search speeds.

For example, you might consider conducting a CFS search with a query that contains exclusion spheres after a CFS search with a query that does not contain exclusion spheres. You might also consider replacing a planarity constraint with an angle constraint. In the examples below, the query with the angle constraint requires much less search time than the query with the planarity constraint:

*	Avoid using unnecessary explicit hydrogens and lone pairs in the query. ISIS requires sprouting time.

*	Omit the bump-checking CFS search. This increases search speed but increases the number of false hits by as much as 10 - 15%.

*	If you perform a bump-checking CFS search over an extremely large list of structures, first conduct the search without sprouting hydrogens at all sites. Then, set the search domain to the hit list from the first bump-checking CFS search and conduct a second bump-checking CFS search with hydrogens sprouted at all sites. Sprouting hydrogens on retrieved 3D structures can require a long time.

Note: If you want to export your fitted structures to modeling software programs that cannot sprout hydrogens, you must sprout hydrogens during the bump-checking CFS search.

*	Avoid using Rgroups.

*	Avoid ring flexing. Ring flexing calculations can require a long time. Also, you must increase the maximum number of attempted fittings for ring flexing, which also slows search speed.

*	Avoid rotating bonds between unsaturated atoms. Rotating bonds between unsaturated atoms increases the calculation time during conformational fitting.

*	Use a small value for the maximum number of attempted fittings. This avoids spending time to fit flexible and highly functional compounds (for example, peptides) that might not interest you.

*	If you want to use a TDF search cutoff to eliminate highly flexible molecules, use it in the early stages of query development. The TDF cutoff eliminates flexible molecules before conformational fitting begins.

In the later stages of multistep search strategies:

*	During bump checking, sprout hydrogens at all sites on the fitted 3D structure and lone pairs at sites that match the query. This produces fitted structures that are more realistic.

*	Activate global relaxation during bump checking to avoid excluding valid hits. Global relaxation prevents atoms in other parts of the molecule from interfering with bond rotation in the region that fits the query.

*	Create highly specific queries. You can use Rgroups and other query features to create highly specific chemical environments. For examples of how to use Rgroups to create specific chemical environments, see Section 32.4.

32.11 Searching Example 1: Searching For Pharmacophores with 3D Substructure Queries

This example uses the 3D query that is based on a pharmacophore hypothesis proposed by Kato and coworkers (Kato, K., et al., J. Med. Chem. 1985, 28, 287-294). The 3D query contains a 3D substructure. These results are compared with those of the SSS3D search.

This example uses the ISISMX3D database.

32.11.1 Problem

Find compounds that inhibit thromboxane synthetase and have the following characteristics:

*	1-imidazolyl or 3-pyridyl on one end

*	Carboxylic acid at the other end

*	A distance of 8.5 to 10.0 Angstroms between the oxygen of the carboxylic acid and the nitrogen of the imidazole or pyridine ring

32.11.2 Approach

Draw a query that contains two fragments: one to represent the carboxylic acid and the other to represent the aromatic nitrogen. Add a distance constraint between the oxygen of the carboxylic acid and the nitrogen of the ring.

32.11.3 Query

32.11.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for CFS, how to/examples.

Search Domain (Step 1)

Set the search domain to the entire database.

Initial CFS Search (Step 6)

Specify the default CFS options.

Specify the following sorting instruction:

Sort each MODEL by >CFS_TDF from low to high

In CFS Options, specify Calculate TDF for sorting ( [image])

Specify a TDF search cutoff of 10.

Bump-checking CFS search (Step 8)

Perform the bump-checking CFS search.

32.11.5 Results

The CFS search retrieves five 3D models in ascending order by TDF values (see the table that follows). The higher the TDF value, the more flexible the 3D model.

The following table compares the results of the CFS and SSS3D searches:

In this searching example, the SSS3D search retrieves Model Regnos 80 and 95. The CFS search retrieves three additional Model Regnos: 25, 54, and 74. The following results sample includes Model Regnos 80, 25, and 74.

32.12 Searching Example 2: Searching For Pharmacophores with Submodel Queries

This example uses the 3D query by Petrillo and coworkers (Petrillo, E. W., and Ondetti, M. A. Med. Res. Rev. 1982, 2, 1-41) to retrieve compounds with the CFS search. The 3D query contains both a 3D substructure and a submodel.

This example uses the ISISMX3D database.

32.12.1 Problem

Find compounds that inhibit angiotensin-converting enzyme (ACE) and have the following features in common with Spirapril:

*	A fixed spatial arrangement of the alpha carboxylic acid group with respect to the ring nitrogen.

*	Similar distance constraints among two oxygens and a nitrogen in the aliphatic group.

32.12.2 Approach

To create the submodel query, retrieve Spirapril from the database, and then eliminate all but two portions of the 3D structure. Fix the three atom positions, and then add the three distance constraints. The following figure shows how to construct the query (atoms in boldface in the structure of Spirapril are also present in the query):

32.12.3 Query

32.12.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for CFS, how to/examples.

Search Domain (Step 1)

Set the search domain to the entire database.

Fixed-Atom Tolerances (Step 4)

You require the following settings:

*	Maximum atomic displacement: 0.5. The individual atoms in the 3D models that correspond to the three fixed atom positions in the query will be checked for deviations that are within 0.5 Angstroms.

*	Maximum RMS deviation: 0.5. The overall spatial arrangement of atoms in the 3D models that correspond atoms in the submodel in the query will be checked for deviations that are within 0.5 Angstroms.

Initial CFS Search (Step 6)

Specify the default CFS options.

Specify the following sorting instruction (automatic sorting):

Sort each MODEL by >CFS_TDF from low to high

In CFS Options, specify Calculate TDF for sorting ( [image])

Specify a TDF search cutoff =10.

Bump-Checking CFS Search (Step 8)

Perform the bump-checking CFS search.

32.12.5 Results

In this example, the CFS search results differ from the results of the SSS3D search.

The CFS Search

The CFS search retrieves nine 3D models in ascending order by TDF values. The higher the TDF value, the more flexible the 3D model. The bump-checking CFS search removes three of the twelve hits from the initial CFS search. Four of the nine 3D models from the bump-checking CFS search are known ACE inhibitors. Therefore, the other five 3D models might be valid conformations and can be tested for activity.

The SSS3D Search

The SSS3D search retrieves four 3D models in ascending order by Model Regno. The first three 3D models are known ACE inhibitors. Therefore, the last 3D model might a be valid conformation and can be tested for activity.

The CFS and SSS3D searches retrieved both Spirapril (Model Regno 92) and the following ACE inhibitor:

The fixed atom positions, (F), shown here are for illustrative purposes and do not appear when the query is overlaid onto the 3D model. The following 3D model (Model Regno 95) was retrieved from both searches. This 3D model might be a valid conformation, although it has not been tested for activity:

Although a stored conformation can fit the query, it might be prohibited from being retrieved because of interactions between nonbonded atoms or bonds. The following 3D model is an example of a conformation that could not be fit to the query solely because of nonbonded interactions between the methyl and methylene groups that are circled (For clarity, one of the distance constraints is not displayed):


Remote SBF for 3D Databases: Searching Concepts/Examples

Click [image] to print Part 1.    Click [image] to go to Part 2.    Click [image] to close this Request-A-Document.

This Request-A-Document contains:

Part 1:

*	Definition of a Remote SBF Search in a 3D Database	41.1

*	Specifying Query Features on Atoms and Bonds	41.2

*	Specifying Rgroup Query Features	41.3

*	Specifying Chemical Environments	41.4

*	Specifying Stereochemistry in 2D Graphical Queries	41.5

*	Specifying Submodel Components	41.6

---------------------------------------------------------------------------------------------------------------------

Part 2:

*	Specifying 3D Objects and Constraints	41.7

*	Using Receptor Information	41.8

*	Sprouting Hydrogens and Lone Pairs on 3D Structures	41.9

*	Guidelines for Revising the Query	41.10

*	Searching Example 1: Combining Text/Numeric
Queries	41.11

*	Searching Example 2: Combining Text/Numeric and
2D Graphical Queries	41.12

*	Searching Example 3: Combining Text/Numeric and
3D Graphical Queries	41.13

We recommend that you print this Request-A-Document, and then browse through it. For technical reasons, this 57-page Request-A-Document has been divided into two parts. To print Part 1, click the Printer icon at the top of the screen. To print Part 2, first click the Part 2 icon, and then click the Printer icon at the top of the screen.

For step-by-step instructions on conducting an SBF for 3D Databases search, click here.

41.1 Definition of a Remote SBF Search in a 3D Database

A remote Search By Form (SBF) search finds 3D records in your remote 3D database that contain your text/numeric query exactly as you specify it or your graphical query as a substructure wholly within a larger structure.

Note: If your database contains the exact match of your substructure query, you also retrieve the exact match.

In addition, you can combine text/numeric and graphical queries. For example, you want to find all 3D structures that contain a specific 2D steroid substructure wholly within them and that have a melting point that is greater than 220 degrees Centigrade and that contain a compound name that ends in "one":

Your text/numeric query can also contain wildcards. A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: (The wildcard % is a placeholder for at least one unspecified character.) To find the exact match of the data of interest, enter the search operator LIKE and place your target text in double quotes. A search operator is the command that specifies the type of search. For more information on search operators, see Section 41.1.2.

You can use a graphical query to search for either 3D structures or 2D structures in a 3D database. A 3D structure defines the spatial arrangement of atoms in a molecule. In contrast, a 2D structure specifies solely the number, type, and connectivity of atoms in a molecule, without any information on spatial arrangement. For example:

Note: A 2D structure or graphical query can contain Up and Down stereo bonds that specify stereoconfiguration at an asymmetric center. Do not use Up and Down stereo bonds in 3D structures or graphical queries. In a 3D structure, the 3D spatial arrangement of atoms specifies the stereochemistry.

Your 3D and 2D graphical queries can also contain restrictions (called query features) on atoms and bonds. For example, you can use the ISIS bond-query feature Ch to specify that a bond is part of an acyclic structure in the records retrieved. You can also add hydrogens with visible bonds (called explicit hydrogens) to your query to block substituents on specific atoms.

For more information on 2D graphical queries, see Section 41.1.4. For more information on 3D graphical queries, see Section 41.1.5.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

41.1.1 Specifying a Text/Numeric String as a Query

A text/numeric string as an SBF query is a phrase in a box or column on the form that specifies the retrieval of data. For example, to find structures with a molecular weight greater than 350, enter the text/numeric string > 350 into the Molecular Weight box on the form.

Each phrase in a text/numeric string contains:

*	A search operator that specifies the type of search. For example, the search operators = (equal sign) and LIKE specify the retrieval of the exact match of your query. Use = when you want to retrieve data with numeric values. Use LIKE when you want to retrieve data with text. For details on search operators, see Section 41.1.2.

*	A text or numeric target value that you want to find (such as 350 for the molecular weight or ANTIBIOTIC for the activity).

Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

Specifying Numeric String Queries

Do not include the units, such as a percent sign (%) or the degrees Centigrade (C). For example, to retrieve all compounds with a molecular weight greater than 350, enter:

> 350

where the search operator is > and the target value is 350.

Specifying Text/Numeric String Queries

Always use a wildcard, such as %, in queries that contain text (with or without numeric values). Double quotes around the text string are optional. For example, to retrieve all compounds from the author Smythe, enter one of the following:

LIKE %Smythe%
LIKE "%Smythe%"

where the search operator is LIKE and the target value is Smythe.

A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. The wildcard _ is a placeholder for solely one unspecified character. Without a wildcard, you retrieve solely those records that contain exactly the target value that you specified. For example:

Query Without a Wildcard	Example of a Record Retrieved

LIKE "antibiotic"	Antibiotic

Query With the Wildcard %	Examples of Records Retrieved

LIKE "%antibiotic%"	Antibiotic

Antibiotic activity

Resistance to extracellular products such as antibiotics

Note: If you want to retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

41.1.2 The Search Operators

<, <=, >, >=, and <>

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Search Operator	Definition	Examples

=	equal (numeric)	= 350

<	less than (numeric)	< 350

<=	less than or equal to (numeric)	= 350

>	greater than (numeric)	> 350

>=	greater than or equal to (numeric)	>= 350

<>	not equal to (text or numeric)	<> 350

<> "initiator"

LIKE

Use LIKE with text enclosed in double quotation marks. Enter your query as follows:

Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. For example:

Query	Examples of Records Retrieved

LIKE "methane"	Methane

LIKE "benzoic acid"	Benzoic Acid

LIKE "%acid"	Benzoic Acid

Acetic Acid

LIKE "%acid%"	Benzoic Acid Sodium Salt

Acetic Acid Sodium Salt

LIKE "%but_ne"	Trans 2-Butene

2-Butene

N-Butane

Butane

Butene

LIKE "_ethyl"	Methyl

Ethyl

LIKE "antibiotic"	Antibiotic

LIKE "%antibiotic%"	Antibiotic activity

Resistance to extracellular products such as antibiotics

Note: To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice. To retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

BETWEEN

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks. For example:

BETWEEN "XR11" "XZ15"

BETWEEN 95 100

EXISTS

Use EXISTS to retrieve all records in the database that contain data in a specific database field. For example:

EXISTS

Note: You can only use the EXISTS search operator for database fields that do not give you an error message.

41.1.3 Specifying a Molecular Formula as a Query

To search the data in Formula box (that is, a box that is connected to a MOLFORMULA field), you can specify the following text/numeric queries:

*	An exact formula. Use an exact formula query to find records that contain solely the exact atoms that you specify.

*	A subformula. Use a subformula query to find records that contain the specific atoms that you specify, and any additional atoms.

Exact Formula Query

To specify an exact formula query, specify the target value for the formula. The target value must include all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required. The equals operator (=) and quotes are optional. For example:

Exact Formula Query	Examples of Records Retrieved

c6 h6 O	Phenol

c6h6o

C20 H12 Na2 O4	Sodium salt of phenolphthalein

C20H12Na2O4

= C20 H12 Na2 O4

= C20H12Na2O4

= "C20 H12 Na2 O4"

= "C20H12Na2O4"

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Exact Formula Query	Examples of Records Retrieved

C17 H19 N 03	Piperine

C17H19N 03	Piperine

C17H19N103	Piperine

C17H19N03	No molecules retrieved. ISIS interprets "NO3" as 3 Nobelium atoms.

Subformula Query

To specify a subformula query, use the LIKE operator with a target value for the subformula. The target value can include a range of atom counts, and typically excludes the hydrogens. To exclude specific atoms from the molecules that you retrieve, specify zero for that atom. You can use a single space to separate atoms. Capital letters are not required. Quotes are optional.

Subformula Query	Examples of Records Retrieved

LIKE Na	All sodium salts

LIKE c12 Br(1-2) S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE "C12Br(1-2)S2"	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE c6 h6	All molecules that contain six carbon atoms, six hydrogen atoms, and any number of other atoms

LIKE C5 H10 N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

LIKE C5H10N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Subformula Query	Examples of Records Retrieved

LIKE C12 Br S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12Br1S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12BrS2	No molecules retrieved. ISIS interprets "BrS" as an atom symbol, and gives an error message.

41.1.4 Specifying a 2D Graphical Substructure as a Query

A 2D graphical substructure query retrieves 2D structures that contain your graphical query embedded wholly within them. For example:

You can also increase the power of an SBF search by the addition of specific restrictions (called query features) on atoms and/or bonds. There are a number of query features available for use.

In the following example, the ISIS atom-query feature (H0) prohibits the attachment of hydrogens on a specific atom in the records retrieved:

In addition, the hydrogens block substitutions at the specified positions.

To use a 2D graphical query, you must have a box or table cell on the form that connects to the database field MOLSTRUCTURE.

For more information on query features for 2D graphical queries, see Section 41.2.

Notes: You do not use a search operator with a graphical query.

41.1.5 Specifying a 3D Graphical Substructure as a Query

A 3D graphical substructure query retrieves 3D records from your 3D database that contain your graphical query embedded wholly within them. You can increase the power of an SBF search by adding specific restrictions (called query features). There are a number of query features available for use. A 3D graphical substructure query can contain any of the following 3D query features:

*	Submodel. A submodel is a three-dimensional (3D) representation of a portion of a molecule. A submodel contains two or more atoms in a fixed spatial arrangement (F). You construct a submodel from an existing 3D structure. For example:

For more information on submodels, see Section 41.6.

*	3D geometric constraints. You construct geometric constraints from atoms or from 3D objects such as points, lines, and centroids. For example, you can specify that the centers (centroids) of two rings must be separated by a distance of 2 to 10 Angstroms:

For more information on 3D geometric constraints, see Section 41.7.

*	3D data constraints that you apply to individual atoms or to pairs of atoms. The following example shows calculated values (in Hz) for the ring proton spin-spin couplings of methyl 2-furoate:

For more information on 3D data constraints, see Section 41.7.

A 3D graphical search query can also contain 2D query features. A 2D query feature is a restriction on an atom or bond that specifies solely the number, type, and connectivity of atoms in a molecule, without any information on spatial arrangement. 2D query features can include:

*	Query features on atoms and bonds. You can allow or exclude specific atoms at certain locations, allow or exclude specific types of bonds, and so on. For example, the following query specifies that only carbon, nitrogen, or oxygen can be present at a specific position on the ring:

For more information on atom and bond query features, see Section 41.2.

*	Rgroups. An Rgroup query contains a root structure with defined Rgroup substituents attached to it at specific positions. An Rgroup consists of the molecule fragments (substituents) that can attach to the corresponding Rgroup sites on the root. That is, any Rgroup substituents that are members of the Rgroup R1 can attach to any position with the Rgroup label R1.

For example, you can specify that the Rgroup label R1 on the root structure allows a carboxyl group at its position and that R2 allows either a chloride atom or a sulfonic acid group at its position:

For more information on Rgroups, see Section 41.3.

You can combine 2D and 3D query features to specify:

*	Chemical environments. You can use 2D query features to specify chemical environments such as basic nitrogens, acidic centers, hydrogen-bond donors, or hydrogen-bond acceptors on the molecules that you retrieve. For example, the following is can be considered a hydrogen-bond donor:

For more information on chemical environments, see Section 41.4.

*	Information on the receptor with which active structures interact. For example, you can specify a distance constraint between a hydrogen-bond donor and a hydrogen-bond acceptor on the receptor:

For more information on queries that use information on the receptor, see Section 41.8.

In the following example, you want to find all molecules with a specific 3D substructure wholly within them and that have a molecular weight that is less than 400:

Notes: (1) To use a 3D graphical query, you must have a box or table cell on the form that connects to the database field MODELSTRUCTURE. (2) An SBF search with a single 3D graphical substructure query is equivalent to an SSS3D search with the same graphical query. (3) You do not use a search operator with a graphical query.

41.1.6 Specifying Multiple Queries in a Single SBF Search

When you combine two or more queries of any type into a single SBF search, the search results that you obtain depend on both the specifications and accuracy of your query and the way that information is stored in your database. For more information on how to create an adequate query, see Section 41.1.1 and Section 41.1.2.

Information in a database is stored either in a single level (called a flat database) or in multiple levels (called a hierarchical database). Storage in a hierarchical database is more efficient, but it requires you to enter your queries in the correct location on the form to obtain the search results that you want.

For example, the following hierarchical database stores data for multiple decomposition tests that are conducted under different atmospheric conditions:

(In this database, structures are stored at the top (or root) level, and the percentage of oxygen and the number of peaks are stored at a lower level, under the parent field Decomposition. A parent field is a branch in the hierarchy that contains a set of child fields, such as percent O2 and number of peaks.)

You want specific decomposition data from different tests. Your multiple query in a single SBF search specifies that you want all compounds within a single test that contain: Query 1, greater than 65% O2; Query 2, less than three peaks.

To obtain search results that match all queries (Query 1 AND Query 2), you can either (a) enter each search query into separate boxes or (b) enter each search query into the same row in a single table. This search gives you all compounds within a single test that meet both requirements in your query:

Caution: For all versions of ISIS before 2.0, multiple queries in boxes might give different results than multiple queries in tables. In the previous example, the SBF query in the box on the form at the left retrieves records in which at least one decomposition test that matches both conditions. The SBF query in the table on the form at the right, however, retrieves additional records in which one decomposition test matches one condition, and another decomposition test matches the other condition. In ISIS 2.0, both queries retrieve only those records in which both conditions are met within the same decomposition test.

To obtain search results that match either one query or the other (Query 1 OR Query 2), you must enter each search query into different rows of a single table. You must be certain that the first column in the table is a field at the same database level that you want to search. This search gives you all compounds within a single test that meet either requirement in your query (but not necessarily both requirements):

When you filter your search results, you see solely those lower-level records that meet your search requirements.

Note: A box retrieves data from a single database field. A table retrieves data from multiple database fields. Also, you can enter as many as 25 queries into the same table.

41.1.7 Specifying Searchable Keys as a Query

If your database contains the database field MOLSKEYS, you can use numbered keys to retrieve specific substructures or chemical representations. Separate multiple keys with a comma (with no spaces):

*	Use parentheses to specify the retrieval of all the keys in your query. Example: To specify the retrieval of molecules that contain 6-membered rings and bromine, enter (163,46) into the box or table cell on the form in ISIS/Base that connects to the database field MOLSKEYS.

*	Use square brackets to specify the retrieval of one ore more keys in your query. Example: To specify the retrieval of molecules that contain 6-membered rings or bromine, enter [163,46] into the box or table cell on the form in ISIS/Base that connects to the database field MOLSKEYS.

*	Use angle brackets to specify the retrieval of none of the keys in your query. Example: To specify the retrieval of molecules that do not contain 6-membered rings or bromine, enter <163,46> into the box or table cell on the form in ISIS/Base that connects to the database field MOLSKEYS.

*	Use braces to specify the retrieval of solely one of the keys in your query but not any others in your query. Example: To specify the retrieval of molecules that contain either 6-membered rings or bromine but not both 6-membered rings and bromine, enter {163,46} into the box or table cell on the form in ISIS/Base that connects to the database field MOLSKEYS.

*	Use no restrictors to specify the retrieval of one and/or any other keys in your query. Example: To specify the retrieval of molecules that contain 6-membered rings and/or bromine, enter 163,46 into the box or table cell on the form in ISIS/Base that connects to the database field MOLSKEYS.

Additional Examples

The query 161,[11,96] specifies the retrieval of N and a 4- or 5-membered ring.

The query [(161,96),(164,163)] specifies the retrieval of N and a 5-membered ring or O and a 6-membered ring. Both sets of molecules can be retrieved.

The query [42,46,103],<27> specifies the retrieval of at least one halogen, which cannot be iodine.

The List of Searchable Keys

If you search a MACCS-II database, there are 166 numbered keys that you can use. If you do not recognize the words for a specific key, the words might be in a special type of language called query language. (For more information on query language, see your ISIS Administrator.) The list of searchable keys is as follows:

Key	Description	Key	Description

1	ISOTOPE	84	NH2

2	103 < ATOMIC NO. < 256	85	CN(C)C

3	GROUP IVA,VA,VIA PERIODS 4-6 (GE..)	86	CH2QCH2

4	ACTINIDE	87	X!A$A

5	GROUP IIIB,IVB (SC..)	88	S

6	LANTHANIDE	89	OAAAO

7	GROUP VB,VIB,VIIB (V..)	90	QHAACH2A

8	QAAA@1	91	QHAAACH2A

9	GROUP VIII (FE..)	92	OC(N)C

10	GROUP IIA (ALKALINE EARTH)	93	QCH3

11	4M RING	94	QN

12	GROUP IB,IIB (CU..)	95	NAAO

13	ON(C)C	96	5M RING

14	S-S	97	NAAAO

15	OC(O)O	98	QAAAAA@1

16	QAA@1	99	C=C

17	CTC	100	ACH2N

18	GROUP IIIA (B..)	101	8M RING OR LARGER

19	7M RING	102	QO

20	Si	103	CL

21	C=C(Q)Q	104	QHACH2A

22	3M RING	105	A$A($A)$A

23	NC(O)O	106	QA(Q)Q

24	N-O	107	XA(A)A

25	NC(N)N	108	CH3AAACH2A

26	C$=C($A)$A	109	ACH2O

27	I	110	NCO

28	QCH2Q	111	NACH2A

29	P	112	AA(A)(A)A

30	CQ(C)(C)A	113	Onot%A%A

31	QX	114	CH3CH2A

32	CSN	115	CH3ACH2A

33	NS	116	CH3AACH2A

34	CH2=A	117	NAO

35	GROUP IA (ALKALI METAL)	118	ACH2CH2A>1

36	S HETEROCYCLE	119	N=A

37	NC(O)N	120	HETEROCYCLICATOM>1 (&..)

38	NC(C)N	121	N HETEROCYCLE

39	OS(O)O	122	AN(A)A

40	S-O	123	OCO

41	CTN	124	QQ

42	F	125	AROM RING>1

43	QHAQH	126	A!O!A

44	OTHER	127	A$A!O>1 (&..)

45	C=CN	128	ACH2AAACH2A

46	BR	129	ACH2AACH2A

47	SAN	130	QQ>1 (&..)

48	OQ(O)O	131	QH>1

49	CHARGE	132	OACH2A

50	C=C(C)C	133	A$A!N

51	CSO	134	X (HALOGEN)

52	NN	135	Nnot%A%A

53	QHAAAQH	136	O=A.1

54	QHAAQH	137	HETEROCYCLE

55	OSO	138	QCH2A>1 (&..)

56	ON(O)C	139	OH

57	O HETEROCYCLE	140	O>3 (&..)

58	QSQ	141	CH3>2 (&..)

59	Snot%A%A	142	N>1

60	S=O	143	A$A!O

61	AS(A)A	144	Anot%A%Anot%A

62	A$A!A$A	145	6M RING>1

63	N=O	146	O>2

64	A$A!S	147	ACH2CH2A

65	C%N	148	AQ(A)A

66	CC(C)(C)A	149	CH3>1

67	QS	150	A!A$A!A

68	QHQH (&..)	151	NH

69	QQH	152	OC(C)C

70	QNQ	153	QCH2A

71	NO	154	C=O

72	OAAO	155	A!CH2!A

73	S=A	156	NA(A)A

74	CH3ACH3	157	C-O

75	A!N$A	158	C-N

76	C=C(A)A	159	O>1

77	NAN	160	CH3

78	C=N	161	N

79	NAAN	162	AROM

80	NAAAN	163	6M RING

81	SA(A)A	164	O

82	ACH2QH	165	RING

83	QAAAA@1	166	FRAGMENTS

Where (&..) is equivalent to "and other rare features;" and Key 166 corresponds to molecules that consist of more than one fragment. (A molecule has more than one fragment if its structure cannot be drawn in one connected set of bonds.) Structural keys specify 2D structural features only. You cannot use searchable keys to specify the 3D spatial arrangement of atoms in the structures that you retrieve.

Some of the keys that you see are encoded in a substructure-search query language, such as QAAAA@1 for Key 83. This language allows atoms to be expressed as follows:

*	Unbracketed for C, N, O, P, and S; but bracketed for all other single element symbols, such as [CL] for chlorine, or multiple element symbols in lists, such as [N,O] for nitrogen and oxygen, or [F,CL,BR,I] for halogens.

*	A for any atom except hydrogen, and Q for any atom except carbon or hydrogen.

*	Substituted with a specific number of hydrogens: H0 on an atom prohibits hydrogens at that position, such as CH0; and Hn allows at least that number (n) of hydrogens, such as CH2 (methyl or methylene).

*	Charged: A plus sign (+) on an atom is a positive charge, such as +, +2, or +3; a single quote (') is a monoradical; a double quote (") is a negative charge; and an asterisk (*) is a neutral atom.

*	Variable in mass: The isotopic label M+n indicates a difference of n from the standard mass, such as CM+1 to indicate the isotope carbon 13, or OM-1 to indicate the isotope oxygen 15.

*	Variable in atom number: The notation @n at the end of the atom to which it refers indicates that atom number (n) is attached here. Atoms (except hydrogen) are numbered from left to right, such as C-C-C-@1 (but not @3-C-C-C) to indicate a three-membered ring, or CH3-C-C-C-@2 to indicate (methyl or methylene).

*	Branched: The parentheses around an atom or group indicates that the atom or group branches from the atom at its left (but not its right) in the string. For example, C-C-C-C is butane, while C-C(C)-C-C is 2-methyl butane. N+(-C)(-C)(-C)(-C) is a quaternary ammonium salt.

This language allows bonds to be expressed as follows:

*	Variable bond type: A hyphen (-) is a single bond; an equal sign (=) is a double bond; a (T) is a triple bond; a percent sign (%) is an aromatic bond; a tilde (~) is either a single or a double bond; and an unspecified bond type is the omission a bond marker. For example, the two carbon chain CC contains any type of bond.

*	Variable numbers of fragments: A space between strings indicates that there is no connection between the groups. For example, C=O C-OH retrieves a carbonyl and a hydroxyl, but the groups cannot be centered on the same carbon (the fragments cannot overlap).

*	Part of a ring: A dollar sign ($) that precedes a bond indicates that the bond is part of a ring.

*	Part of a chain: An exclamation sign (!) that precedes a bond indicates that the bond is part of a chain.

41.2 Specifying Query Features on Atoms and Bonds

A query feature on an atom and/or a bond in a molecule is a restriction that specifies the retrieval of certain types of molecule records from an ISIS/Base database. If you do not use query features, the molecules retrieved contain solely your exact substructure query embedded wholly within them. For example:

You can also define Rgroups that specify a root structure with defined Rgroup substituents attached to it at specific positions. For more information on Rgroups, see Section 41.3.

Note: Atom and bond query features are 2D query features. 2D query features specify solely the number, type, and connectivity of atoms in a molecule. You can use atom and bond query features in both 2D and 3D graphical queries. However, a 3D graphical query should contain at least one component that specifies the spatial distribution of atoms in a 3D structure. To specify the spatial distribution of atoms, you can use a submodel with two or more fixed atoms, and/or use 3D geometric constraints such as distances and angles. For more information on submodels, see Section 41.6. For more information on 3D geometric constraints, see Section 41.7.

41.2.1 Definition of Aromaticity

For remote databases: ISIS interprets the following ring systems as aromatic:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:

Note: The bonds of six-membered aromatic ring systems and the perimeter bonds of azulenes are stored as aromatic bonds in the database. The bonds of five-membered aromatic rings, however, are stored as single and double bonds and interpreted as aromatic during a search. The differences between five-membered rings and other types of aromatic rings can cause different search results for five- and six-membered rings/azulenes when you use the following bonds in queries: Single, Double, and Single/Double query bonds. For more information on the Single/Double query bond, see Section 41.2.8.

41.2.2 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except implicit or explicit hydrogens:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

41.2.3 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of implicit hydrogens. For example:

41.2.4 Allowing an Unsaturated Atom

Use an atom query feature to specify that an atom is unsaturated, or attached to at least one multiple bond: double, triple, or aromatic.

Atom Query Feature: Unsaturated Atom (u)

Specifies that the atom of your choice is unsaturated. For example, the following query specifies both an unsaturated atom and single or double bonds (the double dashed lines).

41.2.5 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

Use explicit hydrogens to block non-hydrogen attachments on atoms. For example:

Atom Query Feature: Substitution Count of Zero, s0

Specifies that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of an isolated atom.

Atom Query Feature: Substitution Count of One, s1

Specifies that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Two, s2

Specifies that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Three, s3

Specifies that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Four, s4

Specifies that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Five, s5

Specifies that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of at Least Six, s6

Specifies that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count as Drawn, s*

Specifies that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:

41.2.6 Allowing a Specific Number of Ring Bond Attachments

Use atom query features to specify the number of ring bond attachments.

Atom Query Feature: Ring Bond Count of Zero, r0

Specifies that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:

Atom Query Feature: Ring Bond Count of Two, r2

Specifies that the records retrieved have solely two ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of Three, r3

Specifies that the records retrieved have solely three ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of at Least Four, r4

Specifies that the records retrieved have at least four ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count as Drawn, r*

Specifies that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:

41.2.7 Allowing Additional Atoms and/or Bonds in a Chain or a Ring

Use a query feature that is for either atoms or bonds to specify the addition of atoms and/or bonds in a chain or a ring.

Atom or Bond Query Feature: Link Node

Use a link node to specify the addition of variable numbers repeating units (atoms and/or bonds) to a ring or chain. A repeating unit must be attached to two adjacent bonds. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the link node [L1-3]:

Or, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the link node [L1-3]:

41.2.8 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Note: An aromatic query bond hits any bond in all types of aromatic rings: 6-membered ring bonds, 5-membered ring bonds, and azulene perimeter bonds. For more information on the structures that ISIS interprets as aromatic, see Section 41.2.1.

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

Note: A Single/Double query bond does not hit bonds in 6-membered aromatic rings, or perimeter bonds of azulenes, because bonds in these structures are stored in the database as aromatic bonds. However, a Single/Double query bond does hit bonds in 5-membered rings that ISIS interprets as aromatic. For more information on the structures that ISIS interprets as aromatic, see Section 41.2.1.

Bond Query Feature: Single/Aromatic Bond

Specifies either a single or an aromatic bond at that position:

Bond Query Feature: Double/Aromatic Bond

Specifies either a double or an aromatic bond at that position:

41.2.9 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is attached to a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

41.2.10 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is attached to a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

41.3 Specifying Rgroup Query Features

An Rgroup query finds structures that contain your query as a root structure with defined Rgroup substituents attached to it at specific positions. Your query can contain restrictions on the Rgroup substituents, called Rgroup conditions: You can specify the number of Rgroup sites that must be occupied in the records retrieved, specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site, or specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

Your Rgroup query can also contain restrictions on atoms and bonds of the root structure and Rgroup substituents. For example, you can use the atom query feature H(0) to prohibit the attachment of implicit hydrogens on a specific atom in the structures retrieved.

An example of an Rgroup query is as follows:

You can use Rgroups and atom and bond query features to specify chemical environments such as basic nitrogens and acidic centers. For more information on chemical environments, see Section 41.4.

Note: Rgroup query features are 2D query features. 2D query features specify solely the number, type, and connectivity of atoms in a molecule. You can use atom and bond query features in both 2D and 3D graphical queries. However, a 3D graphical query should contain at least one component that specifies the spatial distribution of atoms in a 3D structure. To specify the spatial distribution of atoms, you can use a submodel with two or more fixed atoms, and/or use 3D geometric constraints such as distances and angles. For more information on submodels, see Section 41.6. For more information on 3D geometric constraints, see Section 41.7.

41.3.1 The Root Structure

The root structure contains the portion of the structure that does not vary among the structures retrieved. For example, if you want to find 2, 5-Dihydroxypyridine in which the substituent at position 2 can be COOH, CN, or Ph, and the substituent at position 5 can be OH or CH3, the root structure is 2, 5-Dihydroxypyridine with Rgroups (such as R1 and R2):

Rgroups

On the root structure, Rgroups (R1 through R32) are placeholders that designate where the lists of functional groups and atoms that can attach to the root structure. In the example above, the Rgroup R1 designates that the members of the list R1 (the Rgroup substituents) are allowed at position 5 on the root structure. The Rgroup R2 designates that the members of the list R2 (the Rgroup substituents) are allowed at position 2 on the root structure.

Multiple Rgroups at One Position

You can specify multiple Rgroups at a single site on the root structure. For example:

One Rgroup at Multiple Positions

You can specify a single Rgroup (such as R1) at multiple positions on the root structure. For example:

Note: See Section 41.3.3 to restrict the number of Rgroups that must be occupied in the records retrieved. A molecule might not have to satisfy all the Rgroup sites on the root structure to be retrieved. For example, the Rgroup condition R1 > 0 specifies that any molecule in which at least one of the R1 sites is filled by an R1 member will be retrieved. In addition, the Rgroup condition RestH determines whether the unsatisfied sites must be filled with hydrogen atoms or if other molecule fragments are allowed to be attached if they are not on the list.

41.3.2 Rgroup Substituents

Rgroup substituents are the members of the list of Rgroups. You define the Rgroup substituents that you will allow to be found at specified positions in the molecules retrieved. Rgroup substituents can be any structural fragment, including functional groups and single atoms.

In the example below, the Rgroup substituents COOH, CN, or Ph are allowed at position 5 (R1) on the root structure and the Rgroup substituents OH or CH3 are allowed at position 2 (R2) on the root structure:

Attachment Points

An attachment point (marked with an arrow and an asterisk) designates the atom on the Rgroup substituent that is attached to the root structure:

You must designate an attachment point on an Rgroup substituent for each bond that is attached to the substituent. If an Rgroup is attached to two bonds on the root structure, you must designate two attachment points. The bond on the root structure that is marked with double quotes corresponds to the attachment point on the Rgroup substituent that is marked with double quotes. The other attachment point on the Rgroup substituent is marked with a single quote:

Nested Rgroups

A nested Rgroup is an Rgroup that is a placeholder within another Rgroup rather than within the root structure. (You cannot nest an Rgroup any lower than this level.) In the following example, Rgroup R2 is nested within the Rgroup R1:

Nested Rgroups are equivalent to the following structures:

41.3.3 Rgroup Conditions

You can apply restrictions to each Rgroup in your query after you assemble all the Rgroups. The set of restrictions is called the Rgroup conditions.

If you do not apply Rgroup conditions, ISIS assigns the default conditions: Occurrence > 0 and RestH off for each Rgroup.

Occurrence

With the Rgroup condition Occurrence, you can specify the number of Rgroup sites that must be occupied in the records retrieved. For example, the occurrence designation R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved. Type one of the following values in the Occurrence range text box:

Value	Explanation

0	All members of the Rgroup are excluded from the Rgroup site (such as R1). To allow any other Rgroup substituent at the Rgroup site, set RestH to off.

> 0	At least one Rgroup must be satisfied. If RestH is off, any other substituent can attach to unsatisfied sites. If RestH is on, unsatisfied sites must be filled solely by hydrogens.

n	Exactly n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

< n	Less than n number of sites (including zero) must be satisfied. RestH controls substitution at unsatisfied sites.

m - n	Any number of sites falling within the range of m to n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

m,n,...	Any combination of the above expressions, separated by commas. For example: 1, 3-5, 9, >12.

For example, the Rgroup condition R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved.

In another example, the Rgroup condition R1 > 0 and R2 > 0 specifies that an Rgroup substituent from the R1 list AND an Rgroup substituent from the R2 list must occupy at least one site on the root structure in the records retrieved.

Finally, the Rgroup conditions R1 = 1, 3-5, 9, >12 specify that either 1, 3, 4, 5, 9, or more than 12 sites must be satisfied:

RestH

With the Rgroup condition RestH, you can specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site.

An unsatisfied Rgroup site is an Rgroup site on the root structure that does not have an Rgroup member attached: If RestH is off, any functional group or atom may be attached at unsatisfied Rgroup sites on the root structure. If RestH is on, solely hydrogens are allowed to be attached at unsatisfied Rgroup sites on the root structure.

If/Then

With the Rgroup condition If/then, you can specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

For example, If R1 then R2 specifies that if the conditions for R1 are satisfied, then the conditions for R2 must also be satisfied. (If the conditions for R1 are not satisfied, then the conditions for R2 are ignored.) The If/then condition implies that a molecule may be retrieved even though R1 is not satisfied.

In the following query, R1 contains a nitro group and a sulfonic acid group. R2 contains a chlorine atom. The condition If R1 then R2 specifies that if a nitro group or a sulfonic acid group is attached at R1 on the root structure, then a chlorine must also be attached at R2. However, if the R1 site on the root structure does not have either the nitro or the sulfonic acid group (R1 is unsatisfied), then R2 can have any substituent (R2 is ignored):

41.4 Specifying Stereochemistry in 2D Graphical Queries

For 2D graphical queries, you can specify stereochemistry with Up and Down bonds, stereo boxes on cis or trans configurations, and chiral flags on molecules.

Note: You can not use the query features in this section in a 3D graphical query.

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

An SBF search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve molecules with matching cis or trans stereochemistry. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An SBF search produces the following results:

Chiral Flags on Molecules

In a remote database, you can create a query with a chiral flag on a molecule with at least one asymmetric center or on a molecule that is asymmetric to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

41.5 Specifying Chemical Environments

You can incorporate specific chemical environments into your graphical query. This section contains examples of several chemical environments that you can create with 2D query features and Rgroups. MDL supplies ISIS/Draw sketch files that contain specific types of chemical environments. You can incorporate these structures into your own queries and modify them if desired.

Note: The chemical environments in this section use 2D query features only. 2D query features specify solely the number, type, and connectivity of atoms in a molecule. You can use 2D query features in both 2D and 3D graphical queries. However, a 3D graphical query should contain at least one component that specifies the spatial distribution of atoms in a 3D structure. To specify the spatial distribution of atoms, you can use a submodel with two or more fixed atoms, and/or use 3D geometric constraints such as distances and angles. For more information on submodels, see Section 41.6. For more information on 3D geometric constraints, see Section 41.7.

41.5.1 Acidic Center

The file ACID_CTR.SKC contains the following definition of an acidic center:

This query defines an acidic center as either an oxygen of a carboxylic acid or any nitrogen of an unsubstituted tetrazole.

41.5.2 Basic Nitrogen

BSC_N_1.SKC File

The file BSC_N_1.SKC contains a definition of a basic nitrogen that includes alkyl amines (nsp3), amidines (nsp2), and guanidines (nsp2). This definition excludes other nitrogens such as aromatic nitrogens, aniline-type nitrogens, N=O, NHC=O, and NHC=C:

You can change this definition to fit your needs. For example, if you want to include aromatic nitrogens, delete R2 from the definition.

BSC_N_2.SKC File

The definition of basic nitrogen in the file BSC_N_2.SKC excludes all amides or anilines, and other conjugated systems that reduce the accessibility of the electron pair on the nitrogen atom:

Simple Definition

The following is a simple definition of a basic nitrogen:

41.5.3 Hydrogen-Bond Acceptor

The definition of a hydrogen bond acceptor in the file H_ACCEPT.SKC extends the definition of a basic nitrogen to include oxygen and sulfur:

Note: There are two different conventions for defining hydrogen-bond donors and acceptors. This help file uses the definition of a hydrogen-bond donor that is generally used by medicinal chemists. By this convention, the donor of a hydrogen bond is the group to which the hydrogen atom is attached:

An alternative definition of hydrogen-bond donors and acceptors defines a hydrogen-bond donor as the group that provides the lone-pair electrons (LP) to the hydrogen bond.

41.5.4 Hydrogen-Bond Donor

The following is an example of a hydrogen bond donor:

41.6 Specifying Submodel Components

Note: You can not use the query features in this section in a 2D graphical query.

A submodel is a three-dimensional (3D) representation of a portion of a molecule. A submodel search retrieves all models that contain the same spatial arrangement of atoms as those specified in your submodel query, within specified deviations of the individual and overall atoms.

You specify the spatial arrangement of atoms in a submodel query by fixing the 3D coordinates of two or more atoms in the structure. To create a submodel, you eliminate parts of an existing 3D structure until you have the submodel that you want to find in other 3D structures. Then, you fix the positions of the atoms of your choice. The figure below shows how you create a submodel query from the 3D structure of Trandolapril. Circles mark the atoms in Trandolapril that are fixed (F) in the query:

When you conduct a search with a submodel query, you must specify how closely the 3D structures that you retrieve must match the spatial arrangement of the fixed atoms in the submodel query. Two fixed-atom tolerances specify how closely the structures must match the query:

*	Maximum atomic displacement specifies the maximum allowed deviation of individual fixed atoms in the query from those in the structures that you retrieve.

*	Maximum RMS deviation specifies the maximum allowed deviation of all fixed atoms in the query from fixed atoms in the structures that you retrieve. During the search, ISIS superimposes the fixed atoms in the 3D structure on those of the query and performs a least-squares calculation.

When your query contains fixed atoms, you must specify at least one fixed-atom tolerance for the SSS3D search. You can specify:

*	Maximum atomic displacement only (structures with 2 or 3 fixed atoms)

*	Maximum RMS deviation only (structures with at least 4 fixed atoms)

*	Both fixed-atom tolerances (structures with at least 4 fixed atoms)

Your ISIS Administrator sets default fixed-atom tolerances that your site uses to register 3D structures to the database. These tolerances are specified in the Session Settings file that your ISIS Administrator supplies you. To change fixed-atom tolerances for searching, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for fixed-atom tolerances, changing.

Caution: If you change the default fixed-atom tolerances for searching, you must restore the default fixed-atom tolerances before you register 3D structures.

The following are examples of the 3D structures that you retrieve from a search with the query that you derive from Trandolapril, with both fixed-atom tolerances set to 0.5:

Note: Queries that contain fixed atoms produce slower search speeds than queries that do not contain fixed atoms. As an alternative to the fixed-atom query shown previously, you can use a query with distance constraints that incorporate the fixed-atom tolerances:

You can also use other 3D query features to specify the spatial distribution of atoms within a 3D structure. For more information on distance constraints and other 3D constraints, see Section 41.7.

(Continued in Part 2)


Remote SBF for 3D Databases: Searching Concepts/Examples Part 2

Click [image] to print Part 2.    Click [image] to return to Part 1.    Click [image] to close this Request-A-Document.

To print Part 2 of this Request-A-Document, click the Printer icon at the top of the screen.

To return to Part 1, click the Part 1 icon at the top of the screen.

---------------------------------------------------------------------------------------------------------------------

41.7 3D Objects and Constraints

Note: You can not use the query features in this section in a 2D graphical query.

To specify the spatial relationships between atoms in a 3D graphical query, you can construct 3D objects and create 3D constraints that use atoms and/or constructed 3D objects.

41.7.1 Specifying 3D Objects

You can set geometric constraints on various molecular or constructed geometric 3D objects. These objects can be points, lines, planes, centroids, and normal vectors. Lines, planes, and normal vectors actually extend infinitely, but are represented in ISIS as shown below:

Centroid

Use a centroid to define the geometric center of a set of reference points or atoms of your choice. For example, the centroids in the structures below (depicted by the triangles) are the geometric centers of selected atoms. The centroid on the left is created when all six ring atoms are selected. The centroid on the right is created when the atoms in the box are selected (the box is used here to indicate atoms selected, and does not appear in the query):

Line

Use a line to define a path through two or more reference positions, such as points, atoms, or centroids:

ISIS derives a best-fit line if you use at least three reference positions to define the line. You can specify a linearity constraint for a best-fit line. For more information, see 41.7.2.

Normal

Use a normal to specify a line (with an arrowhead) that is perpendicular to a plane and that passes through a reference position (a point, atom, or centroid):

In ISIS, the direction of the normal arrow is defined by the sequence in which you selected the first three components of the plane. To reverse the direction of the arrow, simply reverse the order in which you define the components of a plane.

Note: If you define a normal through a point that lies in the same plane, the direction of the normal is undefined.

Plane

Use a plane to define a surface that consists of three or more reference positions (points, atoms, or centroids). A plane actually extends infinitely in all directions, but is depicted in ISIS as a small rectangular surface. In the following figure, the entire molecule specifies the plane:

ISIS derives a best-fit plane if you use at least four reference positions to define the line. You can specify a planarity constraint for a best-fit plane. For more information, see Section 41.7.2.

Point

A point is a reference position. You specify a point at a defined distance and direction from a distance reference position (another point, atom or centroid). To specify the direction, you can use either another reference position (called the direction reference position) or a normal.

You can specify the distance from the distance reference position to the direction reference position in Angstroms or as a percentage. Angstrom distances must lie between -100 and +100 Angstroms. Percentage distances must lie between -1,000% and +1,000%, and must include the % sign.

The following example defines a point at a distance of 1.4 Angstroms from a ring nitrogen (the distance reference position) to a ring oxygen (the direction reference position):

The point that you specify need not lie between the two reference positions. The following example shows a point projected 2.8 Angstroms along a line between the nitrogen atom (the distance reference position) and the hydrogen (the direction reference position):

When you use a normal to specify the direction of the point from the distance reference position, you must specify the distance from the distance reference position in Angstroms.

The following example uses a normal to create points that lie 2.8 Angstroms above and below the center of a phenyl ring. The normal is perpendicular to the plane of the ring and passes through the ring centroid. The direction of the normal is undefined, because the point that defines it lies in the plane. To define points on both sides of the plane, use plus (+) and minus (-) signs with Angstrom values to specify the distances:

To create a point on only one side of the plane, specify a distance of 2.8 Angstroms without the plus (+) or minus (-) sign:

Note: You can use points to represent features on a receptor. For examples, see Section 41.8.

41.7.2 Specifying 3D Constraints

You can apply 3D geometric constraints to 3D objects. 3D geometric constraints include distances, angles, dihedral angles, exclusion spheres, linearity constraints, and planarity constraints:

You can also apply 3D data constraints to atoms and atom pairs. Data constraints are listed under “Atom" and “Atom Pair" later in this section.

Distance

You can define a distance constraint between two reference positions (atoms, centroids, or points), from a reference position to a line or normal, or from a reference position to a plane:

The distance constraint is a range of values. Both values in the range must be greater than zero and equal or less than 1,000. The following query has a distance constraint of 2 to 10 Angstroms between the center of a phenol ring and the center of a phenyl ring:

The following are examples of the 3D structures that you retrieve:

Angle

You can define an angle constraint with three points, centroids, or atoms; or with two planes, lines, or normals:

The vertex of the angle for two planes, lines, or normals that do not intersect is an imaginary point. An angle drawn with two lines that do not intersect is equivalent to a dihedral angle through an imaginary line that connects the two lines with the shortest distance.

The angular range that you specify depends on the way that you defined the angle:

*	If you used lines or planes to define the angle, the range must lie between 0 and 90 degrees.

*	If you used three points to define the angle, the range must lie between 0 and 180 degrees.

The following query has a constraint of 30- 65 degrees on the angle between the line between two phenyl centers and a phenol oxygen:

The following are examples of the 3D structures that you retrieve:

Exclusion sphere

Use an exclusion sphere to exclude atoms within a sphere surrounding a reference position. You define the radius of the exclusion sphere. You can ignore unconnected atoms within the radius of the sphere or specify exactly which atoms that you want to be included. The radius of the sphere must be between 0.1 and 20 Angstroms.

Note: You cannot use a 3D graphical query that consists solely of exclusion spheres. A 3D graphical query should contain at least one of the following 3D query components: distance, angle, dihedral angle, linearity constraint, planarity constraint, or two or more fixed atoms.

For example, the exclusion spheres in the following query ensure that you select compounds that have no atoms within the circled areas of 1.0-Angstrom radius:

The following is an example of the 3D structures that you retrieve (For clarity, the measured values of the four distance constraints are not displayed):

You can specify that atoms that are part of the query can lie within the exclusion sphere. In the following query, for example, you might want to allow atoms from the carboxyl group within the exclusion spheres, but exclude all other atoms:

To allow other atoms in the query within the exclusion sphere, you must include these atoms in the basis of the exclusion sphere. (The basis of a 3D object or constraint is the set of atoms or 3D objects that comprise the object.) For an exclusion sphere, the basis always includes the reference position at the center of the sphere. To include additional atoms, you edit the basis to include these atoms. For example, you can edit the basis of the exclusion spheres in the previous query to include the carboxyl group. The following are examples of the 3D structures that you retrieve (For clarity, the measured value of one distance constraint is not displayed):

You can also specify that unconnected atoms that are not part of the query can lie within the volume of the exclusion spheres. For example, you might want to allow salt ions or water molecules within the volume of the exclusion sphere. To allow these atoms, you specify the following setting when you create the exclusion sphere: Allow nonquery atoms within exclusion sphere.

Note: You can use exclusion spheres to represent regions on a receptor. For examples, see Section 41.7.

Dihedral

When two planes intersect, a dihedral angle is created from the common vertex of reference positions 1 and 2 and reference positions 3 and 4:

Atoms 1 and 2 are adjacent reference points for the phenol structure, and atoms 3 and 4 are adjacent reference points for the phenyl structure. Reference points 1, 2, and 3 lie along the first plane, and reference points 2, 3, and 4 lie along the second plane. Reference points 2 and 3 share both planes and form the vertex of the dihedral angle.

The angular range that you specify must be between -180 and +180 degrees.

The following query specifies a dihedral angle between two atoms on a phenyl ring and two atoms on a phenol ring:

The following are examples of the 3D structures that you retrieve:

Linearity

You can specify that three or more reference positions (atoms, points, or ring centroids) must lie along the same line. To do this, you specify the maximum average distance (RMS deviation) of the reference positions from the best-fit line derived from the reference positions. The following shows a linearity constraint for all atoms in a trialkene:

The value that you specify must lie between 0 and 1,000.

Planarity

You can specify that four or more reference positions (atoms, points, or ring centroids) must lie along the same plane. To do this, you specify the maximum average distance (RMS deviation) of the reference positions from the best-fit plane derived from the reference positions. The following shows a planarity constraint for all atoms in a benzaldehyde:

The value that you specify must lie between 0 and 1,000.

Atom

Use atom data to specify a data constraint for selected atoms in your query, such as spectroscopic and quantum mechanical data or partial charges. For example:

The atom data constraint specifies the partial charge on the oxygen. Rn specifies that the oxygen must appear in a ring. For more information on Rgroups, see Section 41.2.

Atom-Pair

Use atom-pair data to specify a data constraint between two atoms in your query. For example, you can specify bond order, lower/upper distance constraints, and spectroscopic and quantum mechanical data. The following query specifies values for the ring proton spin-spin couplings of methyl 2-furoate:

41.8 Using Receptor Information

Note: You can not use the query features in this section in a 2D graphical query.

The previous sections showed how to use information about active compounds (that is, information about the pharmacophore) to specify constraints in 3D graphical queries. This section shows how you can use information about the receptor to specify geometric constraints in your 3D graphical query. Use these examples as a starting point for creating your own queries.

Note: For simplicity, the queries in this section use a simple definition of a basic nitrogen. For more refined definitions of basic nitrogen, see Section 41.4.2.

41.8.1 Specifying Hydrogen-Bond Interactions

You can use projected points and exclusion spheres to represent hydrogen bond donors and acceptors on the receptor.

Note: There are two different conventions for defining hydrogen-bond donors and acceptors. This help file uses the definition of a hydrogen-bond donor that is generally used by medicinal chemists. By this convention, the donor of a hydrogen bond is the group to which the hydrogen atom is attached:

An alternative definition of hydrogen-bond donors and acceptors defines a hydrogen-bond donor as the group that provides the lone-pair electrons (LP) to the hydrogen bond.

Hydrogen Bond Donor on Receptor

The following example shows how to construct an exclusion sphere that represents a hydrogen-bond donor on the receptor. You construct the exclusion sphere around a point that you construct from two atoms of the corresponding hydrogen-bond acceptor on the ligand.

Hydrogen Bond Acceptor on Receptor

The following example shows how to construct an exclusion sphere that represents a hydrogen-bond acceptor on the receptor. You construct the exclusion sphere around a point that you construct from two atoms of the corresponding hydrogen-bond donor on the ligand.

Distance Constraint Between Features on the Receptor

Specifying distance constraints between points on the receptor rather than the ligand can produce highly specific queries. For example, suppose you know that the receptor contains a hydrogen bond donor that is 10 - 11.5 Angstroms from a basic nitrogen. The following figure schematically shows how two topologically different drugs can bind to the same receptor site:

If you use a query that uses information about the pharmacophore (ligand-based query), you must specify a large distance range (4 - 10 Angstroms) to retrieve both classes of compounds. The ligand-based query retrieves the compounds that you want, but also retrieves many false hits. If you use a query that uses information about the receptor (receptor-based query), you can specify a much narrower distance range. For example:

The greater specificity in the receptor-based query allows you to retrieve the compounds that you want while eliminating many of the false hits that the ligand-based query might produce.

41.8.2 Specifying Pi-Pi Interactions

You can use projected points and exclusion spheres to represent pi-pi interactions with aromatic groups on the receptor.

Pi-Pi Interactions Alone

Use exclusion spheres above and below aromatic rings that interact with aromatic groups on the receptor. The exclusion spheres eliminate 3D structures with atoms that intrude into the excluded area. Consequently, all 3D structures that you retrieve can contain phenyl rings that can interact freely with the receptor.

To create the exclusion spheres, you create a normal to the plane of the phenyl ring. On that normal, you place a point that is 3.0 Angstroms above (+ 3.0 Angstroms) the plane of the ring, and another point that is 3.0 Angstroms below (- 3.0 Angstroms) the plane of the ring. Around each point, you create exclusion spheres that are 1.5 Angstroms in diameter.

The following query uses exclusion spheres and a distance constraint:

Pi-Pi Interactions With a Distance Constraint

To specify a distance constraint between a lipophilic site and another site on the receptor, use a projected point on one side of an aromatic ring. Use exclusion spheres to eliminate 3D structures that do not permit the aromatic ring to interact freely with the receptor.

To construct the exclusion spheres and projected points, create a normal to the plane of the phenyl ring. On that normal, you place a point that is 2.0 Angstroms above (+ 2.0 Angstroms) the plane of the ring, and another point that is 2.0 Angstroms below (- 2.0 Angstroms) the plane of the ring. On the normal, you place another point that is 3.5 Angstroms from the plane of the ring. Around the two points at 2.0 Angstroms from the aromatic ring, you create exclusion spheres that are 1.5 Angstroms in diameter.

The following query specifies a distance constraint of 6 - 10 Angstroms between a lipophilic site on the receptor and a hydrogen-bond donor on the receptor (for clarity, the query uses a simple definition of a basic nitrogen):

41.9 Sprouting Hydrogens and Lone Pairs on 3D Structures

3D structures in a molecule database generally do not contain explicit representations of hydrogen atoms. You can, however, create explicit hydrogen atoms on the structures that you retrieve by sprouting hydrogen atoms on 3D structures. You must sprout hydrogen atoms when you export 3D structures to modeling software programs that cannot sprout hydrogens.

Note: If your 3D graphical query contains lone pairs, sprouting hydrogen atoms also sprouts lone pairs at sites that correspond to lone pairs on your query.

You have three options for displaying hydrogen atoms and lone pairs on the 3D structures that you retrieve:

Off

Prevents sprouting of hydrogens and lone pairs on retrieved 3D structures. Use this setting when the 3D structures in your database already contain sufficient explicit hydrogens and lone pairs, or when your query does not contain explicit hydrogens and lone pairs.

Query Atoms Only

Sprouts hydrogens and lone pairs on retrieved 3D structures, but solely at sites where hydrogens and lone pairs appear on the query.

All

Sprouts hydrogens at all sites on retrieved 3D structures, and sprouts lone pairs on retrieved structures at sites where lone pairs appear on the query. Use this setting when you want to export 3D structures to a modeling software program that does not sprout hydrogens.

41.10 Guidelines for Revising the Query

If your SBF search did not produce the results that you wanted, use the guidelines in this section to:

*	Increase or decrease the number of 3D structure records that you retrieve.

*	Optimize your 3D graphical query for fast search speeds.

*	Use multistep search strategies to refine your 3D graphical query.

41.10.1 Increasing or Decreasing the Number of Retrieved Records

If your SBF search retrieved no records or too few records, you might want to:

*	Conduct an SBF search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the text/numeric strings in your query more general, and then search the same set of records. For example, you can apply operators that partially restrict, such as > or between instead of =, or you can apply wildcards. (A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters.)

*	Make your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, or change bond types to increase bond variation.

*	Increase the range of distance, angle, or other 3D constraints in a 3D graphical query. If your query contains a submodel, you can increase the fixed-atom tolerances.

Note: If you make your query more general, search speed can decrease significantly. For more information on maintaining high search speeds when refining your query, see Section 41.10.3.

If your SBF search retrieved too many records, you might want to:

*	Refine your query, and then search the same set of records. For example, you can restrict atom or bond variation with explicit atoms or bonds or add additional substructures to the query. For 3D graphical queries, you can narrow the ranges of distance, angle, and other 3D constraints. If your 3D graphical query contains a submodel, you can decrease fixed-atom tolerances.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	First, conduct a formula search (or a data search on molecular weight) to screen out large and complex molecules that are stored in your database, and then conduct a search on the less complex molecules. If your query is not able to map a stored molecule within a specific length of time, the molecule is added to the search results.

*	Filter your search results so that you view solely the lower-level records. (This assumes that you are viewing both upper- and lower-level records.)

41.10.2 Optimizing a 3D Graphical Query for Fast Search Speeds

An SBF search with a 3D graphical query is equivalent to an SSS3D search. ISIS conducts the SSS3D search in two stages:

*	2D and 3D key screening. At this stage, ISIS rapidly eliminates compounds that cannot fit the query constraints. You want ISIS to eliminate as many structures as possible at this stage, before the slower atom-atom mapping process begins.

*	Atom-atom mapping. At this phase, ISIS attempts to match the atoms and constraints in the query to each 3D structure that remains after key screening. ISIS might need to map the query to a potential hit structure many times before it can eliminate it. Therefore, you want to design your query so that ISIS performs as few mappings as possible.

Note: An SBF search with a 3D query (that is, an SSS3D search) finds 3D structures that contain your query wholly within a larger structure. In this search, ISIS does not attempt to fit 3D structures to the query by rotating single bonds. For example:

To find 3D structures that can be made to fit the query by rotating single bonds, you require a CFS search. For step-by-step instructions and searching examples for CFS search, click here. Alternatively, choose Help > Index, and search for CFS, how-to/examples.

2D and 3D key screening

Every structure in a database has a set of binary representations of its structural entities, called keys. 2D keys code for 2D structural features, while 3D keys code for 3D features such as distances. To improve search speed, you want your query to contain as many different structural features (that is, to set as many keys) as possible. This reduces number of structures that must be processed by atom-atom mapping.

The following characteristics increase the number of 2D keys in a query:

*	Different atom types

*	Different bond types and connectivity

*	Different types of functional groups

*	Different types and sizes of rings

For example, if you are searching for carbohydrate structures, your query might contain solely carbon and oxygen atoms. You can increase the number of keys by including rings and functional groups that you know are present in the structures that you want, even if they are not part of the pharmacophore.

The following are examples of features that increase the number of 3D keys in a query:

*	Distances between two heteroatoms

*	Distances between a heteroatom and a ring centroid, where the ring contains 3 - 7 atoms

*	Distances between two ring centroids

Key screening and atom-atom mapping

To increase and maintain high search speeds during both the key screening and atom mapping phases of the search:

*	Draw as precise a query as you can, but use the fewest possible points to define lines and planes. ISIS calculates a best-fit line for three or more points and a best-fit plane for four or more points. These calculations can require a long time.

*	Use as many 2D query features as possible, and use as many specific 2D query features as possible if they can replace 3D constraints. For example, to define two atoms that are close together, draw a bond between them instead of using a distance constraint. This sets more keys an eliminates a 3D constraint.

*	Avoid using unconnected atoms in the query. (The slowest atoms are C and A.). ISIS must check all possible combinations of the specified atoms during the slower atom-atom mapping stage of the search.

*	Construct constraints with ring centroids rather than ring atoms. Ring centroids set additional keys and reduce the number of atom-atom mappings.

*	Avoid highly symmetrical queries. Highly symmetrical queries cause ISIS to perform the same mappings many times, with no increase in the number of hits. You can reduce the symmetry of a query by adding atoms or functional groups that are not part of the pharmacophore, but which you know are present in the molecules that you want.

*	Avoid multiple atom and atom-pair data constraints.

41.10.3 Using Multistep Search Strategies to Refine a 3D Graphical Query

You can refine a 3D graphical query by performing successive searches on a smaller and smaller set of retrieved molecules. You can maintain high search speeds by using query features that slow down searches at later stages of query refinement. Use the following strategies during the initial stages of multistep search strategies:

*	If your multistep search strategy includes a 2D structural or 3D data search, perform these searches first. For example, you can conduct a Search By Form for a specific therapeutic activity and then conduct an SBF search for topological differences among the models retrieved from the Search By Form.

*	Avoid using exclusion spheres. Exclusion spheres require calculation time that can slow down your search if you retrieve many structures. You might consider conducting an SBF search with a query that contains exclusion spheres after an SBF search with a query that does not contain exclusion spheres.

*	Avoid using lines and planes. ISIS must calculate the RMS deviation for each compound during the search. For example, you might want to substitute an angle constraint for a planarity constraint. In the examples below, the query with the angle constraint runs ten times faster than the query with the planarity constraint:

*	Avoid using unnecessary explicit hydrogens and lone pairs in the query. ISIS requires sprouting time.

*	Avoid using Rgroups.

*	Avoid using residues (superatoms).

41.11 Searching Example 1: Combining Text/Numeric Queries

This searching example shows you how to conduct a single SBF search with a query that contains two text/numeric strings.

41.11.1 Problem

You want to retrieve all molecules that meet both of the following requirements:

*	Have a molecular weight greater than 250

*	Contain two or three oxygen atoms

41.11.2 Approach

Enter the numeric string query > 250 into the Molecular Weight box or table cell on the form in ISIS/Base that connects to the database field MOLECULAR.WEIGHT. This string contains the search operator > and the target value 250.

Enter the text/numeric string query LIKE "O(2-3)" into the Formula box or table cell on the form that connects to the database field MOL>MOLFORMULA. This string contains the search operator LIKE and the target value o(2-3) in double quotation marks, where o is either in upper- or lower-case characters.

Note: If you enter both queries into different rows in a single table, you retrieve those molecules that meet either requirement (but not necessarily both).

Conduct an SBF search in the remote molecule database of your choice, such as the ISISMX3D demo database.

41.11.3 Query

Note: Your form in ISIS/Base might be entirely different from the one in this example.

41.11.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SBF, how to/examples.

41.11.5 Results

You retrieve records with molecules that have a molecular weight greater than 250 and records with molecules that contain two or three oxygens.

41.12 Searching Example 2: Combining Text/Numeric and 2D Graphical Queries

This searching example shows you how to conduct a single SBF search with a query that contains a text/numeric string and a 2D graphical query.

41.12.1 Problem

You want to retrieve all molecules that meet both of the following requirements:

*	Contain a steroid substructure embedded wholly within them

*	Have a melting point that is greater than 220 degrees Centigrade

41.12.2 Approach

Enter the numeric string query > 220 into the Temperature box or table cell on the form in ISIS/Base that connects to the database field TEMPERATURE (or to an equivalent field with another name). This string contains the search operator > and the target value 220.

Draw the following steroid as your 2D graphical query:

Enter the steroid query into the Structure box or table cell on the form that connects to the database field MOLSTRUCTURE.

Conduct an SBF search in the remote molecule database of your choice, such as the ISISMX3D demo database.

41.12.3 Query

Note: Your form in ISIS/Base might be entirely different from the one in this example.

41.12.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SBF, how to/examples.

41.12.5 Results

You retrieve records with molecules that have a melting point greater than 220 and all records that contain the steroid substructure in your query.

41.13 Searching Example 3: Combining Text/Numeric and 3D Graphical Queries

This example uses the 3D query that is based on a pharmacophore hypothesis proposed by Kato and coworkers (Kato, K., et al., J. Med. Chem. 1985, 28, 287-294). The 3D graphical query contains a 3D substructure.

This example uses the ISISMX3D database.

Note: We provide the ISISMX3D database for demonstration purposes alone. ISISMX3D contains a small number of 3D structures. You generally want to conduct 3D searches in medium to large databases such as MDDR-3D.

41.13.1 Problem

Find compounds that inhibit thromboxane synthetase and have the following characteristics:

*	1-imidazolyl or 3-pyridyl on one end

*	Carboxylic acid at the other end

*	A distance of 8.5 to 10.0 Angstroms between the oxygen of the carboxylic acid and the nitrogen of the imidazole or pyridine ring

*	Molecular weight less than 1000

41.13.2 Approach

Draw a 3D graphical query that contains two fragments: one to represent the carboxylic acid and the other to represent the aromatic nitrogen. Add a distance constraint between the oxygen of the carboxylic acid and the nitrogen of the ring:

Enter the 3D graphical query into the box or table cell on the form that connects to the database field MODELSTRUCTURE.

Enter the numeric string query < 1000 into the Molecular Weight box or table cell on the form in ISIS/Base that connects to the molecular weight field MODEL>MOL>MOL.WEIGHT. This string contains the search operator < and the target value 1000.

Conduct the SBF search.

41.13.3 Query

Note: Your form in ISIS/Base might be entirely different from the one in this example.

41.13.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for SBF, how to/examples.

41.13.5 Results

In this searching example, the SBF retrieves Model Regnos 80 and 95:


ID: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote ID Search	72.1

*	Guidelines for Revising the Query	72.2

*	Searching Example 1: A Record With a Text and Numeric ID Number	72.3

*	Searching Example 2: Records With Text and Numeric ID Numbers	72.4

*	Searching Example 3: A Record With Solely a Numeric ID Number	72.5

*	Searching Example 4: Records With Solely Numeric ID Numbers	72.6

We recommend that you print this 5-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote ID search, click here.

72.1 Definition of a Remote ID Search

A remote ID search finds the records in your remote database that contain the corporate identification numbers that you specify in your query. To do this type of search, you need:

*	An ID field in your database. This is a field in the database that contains corporate identification numbers for the records in your database.

*	A box or table in a form that is linked to the ID field. A form is the set of boxes and/or tables that you use to hold your query and to view the results of a search. (You can enter a maximum of 25 ID numbers into individual table cells on a form.)

If you do not have these items, see your ISIS Administrator.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

72.1.1 Specifying ID Queries

An ID query is a phrase in a box or column on the form that specifies the retrieval of specific ID numbers. For example, to find structures with an ID that is equal to the ID number CL011250, enter the ID query LIKE "CL011250".

Each phrase in an ID query contains:

*	A search operator that specifies the type of search. For example, use the search operator = (an equal sign) with numeric ID numbers or the search operator LIKE in place of = with ID numbers that contain text.

*	The text or numeric target value that you want to find (such as the ID number CL011250). A target value can contain wildcards. A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. For example, you can specify the query LIKE "%CL%" (instead of the query LIKE "CL011250"). The wildcard _ is a placeholder for solely one unspecified character. For example, you can specify the query LIKE "_L011250" (instead of the query LIKE "CL011250"). Target values that contain text or wildcards require double quotation marks.

The Search Operators

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Use LIKE with text enclosed in double quotation marks. Enter your query as follows: Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. (To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice.)

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks (such as BETWEEN "XR11" "XZ15").

Use EXISTS to retrieve all records in the database that contain data in a specific database field.

Note: You can only use this search operator for database fields that do not give you an error message.

72.2 Guidelines for Revising the Query

If your ID search retrieved no records, you might want to check that your search domain is set to the entire database.

72.3 Searching Example 1: A Record With a Text and Numeric ID Number

This searching example shows you how to find a specific record whose ID number has both text and numbers. Any ID query that contains text (or wildcards) requires the search operator LIKE and the ID number to be enclosed in double quotation marks.

72.3.1 Problem

You want to retrieve the record with the ID number MUSE000000001.

72.3.2 Approach

Enter the ID query LIKE "MUSE000000001" into the ID box or table cell on the form that connects to the ID database field. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains text and numbers. Enter the search operator LIKE. Enter a space, and then enter the target value MUSE000000001 in double quotation marks. (You can enter the text in either upper- or lower-case characters.)

Conduct an ID search in the remote molecule demo database ISISMX.

72.3.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

72.3.4 Results

You retrieve solely the record with the ID number MUSE000000001.

72.4 Searching Example 2: Records With a Text and Numeric ID Number

This searching example shows you how to find a specific set of records whose ID numbers have both text and numbers. Any ID query that contains text (or wildcards) requires the search operator LIKE and all ID numbers to be enclosed in double quotation marks.

72.4.1 Problem

You want to retrieve the set of records with ID numbers that are between (and including) MUSE000000001 and MUSE000000009.

72.4.2 Approach

Enter the ID query BETWEEN "MUSE000000001" "MUSE000000009" into the ID box or table cell on the form that connects to the ID database field. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains text and numbers. Enter the search operator BETWEEN. Enter a space. Enter the target value MUSE000000001 in double quotation marks. (You can enter the text in either upper- or lower-case characters.) Enter a space, and then enter the target value MUSE000000009 in double quotation marks.

Conduct an ID search in the remote molecule demo database ISISMX.

72.4.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

72.4.4 Results

You retrieve solely the specific set of records with ID numbers that fall between (and that include) MUSE000000001 and MUSE000000009.

72.5 Searching Example 3: A Record With Solely a Numeric ID Number

This searching example shows you how to find a specific record whose ID number has solely numbers. Any ID query that contains solely numbers uses the search operator = (the equal sign).

72.5.1 Problem

You want to retrieve the record with the ID number 95.

72.5.2 Approach

Enter the ID query = 95 into the ID box or table cell on the form that connects to the ID database field. You can omit the single space between the equal sign and the number. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains solely a number. Enter the search operator = (an equal sign). Enter a space, and then enter the target value 95.

Conduct an ID search in the remote molecule demo database ISISMX.

72.5.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

72.5.4 Results

You retrieve solely the record with the ID number 95.

72.6 Searching Example 4: Records Solely Numeric ID Numbers

This searching example shows you how to find a specific set of records whose ID numbers have solely numbers. Any ID query that contains solely numbers uses the search operator = (the equal sign).

72.6.1 Problem

You want to retrieve the set of records with ID numbers that are between (and including) 95 and 100.

72.6.2 Approach

Enter the ID query BETWEEN 95 100 into the ID box or table cell on the form that connects to the ID database field. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains solely numbers. Enter the search operator BETWEEN. Enter a space. Enter the target value 95. Enter a space, and then enter the target value 100.

Conduct an ID search in the remote molecule demo database ISISMX.

72.6.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

72.6.4 Results

You retrieve solely the specific set of records with ID numbers that fall between (and that include) 95 and 100.


ID: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Local ID Search	76.1

*	Guidelines for Revising the Query	76.2

*	Searching Example 1: A Record With a Text and Numeric ID Number	76.3

*	Searching Example 2: Records With Text and Numeric ID Numbers	76.4

*	Searching Example 3: A Record With Solely a Numeric ID Number	76.5

*	Searching Example 4: Records With Solely Numeric ID Numbers	76.6

We recommend that you print this 5-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a local ID search, click here.

76.1 Definition of a Local ID Search

A local ID search finds the records in your local database that contain the corporate identification numbers that you specify in your query. To do this type of search, you need:

*	An ID field in your database. This is a field in the database that contains corporate identification numbers for the records in your database.

*	A box or table in a form that is linked to the ID field. A form is the set of boxes and/or tables that you use to hold your query and to view the results of a search. (You can enter a maximum of 25 ID numbers into individual table cells on a form.)

If you do not have these items, see your ISIS Administrator.

A local search is a search over a database that typically exists on your hard disk. To do a local search on your hard disk, you do not need to input network information.

Note: To do a local search that is accessed from a shared network, you need to input network information.

76.1.1 Specifying ID Queries

An ID query is a phrase in a box or column on the form that specifies the retrieval of specific ID numbers. For example, to find structures with an ID that is equal to the ID number CL011250, enter the ID query LIKE "CL011250".

Each phrase in an ID query contains:

*	A search operator that specifies the type of search. For example, use the search operator = (an equal sign) with numeric ID numbers or the search operator LIKE in place of = with ID numbers that contain text.

*	The text or numeric target value that you want to find (such as the ID number CL011250). A target value can contain wildcards. A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. For example, you can specify the query LIKE "%CL%" (instead of the query LIKE "CL011250"). The wildcard _ is a placeholder for solely one unspecified character. For example, you can specify the query LIKE "_L011250" (instead of the query LIKE "CL011250"). Target values that contain text or wildcards require double quotation marks.

The Search Operators

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Use LIKE with text enclosed in double quotation marks. Enter your query as follows: Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. (To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice.)

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks (such as BETWEEN "XR11" "XZ15").

Use EXISTS to retrieve all records in the database that contain data in a specific database field.

Note: You can only use this search operator for database fields that do not give you an error message.

76.2 Guidelines for Revising the Query

If your ID search retrieved no records, you might want to check that your search domain is set to the entire database.

76.3 Searching Example 1: A Record With a Text and Numeric ID Number

This searching example shows you how to find a specific record whose ID number has both text and numbers. Any ID query that contains text (or wildcards) requires the search operator LIKE and the ID number to be enclosed in double quotation marks.

76.3.1 Problem

You want to retrieve the record with the ID number MUSE000000001.

76.3.2 Approach

Enter the ID query LIKE "MUSE000000001" into the ID box or table cell on the form that connects to the ID database field. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains text and numbers. Enter the search operator LIKE. Enter a space, and then enter the target value MUSE000000001 in double quotation marks. (You can enter the text in either upper- or lower-case characters.)

Conduct an ID search in the local molecule demo database LOCALMX.

76.3.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

76.3.4 Results

You retrieve solely the record with the ID number MUSE000000001.

76.4 Searching Example 2: Records With a Text and Numeric ID Number

This searching example shows you how to find a specific set of records whose ID numbers have both text and numbers. Any ID query that contains text (or wildcards) requires the search operator LIKE and all ID numbers to be enclosed in double quotation marks.

76.4.1 Problem

You want to retrieve the set of records with ID numbers that are between (and including) MUSE000000001 and MUSE000000009.

76.4.2 Approach

Enter the ID query BETWEEN "MUSE000000001" "MUSE000000009" into the ID box or table cell on the form that connects to the ID database field. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains text and numbers. Enter the search operator BETWEEN. Enter a space. Enter the target value MUSE000000001 in double quotation marks. (You can enter the text in either upper- or lower-case characters.) Enter a space, and then enter the target value MUSE000000009 in double quotation marks.

Conduct an ID search in the local molecule demo database LOCALMX.

76.4.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

76.4.4 Results

You retrieve solely the specific set of records with ID numbers that fall between (and that include) MUSE000000001 and MUSE000000009.

76.5 Searching Example 3: A Record With Solely a Numeric ID Number

This searching example shows you how to find a specific record whose ID number has solely numbers. Any ID query that contains solely numbers uses the search operator = (the equal sign).

76.5.1 Problem

You want to retrieve the record with the ID number 95.

76.5.2 Approach

Enter the ID query = 95 into the ID box or table cell on the form that connects to the ID database field. You can omit the single space between the equal sign and the number. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains solely a number. Enter the search operator = (an equal sign). Enter a space, and then enter the target value 95.

Conduct an ID search in the local molecule demo database LOCALMX.

76.5.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

76.5.4 Results

You retrieve solely the record with the ID number 95.

76.6 Searching Example 4: Records Solely Numeric ID Numbers

This searching example shows you how to find a specific set of records whose ID numbers have solely numbers. Any ID query that contains solely numbers uses the search operator = (the equal sign).

76.6.1 Problem

You want to retrieve the set of records with ID numbers that are between (and including) 95 and 100.

76.6.2 Approach

Enter the ID query BETWEEN 95 100 into the ID box or table cell on the form that connects to the ID database field. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains solely numbers. Enter the search operator BETWEEN. Enter a space. Enter the target value 95. Enter a space, and then enter the target value 100.

Conduct an ID search in the local molecule demo database LOCALMX.

76.6.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

76.6.4 Results

You retrieve solely the specific set of records with ID numbers that fall between (and that include) 95 and 100.


Remote SSS/Poly: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote SSS/Poly Search	99.1

*	Specifying Polymer Queries	99.2

*	Specifying Polymer Mixtures in Queries	99.3

*	Specifying Attached Data in Queries	99.4

*	Specifying Atom and Bond Query Features	99.5

*	Specifying Rgroup Query Features	99.6

*	Specifying Stereochemistry	99.7

*	Guidelines for Revising the Query	99.8

*	Searching Example 1: Allowing Specific Bond Types 	99.9

*	Searching Example 2: Variable Chain Length	99.10

*	Searching Example 3: Polymer Mixture	99.11

We recommend that you print this 38-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

We assume that you know how to draw polymer structures that can be registered to molecule databases and/or used as search queries. We also assume that you know the conventions for polymer representation that your ISIS Administrator has established for registering polymer structures to your corporate database. For more information on requirements for drawing polymers for registration, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

For step-by-step instructions on conducting a remote SSS/Poly search, click here.

99.1 Definition of a Remote SSS/Poly Search

A Polymer Substructure (SSS/Poly) search finds molecule records that contain your polymer query as a substructure wholly within another molecule:

You can also increase the power of an SSS/Poly search by adding specific restrictions (called query features) on atoms and/or bonds. In the following example, the ISIS link atom query feature (L1-9) specifies the retrieval of polyamides of between 1 and 9 carbons in length. In addition, the anypolymer (anyp) polymer brackets specify the retrieval of any polymer that contains the substructure:

For a description of available query features, see Sections 99.5 and 99.6.

A remote search is a search over a database that typically exists on a mainframe.

99.2 Specifying Polymer Queries

Polymer queries can be drawn as structure-based or source-based representations. The following example shows both representations of a simple homopolymer:

Your corporate database might contain structures that are drawn in the structure-based representation, the source-based representation, or both.

Note: Conventions for drawing structure-based and source-based representations of polymers are provided in the Request-A-Document Drawing Polymers: MDL Requirements for Database Searching and Registration.

Study the following sections to learn how to use the different types of polymer brackets to create structure-based and source-based queries.

99.2.1 Structural Repeating Unit (SRU) Brackets (n)

Use Structural Repeating Unit (SRU) brackets to enclose the structural repeating unit of the structure-based search query:

SRU brackets imply that the structure within the brackets can repeat with itself (...AAAAA... can occur). Consequently, you should enclose the structure "A" in SRU brackets solely if the sequence ...AAAAA... can occur.

Each set of SRU brackets has one or two bonds that cross each bracket, called crossing bonds. The crossing bonds of an SRU show where the repeating units connect to each other within the polymer (connectivity).

Polymers With Two Crossing Bonds

The polymer repeat pattern shows how the repeating units are joined together. In structures with two crossing bonds, the repeat pattern of an SRU with respect to the next SRU in sequence can be head-to-tail (the default), head-to-head (hh), or either/unknown (eu).

The following table shows examples of the three repeat patterns:

Note: Use the either/unknown repeat pattern when the repeat pattern is unknown, or when both the head-to-tail and head-to-head repeat patterns might be present. In the following example, poly(1-chloroethylene/2-chloroethylene) consists of units of chloroethylene that can be joined head-to-head (1-chloroethylene) or head-to-tail (2-chloroethylene):

In searching, a polymer with the either/unknown repeat pattern finds all other repeat patterns. Other polymer repeat patterns must match exactly. The following table summarizes the search characteristics of repeat patterns for polymers with two crossing bonds:

Ladder-Type Polymers

Polymers with two crossing bonds on each bracket of the SRU (ladder-type polymers) can have a repeat pattern of head-to-tail, head-to-head, or either/unknown. For the head-to tail and head-to-head repeat patterns, you must also specify how the two crossing bonds on each bracket connect to the corresponding bonds of the adjacent SRU:

*	The head-to-tail repeat pattern has the following two options for connecting the bonds in adjacent SRUs:

*	The head-to-head repeat pattern has the following two options for connecting the bonds in adjacent SRUs:

*	If the repeat pattern is either/unknown, the connections between corresponding bonds might be unknown, or the polymer might contain a mixture of units that are joined head-to-head and other units that are joined head-to-tail (either).

The following table shows examples of the five repeat patterns that are possible for polymers with two crossing bonds on each bracket:

In searching, a polymer with the either/unknown repeat pattern finds all other repeat patterns. Other polymer repeat patterns must match exactly. The following table summarizes the search characteristics of repeat patterns for ladder-type polymers:

For the either/unknown repeat pattern, a structure that contains two brackets with four crossing bonds is equivalent to a structure that contains four brackets with one crossing bond on each bracket. For example, the following structures represent the same polymer:

Polymers With Three or More Brackets

Polymers with 3 or more brackets always have the either/unknown (eu) repeat pattern. The following are additional representations of polymer structures:

Cyclization and "Phase Shifting"

For SRUs that contain a pair of brackets and that have the head-to-tail repeat pattern, you can define the structural repeating unit anywhere along the polymer backbone (that is, you can "phase-shift" the brackets along the polymer backbone). For example:

You can visualize the connectivity between SRUs as a cyclization of the crossing bonds:

The head-to-tail repeat pattern (the default) shows cyclization and "phase-shifting". For example:

The head-to-head repeat pattern does not show cyclization or "phase shifting." For example:

The either/unknown repeat pattern finds structures that have the following:

*	Identical SRUs and any repeat pattern (head-to-tail, head-to-head, or either/unknown):

*	"Phase-shifted" SRUs with the head-to-tail repeat pattern:

99.2.2 Monomer Brackets (mon)

Use Monomer (mon) brackets to draw the repeating unit(s) for the source-based representation of a homopolymer:

Specifying monomer brackets implies that the structure(s) within them comprise all the source materials from which the structural repeating unit of the polymer is made. If the structural repeating unit of a polymer contains two or more monomeric units, you need to enclose all the monomers within the same set of monomer brackets.

99.2.3 Copolymer Brackets (co)

If a structure contains more than one set of SRU and/or monomer brackets, enclose the entire structure within copolymer brackets. Copolymer brackets can have crossing bonds, cyclization, and phase-shifting. The following figure shows cyclization of a structure-based copolymer query:

If the sequence of the repeating units is known (for example, a block copolymer that consists of regular blocks), draw the structure-based representation with connecting bonds between the SRUs. If the sequence repeats, draw the structure so that bonds cross the copolymer brackets:

However, if the sequence of the repeating units is unknown or unspecified (for example, an irregular block copolymer, or a random copolymer), draw the structure-based representation with no connecting bonds between the SRUs:

In searching, copolymers in which the sequence of SRUs is unspecified match structures in which the sequence is specified. The following table summarizes the search characteristics of copolymer structures that contain SRUs:

Note: Always use copolymer brackets when the structure requires more than one set of polymer brackets (monomer or SRU) to represent the structure. For example, polymers that are chemically modified after polymerization are represented as copolymers. For examples of structures that use copolymer brackets, see the Request-A-Document Drawing Polymers: MDL Requirements for Database Searching and Registration.

99.2.4 Mer Brackets (mer)

For source-based polymers only, use Mer brackets (mer) to enclose a monomer that can not repeat with itself. For example, you know that the diol and diacid monomers of the following polyester do not homopolymerize to form polyperoxides and polyanhydrides:

99.2.5 Additional Polymer Bracket Types

ISIS/Draw provides additional polymer and copolymer bracket types that can be used for alternative representations of certain types of polymers. If you are not sure whether your company uses alternative representations of polymers, see your ISIS Administrator.

The additional polymer and copolymer bracket types are as follows:

*	Copolymer bracket types: alternating (alt), block (blk), and random (ran)

*	Polymer bracket types: cross-link (xl), modified (mod), and graft (grf)

*	Mer brackets (mer) can be used to enclose a structural unit that does not repeat with itself, such as a junction unit within a block copolymer

The following are the search characteristics of the additional polymer types:

*	Polymer and copolymer types must match the query exactly. For example:

*	Unspecified copolymer brackets (co) match any type of copolymer (co, blk, ran, alt).

99.2.5 Anypolymer Brackets (anyp)

Use Anypolymer (anyp) brackets when you want your search query to find any polymer that contains your query embedded within it. For example, you might use atom and bond query features to create a generic polymer query that finds both the structure-based and source-based representations of an addition polymer:

In this example, the bond query feature S/D finds both single and double bonds. The anyp brackets allow ISIS to retrieve structures with either monomer (mon) or SRU (n) brackets.

For more information on atom and bond query features, see Section 99.5

99.3 Specifying Mixtures in Queries

You can define both ordered and unordered mixtures of polymers as search queries:

*	If the order of addition of components is not important, specify an unordered mixture (mix). Unordered mixtures contain components (c) that are not numbered:

*	If the order of addition of components of the formulation is important, use an ordered mixture (f). Ordered mixtures contain components that are numbered (c1, c2, c3, and so forth):

A query that contains ordered components finds structures that contain ordered components with the same relative (not necessarily sequential) order. For example:

To find both unordered and ordered mixtures that contain specified components, use an unordered component without brackets. For example:

For an example of a polymer mixture as a search query, see Section 99.11.

99.4 Specifying Attached Data in Queries

Attached data is chemically-significant text that you can associate with an atom, a bond, a set of atoms and bonds, or with a bracket. Attached data differs from chemically-insignificant text (plain text). Attached data can be exported to a molfile, stored in a molecule database, and/or used in a graphical search query in a remote molecule database.

For example, the following structure of a statistical copolymer contains attached data on the type of copolymer (stat), the number-average molecular weight of the copolymer (20,000 Mn), and on the mass percentage of each type of repeating unit (75 mass %, 25 mass %):

99.4.1 Substance Group (Sgroup) Database Fields

Each piece of attached data is associated with a special kind of database field, called a Substance Group (Sgroup) field. The Sgroup field defines what the data means. The following table shows the associated Sgroup field and the meaning of each piece of attached data in the polymer structure in the previous example:

Caution: Your ISIS Administrator defines the Sgroup fields that you can use to specify attached data. When you draw a structure for registration or searching, you must specify the correct Sgroup fields for the data that you attach to the structure. If you do not specify the correct Sgroup fields, you might not be able to retrieve the structures that you want. For more information on the Sgroup fields that are available at your site, see your ISIS Administrator.

99.4.2 Specifying Attached Data in a Query

You can specify a text/numeric query (search operator with conditions) for attached data, a target value (specific data) of attached data, or no attached data. The following sections show the search results that you obtain for each type of query.

Note: In these examples, Ph is an abbreviated structure that represents a phenyl group.

Text/Numeric Query (Search Operator and Target Value)

A query that contains a text/numeric query retrieves structures in which the attached data meets the conditions that are specified by the text/numeric query. A text/numeric query contains a search operator (such as <) and a text or numeric target value (such as 25% mole fraction) that you want to find. For example, to find copolymers that contain less than 25% polystyrene, attach the text/numeric query < 25 to the monomer brackets of polystyrene:

For an example of a text/numeric query in attached data, see Section 99.11.

Target Value (Specific Data)

A query that contains a target value (specific data) retrieves structures in which the attached data matches exactly. For example:

No Attached Data

A query that contains no attached data retrieves structures that contain any attached data. For example:

For more information on search operators for text/numeric queries, see Section 99.4.3.

99.4.3 Search Operators for Text/Numeric Queries in Attached Data

The following search operators are available as text/numeric queries for attached data.

<, <=, >, >=, and <>

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Search Operator	Definition	Examples

<	less than (numeric)	< 50

<=	less than or equal to (numeric)	<= 50

>	greater than (numeric)	> 50

>=	greater than or equal to (numeric)	>= 50

<>	not equal to (text or numeric)	<> 50

<> "blk"

BETWEEN

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks. For example:

BETWEEN "XR11" "XZ15"

BETWEEN 95 100

CONTAINS

Use CONTAINS with text. You retrieve all values that contain the text string that you specify embedded within them. For example:

Query	Examples of Records Retrieved

CONTAINS tactic	Isotactic

Syndiotactic

Tacticity

LIKE

Use LIKE with text enclosed in double quotation marks. The text can include wildcards. A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. The wildcard _ is a placeholder for solely one unspecified character. Without a wildcard, you retrieve solely those records that contain exactly the target value that you specified. For example:

Query Without a Wildcard	Example of a Record Retrieved
LIKE "isotactic"	Isotactic

Query With the Wildcard %	Examples of Records Retrieved
LIKE "%tactic"	Isotactic
Syndiotactic

LIKE "%tactic%"	Isotactic
Syndiotactic
Tacticity

Note1: To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice. To retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

Note2: The CONTAINS operator is a special case of the LIKE operator. For example, the query like "%tactic%" is equivalent to the query contains tactic. ISIS automatically supplies the quotes and wildcard for the target value of the CONTAINS operator.

99.5 Specifying Atom and Bond Query Features

A query feature on an atom and/or a bond in a molecule is a restriction that specifies the retrieval of certain types of molecule records from an ISIS/Base database.

If you do not use query features, the molecules retrieved contain solely your exact substructure query embedded wholly within them. For example:

You can also define Rgroups that specify a root structure with defined Rgroup substituents attached to it at specific positions. For more information on Rgroups, see Section 99.6.

99.5.1 Definition of Aromaticity

For remote databases: ISIS interprets the following ring systems as aromatic:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:

Note: The bonds of six-membered aromatic ring systems and the perimeter bonds of azulenes are stored as aromatic bonds in the database. The bonds of five-membered aromatic rings, however, are stored as single and double bonds and interpreted as aromatic during a search. The differences between five-membered rings and other types of aromatic rings can cause different search results for five- and six-membered rings/azulenes when you use the following bonds in queries: Single, Double, and Single/Double query bonds. For more information on the Single/Double query bond, see Section 99.5.8.

99.5.2 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except implicit or explicit hydrogens:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

99.5.3 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of implicit hydrogens. For example:

99.5.4 Allowing an Unsaturated Atom

Use an atom query feature to specify that an atom is unsaturated, or attached to at least one multiple bond: double, triple, or aromatic.

Atom Query Feature: Unsaturated Atom (u)

Specifies that the atom of your choice is unsaturated. For example, the following query specifies both an unsaturated atom and single or double bonds (the double dashed lines).

99.5.5 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

Use explicit hydrogens to block non-hydrogen attachments on atoms. For example:

Atom Query Feature: Substitution Count of Zero, s0

Specifies that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of an isolated atom.

Atom Query Feature: Substitution Count of One, s1

Specifies that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Two, s2

Specifies that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Three, s3

Specifies that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Four, s4

Specifies that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Five, s5

Specifies that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of at Least Six, s6

Specifies that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count as Drawn, s*

Specifies that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:

99.5.6 Allowing a Specific Number of Ring Bond Attachments

Use atom query features to specify the number of ring bond attachments.

Atom Query Feature: Ring Bond Count of Zero, r0

Specifies that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:

Atom Query Feature: Ring Bond Count of Two, r2

Specifies that the records retrieved have solely two ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of Three, r3

Specifies that the records retrieved have solely three ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of at Least Four, r4

Specifies that the records retrieved have at least four ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count as Drawn, r*

Specifies that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:

99.5.7 Allowing Additional Atoms and/or Bonds in a Chain or a Ring

Use a query feature that is for either atoms or bonds to specify the addition of atoms and/or bonds in a chain or a ring.

Atom or Bond Query Feature: Link Node

Use a link node to specify the addition of variable numbers repeating units (atoms and/or bonds) to a ring or chain. A repeating unit must be attached to two adjacent bonds. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the link node [L1-3]:

Or, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the link node [L1-3]:

99.5.8 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Note: An aromatic query bond hits any bond in all types of aromatic rings: 6-membered ring bonds, 5-membered ring bonds, and azulene perimeter bonds. For more information on the structures that ISIS interprets as aromatic, see Section 99.5.1.

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

Note: A Single/Double query bond does not hit bonds in 6-membered aromatic rings, or perimeter bonds of azulenes, because bonds in these structures are stored in the database as aromatic bonds. However, a Single/Double query bond does hit bonds in 5-membered rings that ISIS interprets as aromatic. For more information on the structures that ISIS interprets as aromatic, see Section 99.5.1.

Bond Query Feature: Single/Aromatic Bond

Specifies either a single or an aromatic bond at that position:

Bond Query Feature: Double/Aromatic Bond

Specifies either a double or an aromatic bond at that position:

99.5.9 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is attached to a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

99.5.10 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is attached to a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

99.6 Specifying Rgroup Query Features

An Rgroup query finds structures that contain your query as a root structure with defined Rgroup substituents attached to it at specific positions. Your query can contain restrictions on the Rgroup substituents, called Rgroup conditions: You can specify the number of Rgroup sites that must be occupied in the records retrieved, specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site, or specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

Your Rgroup query can also contain restrictions on atoms and bonds of the root structure and Rgroup substituents. For example, you can use the atom query feature H(0) to prohibit the attachment of implicit hydrogens on a specific atom in the structures retrieved.

An example of an Rgroup query is as follows:

99.6.1 The Root Structure

The root structure contains the portion of the structure that does not vary among the structures retrieved. For example, if you want to find 2, 5-Dihydroxypyridine in which the substituent at position 2 can be COOH, CN, or Ph, and the substituent at position 5 can be OH or CH3, the root structure is 2, 5-Dihydroxypyridine with Rgroups (such as R1 and R2):

Rgroups

On the root structure, Rgroups (R1 through R32) are placeholders that designate where the lists of functional groups and atoms that can attach to the root structure. In the example above, the Rgroup R1 designates that the members of the list R1 (the Rgroup substituents) are allowed at position 5 on the root structure. The Rgroup R2 designates that the members of the list R2 (the Rgroup substituents) are allowed at position 2 on the root structure.

Multiple Rgroups at One Position

You can specify multiple Rgroups at a single site on the root structure. For example:

One Rgroup at Multiple Positions

You can specify a single Rgroup (such as R1) at multiple positions on the root structure. For example:

Note: See the section 99.5.3 Rgroup Conditions to restrict the number of Rgroups that must be occupied in the records retrieved. A molecule might not have to satisfy all the Rgroup sites on the root structure to be retrieved. For example, the Rgroup condition R1 > 0 specifies that any molecule in which at least one of the R1 sites is filled by an R1 member will be retrieved. In addition, the Rgroup condition RestH determines whether the unsatisfied sites must be filled with hydrogen atoms or if other molecule fragments are allowed to be attached if they are not on the list.

99.6.2 Rgroup Substituents

Rgroup substituents are the members of the list of Rgroups. You define the Rgroup substituents that you will allow to be found at specified positions in the molecules retrieved. Rgroup substituents can be any structural fragment, including functional groups and single atoms.

In the example below, the Rgroup substituents COOH, CN, or Ph are allowed at position 5 (R1) on the root structure and the Rgroup substituents OH or CH3 are allowed at position 2 (R2) on the root structure:

Attachment Points

An attachment point (marked with an arrow and an asterisk) designates the atom on the Rgroup substituent that is attached to the root structure:

You must designate an attachment point on an Rgroup substituent for each bond that is attached to the substituent. If an Rgroup is attached to two bonds on the root structure, you must designate two attachment points. The bond on the root structure that is marked with double quotes corresponds to the attachment point on the Rgroup substituent that is marked with double quotes. The other attachment point on the Rgroup substituent is marked with a single quote:

Nested Rgroups

A nested Rgroup is an Rgroup that is a placeholder within another Rgroup rather than within the root structure. (You cannot nest an Rgroup any lower than this level.) In the following example, Rgroup R2 is nested within the Rgroup R1:

Nested Rgroups are equivalent to the following structures:

99.6.3 Rgroup Conditions

You can apply restrictions to each Rgroup in your query after you assemble all the Rgroups. The set of restrictions is called the Rgroup conditions.

If you do not apply Rgroup conditions, ISIS assigns the default conditions: Occurrence > 0 and RestH off for each Rgroup.

Occurrence

With the Rgroup condition Occurrence, you can specify the number of Rgroup sites that must be occupied in the records retrieved. For example, the occurrence designation R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved. Type one of the following values in the Occurrence range text box:

Value	Explanation

0	All members of the Rgroup are excluded from the Rgroup site (such as R1). To allow any other Rgroup substituent at the Rgroup site, set RestH to off.

> 0	At least one Rgroup must be satisfied. If RestH is off, any other substituent can attach to unsatisfied sites. If RestH is on, unsatisfied sites must be filled solely by hydrogens.

n	Exactly n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

< n	Less than n number of sites (including zero) must be satisfied. RestH controls substitution at unsatisfied sites.

m - n	Any number of sites falling within the range of m to n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

m,n,...	Any combination of the above expressions, separated by commas. For example: 1, 3-5, 9, >12.

For example, the Rgroup condition R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved.

In another example, the Rgroup condition R1 > 0 and R2 > 0 specifies that an Rgroup substituent from the R1 list AND an Rgroup substituent from the R2 list must occupy at least one site on the root structure in the records retrieved.

Finally, the Rgroup conditions R1 = 1, 3-5, 9, >12 specify that either 1, 3, 4, 5, 9, or more than 12 sites must be satisfied:

RestH

With the Rgroup condition RestH, you can specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site.

An unsatisfied Rgroup site is an Rgroup site on the root structure that does not have an Rgroup member attached: If RestH is off, any functional group or atom may be attached at unsatisfied Rgroup sites on the root structure. If RestH is on, solely hydrogens are allowed to be attached at unsatisfied Rgroup sites on the root structure.

If/Then

With the Rgroup condition If/then, you can specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

For example, If R1 then R2 specifies that if the conditions for R1 are satisfied, then the conditions for R2 must also be satisfied. (If the conditions for R1 are not satisfied, then the conditions for R2 are ignored.) The If/then condition implies that a molecule may be retrieved even though R1 is not satisfied.

In the following query, R1 contains a nitro group and a sulfonic acid group. R2 contains a chlorine atom. The condition If R1 then R2 specifies that if a nitro group or a sulfonic acid group is attached at R1 on the root structure, then a chlorine must also be attached at R2. However, if the R1 site on the root structure does not have either the nitro or the sulfonic acid group (R1 is unsatisfied), then R2 can have any substituent (R2 is ignored):

99.7 Specifying Stereochemistry

You can specify the following types of stereochemistry:

*	Stereoregularity in polymers.

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond). Use this for non-polymer components of your query.

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

99.7.1 Stereoregularity in Polymers

Polymer structures that are stored in a database do not use Up and Down stereo bonds to show stereoregularity, because these bonds can cause inaccurate search results in certain types of searches, such as POLY/Both and POLY/Co. Instead, polymer structures use attached data to show stereoregularity. In the following example, attached data (associated with the Sgroup field STEREO) shows tacticity in polystyrene (Ph is an abbreviated structure that represents a phenyl group):

Use attached data on your query to retrieve the structures of your choice. For example:

To retrieve all structures, regardless of stereoregularity, use a query without attached data:

For more information on attached data, see Section 99.5.

99.7.2 Geometric Stereochemistry

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve molecules with matching cis or trans stereochemistry. Without the stereo boxes, you retrieve both the cis and trans configuration, and any structures that contain Double Either bonds ( [image]). For example:

The cis configuration is not retrieved:

A SSS/Poly search produces the following results:

99.7.3 Tetrahedral Stereochemistry in Non-Polymer Structures

If you want to retrieve structures that contain non-polymer components that are optical stereoisomers, use Up and Down bonds with chiral flags to show stereochemistry.

Up and Down Bonds

In non-polymer structures, you can use Up and Down stereo bonds to show stereochemistry. An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

An SSS/Poly search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Chiral Flags on Molecules

If your structure contains Up and Down stereo bonds, you can create a query with a chiral flag on a molecule with at least one asymmetric center. The chiral flag ensures that you retrieve solely the absolute stereoconfiguration, and eliminates the relative. stereoconfigurations. (In a local database, the chiral flag is ignored.) For example:

99.8 Guidelines for Revising the Query

If your SSS/Poly search retrieved no records or too few records, you might want to:

*	Conduct an SSS/Poly search on a different set of records with the same query.

*	Verify that your search domain is set to the entire database.

*	Verify that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, remove substituent limits, remove stereochemical requirements, or specify anypolymer (anyp) for all polymer brackets.

*	Remove the attached data from your query, and then search the same set of records. For example, if your query contains the attached data value 0.7 attached to polymer brackets, you can delete the attached data.

*	Make the Rgroup conditions in your query more general, and then search the same set of records. For example, you can decrease the number of Rgroup sites that must be satisfied or allow unsatisfied Rgroup sites to be filled with non-Rgroup substituents (instead of with hydrogens solely).

If your SSS/Poly search retrieved too many records, you might want to:

*	Refine your query by specifying atom and bond query features that limit the types of structures that you retrieve, and then search the same set of records. For example, you can limit substitution at specific positions, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Refine your query by adding restrictions to the attached data in the structures that you retrieve. For example, if your query contains no attached data, you can attach a target value or a text/numeric query (such as < 90) to your query structure.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	Make the Rgroup conditions in your query more specific, and then search the same set of records. For example, you can increase the number of Rgroup sites that must be satisfied or restrict unsatisfied Rgroup sites to be filled solely with hydrogens.

*	If you are interested in additional properties of the polymers that you want to find, conduct a Search By Form (SBF) search for those properties (for example, number-average molecular weight > 30000) over the entire database. Then, save the list from that search and conduct the SSS/Poly search over the saved list.

99.9 Searching Example 1: Allowing Specific Bond Types

To retrieve a general class of compounds, draw a substructure query that contains the minimum structural features that define the class of compounds. If you draw too many specific features, you might unintentionally eliminate some molecules.

99.9.1 Problem

You want to retrieve all polymers that contain 1-methyl-4-vinylpyridinium.

99.9.2 Approach

Conduct an SSS/Poly search with a query that consists of:

*	1-methyl-4-vinylpryidinium within anypolymer (anyp) brackets

*	A single/double query bond in the vinyl group. This allows your query to match the bonds in both structure-based (SRU) and source-based (mon) polymer representations.

99.9.3 Query

The anyp polymer bracket specifies any polymer type.

The bond query feature S/D specifies a single or double bond.

99.9.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for SSS/Poly, how to/examples.

99.9.5 Results

The search retrieves the following structures:

*	The source-based and structure-based representations of poly(1-methyl-4-vinylpyridinium chloride):

*	An N-methylated modification of poly(4-vinyl-pyridine):

*	Three block copolymers of 4-vinylpryidine and 1-methyl-4-pyridinium chloride with varying information on how the repeating units are linked together (connectivity):

*	A random copolymer of 4-vinylpyridine and 1-methyl-4-pyridinium chloride:

99.10 Searching Example 2: Variable Chain Length

To retrieve a general class of compounds, draw a substructure query that contains the minimum structural features that define the class of compounds. If you draw too many specific features, you might unintentionally eliminate some molecules.

99.10.1 Problem

You want to retrieve all polyamides that contain alkylamines.

99.10.2 Approach

Conduct an SSS/Poly search using a polymer query that contains:

*	An amide, N-substituted with a link node [L1-9] that specifies 1 to 9 units. (The link atom must be long enough to find any alkylamine substructures that are likely to be in the database.)

*	A Ring bond count of zero (r0) on the amide nitrogen. The r0 excludes cyclic amides.

*	Anypolymer brackets (anyp)

99.10.3 Query

The ring atom query feature r0 excludes cyclic alkylamines.

The atom and/or bond query feature link node [L1-9] allows alkylamine chains of from 2 to 10 carbons.

The polymer repeat pattern head-to-tail allows the repeating unit to be defined anywhere along the polymer backbone ("phase-shifting" the repeating unit).

99.10.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for SSS, how to/examples.

99.10.5 Results

Molecules Retrieved

Some of the molecules that might be retrieved from the remote molecule database of your choice are as follows:

*	Three versions of Nylon 3 (poly(3-aminopropionic acid)):

These three structures represent the same polymer, but the repeating unit is defined at different points along the backbone of the polymer. These structures were retrieved because the query has a polymer repeat pattern of head-to-tail.

*	Other polyamides of varying chain length, such as poly(caprolactam):

Molecules Not Retrieved

The following structures are not retrieved:

*	The ring atom query feature r0 excludes cyclic alkylamines, such as this lactam version of Nylon 3:

*	The head-to-tail repeat pattern on the query excludes the following structure, because polymers with the either/unknown (eu) repeat pattern are not checked for phase-shifting:

99.11 Searching Example 3: Polymer Mixture

To retrieve a general class of compounds, draw a substructure query that contains the minimum structural features that define the class of compounds. If you draw too many specific features, you might unintentionally eliminate some molecules.

99.11.1 Problem

Find all polymer mixtures that contain up to 20% poly(ethylene oxide).

99.11.2 Approach

Perform an SSS/Poly search using a query that consists of the following:

*	Poly(ethylene oxide) as a component in an unordered mixture.

*	Attached data that specifies a poly(ethylene oxide) concentration range of 0-20%.

99.11.3 Query

The unordered mixture (mix) contains a single component, poly(ethylene oxide). The mixtures that you retrieve can contain additional components.

The attached data (between 0 20) specifies the concentration range.

99.11.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for SSS/Poly, how to/examples.

99.11.5 Results

Some of the molecules that might be retrieved from the remote molecule database of your choice are as follows:


Remote POLY/Exact: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote POLY/Exact Search	121.1

*	Specifying Text/Numeric Queries	121.2

*	Specifying Polymer Structures in Queries	121.3

*	Specifying Polymer Mixtures in Queries	121.4

*	Specifying Attached Data in Queries	121.5

*	Specifying Stereochemistry	121.6

*	Guidelines for Revising the Query	121.7

*	Searching Example 1: Structure-Based Polymer	121.8

*	Searching Example 2: Source-Based Polymer	121.9

We recommend that you print this N-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote POLY/Exact search, click here.

121.1 Definition of a Remote POLY/Exact Search

A Exact Polymer (POLY/Exact) search finds molecule records that match your polymer query exactly:

In addition, you can combine text/numeric and graphical queries. For example, you can find structures that match your query exactly and have a number-average molecular weight greater than 20000 (> 20000 number-average molecular weight).

For more information on text/numeric queries, see Section 121.2. For more information on graphical queries, see Section 121.3.

121.2 Specifying Text/Numeric Queries

A text/numeric query is a phrase in a box or column on the form that specifies the retrieval of data. For example, to find structures with a number-average molecular weight greater than 20,000, enter the text/numeric string > 20000 into the Number-Average Molecular Weight box on the form.

Each phrase in a text/numeric query contains:

*	A search operator that specifies the type of search. For example, the search operators = (equal sign) and LIKE specify the retrieval of the exact match of your query. Use = with numeric values. Use LIKE with text values.

*	A text or numeric target value that you want to find (such as 350 for the molecular weight or ANTIBIOTIC for the activity).

Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

121.2.1 Specifying Numeric Data in Queries

Do not include the units, such as a percent sign (%) or the degrees Centigrade (C). For example, to retrieve all compounds with a molecular weight greater than 350, enter:

> 350

where the search operator is > and the target value is 350.

121.2.2 Specifying Text/Numeric Strings in Queries

Enclose queries that contain text (with or without numeric values) in double quotes and always use a wildcard, such as %. For example, to retrieve all compounds from the author Smythe, enter:

LIKE "%Smythe%"

where the search operator is LIKE and the target value is Smythe.

A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. The wildcard _ is a placeholder for solely one unspecified character. Without a wildcard, you retrieve solely those records that contain exactly the target value that you specified. For example:

Query Without a Wildcard	Example of a Record Retrieved

LIKE "antibiotic"	Antibiotic

Query With the Wildcard %	Examples of Records Retrieved

LIKE "%antibiotic%"	Antibiotic

Antibiotic activity

Resistance to extracellular products such as antibiotics

Note: If you want to retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

121.2.3 The Search Operators

<, <=, >, >=, and <>

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Search Operator	Definition	Examples

=	equal (numeric)	= 350

<	less than (numeric)	< 350

<=	less than or equal to (numeric)	= 350

>	greater than (numeric)	> 350

>=	greater than or equal to (numeric)	>= 350

<>	not equal to (text or numeric)	<> 350

<> "initiator"

LIKE

Use LIKE with text enclosed in double quotation marks. Enter your query as follows:

Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. For example:

Query	Examples of Records Retrieved

LIKE "methane"	Methane

LIKE "benzoic acid"	Benzoic Acid

LIKE "%acid"	Benzoic Acid

Acetic Acid

LIKE "%acid%"	Benzoic Acid Sodium Salt

Acetic Acid Sodium Salt

LIKE "%but_ne"	Trans 2-Butene

2-Butene

N-Butane

Butane

Butene

LIKE "_ethyl"	Methyl

Ethyl

LIKE "antibiotic"	Antibiotic

LIKE "%antibiotic%"	Antibiotic activity

Resistance to extracellular products such as antibiotics

Note: To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice. To retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

BETWEEN

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks. For example:

BETWEEN "XR11" "XZ15"

BETWEEN 95 100

EXISTS

Use EXISTS to retrieve all records in the database that contain data in a specific database field. For example:

EXISTS

Note: You can only use the EXISTS search operator for certain types of database fields. Using EXISTS with other types of fields produces an error message.

121.3 Specifying Polymer Structures in Queries

Polymer structures can be drawn as structure-based or source-based representations. The following example shows both representations of a simple homopolymer:

Your corporate database might contain structures that are drawn in the structure-based representation, the source-based representation, or both.

Note: This document assumes that your company uses MDL's recommended conventions for drawing structure-based and source-based representations of polymers. If you are not sure whether your company uses these conventions, see your ISIS Administrator.

A POLY/Exact search retrieves only the representation that matches the query exactly. That is, use a source-based query to retrieve the source-based representation, and a structure-based query to retrieve the structure-based representation.

Use the information in this section to learn how to draw source-based and structure-based queries for your database.

121.3.1 Structural Repeating Unit (SRU) Brackets (n) in Structure-Based Polymers

Use Structural Repeating Unit (SRU) brackets to enclose the structural repeating unit of the structure-based search query:

SRU brackets imply that the structure within the brackets can repeat with itself (...AAAAA... can occur). Consequently, you should enclose the structure "A" in SRU brackets solely if the sequence ...AAAAA... can occur.

Each set of SRU brackets has one or two bonds that cross each bracket, called crossing bonds. The crossing bonds of an SRU show where the repeating units connect to each other within the polymer (connectivity).

Polymers With Two Crossing Bonds

The polymer repeat pattern shows how the repeating units are joined together. In structures with two crossing bonds, the repeat pattern of an SRU with respect to the next SRU in sequence can be head-to-tail (the default), head-to-head (hh), or either/unknown (eu).

The following table shows examples of the three repeat patterns:

Note: Use the either/unknown repeat pattern when the repeat pattern is unknown, or when both the head-to-tail and head-to-head repeat patterns might be present. In the following example, poly(1-chloroethylene/2-chloroethylene) consists of units of chloroethylene that can be joined head-to-head (1-chloroethylene) or head-to-tail (2-chloroethylene):

In a POLY/Exact search, polymer repeat patterns must match exactly.

Ladder-Type Polymers

Polymers with two crossing bonds on each bracket of the SRU (ladder-type polymers) can have a repeat pattern of head-to-tail, head-to-head, or either/unknown. For the head-to tail and head-to-head repeat patterns, you must also specify how the two crossing bonds on each bracket connect to the corresponding bonds of the adjacent SRU:

*	The head-to-tail repeat pattern has the following two options for connecting the bonds in adjacent SRUs:

*	The head-to-head repeat pattern has the following two options for connecting the bonds in adjacent SRUs:

*	If the repeat pattern is either/unknown, the connections between corresponding bonds might be unknown, or the polymer might contain a mixture of units that are joined head-to-head and other units that are joined head-to-tail (either).

The following table shows examples of the five repeat patterns that are possible for polymers with two crossing bonds on each bracket:

In a POLY/Exact search, polymer repeat patterns -- including flip/no flip -- must match exactly.

For the either/unknown repeat pattern, a structure that contains two brackets with four crossing bonds is equivalent to a structure that contains four brackets with one crossing bond on each bracket. For example:

Polymers With Three or More Brackets

Polymers with 3 or more brackets always have the either/unknown (eu) repeat pattern. For example:

Cyclization and "Phase Shifting"

For SRUs that contain a pair of brackets and that have the head-to-tail repeat pattern, you can define the structural repeating unit anywhere along the polymer backbone (that is, you can "phase-shift" the brackets along the polymer backbone). For example:

You can visualize the connectivity between SRUs as a cyclization of the crossing bonds:

A POLY/Exact search ignores cyclization. That is, a POLY/Exact search retrieves solely structure-based representations that match the query exactly. For example:

To retrieve all three representations of the polymer (the query and "phase-shifted" versions), use POLY/Both search. For information on POLY/Both search, click here.

121.3.2 Monomer Brackets (mon) and Mer Brackets (mer)

Use Monomer (mon) brackets to draw the repeating unit(s) for the source-based representation of a homopolymer:

Enclose a monomer within monomer brackets solely if the monomer molecule is homopolymerizable. If the structural repeating unit consists of one or more monomers that cannot homopolymerize, use mer brackets (mer) to enclose each of these monomers. Then, enclose the mer brackets within monomer brackets. For example:

In this polymer, enclosing the diol and diacid monomers of the polyester in mer brackets shows that these monomers do not homopolymerize to form polyperoxides and polyanhydrides.

121.3.3 Copolymer Brackets (co)

If a structure contains more than one set of SRU and/or monomer brackets, enclose the entire structure within copolymer brackets. Always use copolymer brackets when the structure requires more than one set of polymer brackets (monomer or SRU) to represent the structure. This includes both true copolymers and polymers that are modified after polymerization. For examples of structures that use copolymer brackets, see the Request-A-Document Drawing Polymers: MDL Requirements for Database Searching and Registration.

121.3.4 Additional Polymer Bracket Types

ISIS/Draw provides additional polymer and copolymer bracket types that can be used for alternative representations of certain types of polymers. Use these brackets in search queries only if you know that your company uses these alternative representations. If you are not sure whether your company uses alternative representations of polymers, see your ISIS Administrator.

The additional polymer and copolymer bracket types are as follows:

*	Copolymer bracket types: alternating (alt), block (blk), and random (ran)

*	Polymer bracket types: cross-link (xl), modified (mod), and graft (grf)

*	Mer brackets (mer) can be used to enclose a structural unit that does not repeat with itself, such as a junction unit within a block copolymer

The following are the search characteristics of the additional polymer types:

*	Polymer and copolymer types must match the query exactly. For example:

*	Unspecified copolymer brackets (co) match any type of copolymer (co, blk, ran, alt).

121.3.5 Abbreviated Structures and Multiple Groups

For complex polymers, you might want to abbreviate parts of the structure. An abbreviated structure is all or part of a molecule that has been abbreviated to a text label. Structures that you abbreviate keep their chemical significance, but the underlying structure is hidden. In this example, the phenyl ring in polystyrene is abbreviated to the text string Ph:

A POLY/Exact search finds the underlying chemistry and ignores the name. For example:

For more information on abbreviated structures, click here. Alternatively, choose Help > Index, and search for abbreviated structures, definition of.

You can also use multiple groups to abbreviate structures. A multiple group is a pair of brackets that represents a fixed number of replications of the structure within the brackets. For example:

A POLY/Exact search finds the underlying chemistry of a multiple group. For example:

For step-by-step instructions on creating multiple groups, click here. Alternatively, choose Help > Index, and search for multiple groups, drawing.

121.3.6 Polymer End Groups

The end groups of polymers are generally unknown. Use *atoms (star atoms) to represent unknown or unspecified end groups. For example:

In a POLY/Exact search, you can choose whether polymer end groups must match:

*	To specify that polymer end groups must match in a POLY/Exact search, set [image] End Groups Must Match in the Polymer dialog.

*	To ignore end groups during the search, set [image] End Groups Must Match

121.4 Specifying Polymer Mixtures in Queries

You can define both ordered and unordered mixtures in polymer queries:

*	If the order of addition of components is not important, specify an unordered mixture (mix). Unordered mixtures contain components (c) that are not numbered:

*	If the order of addition of components of the formulation is important, use an ordered mixture (f). Ordered mixtures contain components that are numbered (c1, c2, c3, and so forth):

In a POLY/Exact search, all characteristics of a mixture (number of components, order of ordered components, and structures within component brackets) must match the query exactly.

For more information and examples of structures that use mixtures, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

121.5 Specifying Attached Data in Queries

Attached data is chemically-significant text that you can associate with an atom, a bond, a set of atoms and bonds, or with a bracket. Attached data differs from chemically-insignificant text (plain text). Attached data can be stored in a molecule database and/or used in a graphical search query in a remote molecule database.

For example, the following structure of a statistical copolymer contains attached data on the type of copolymer (stat), the number-average molecular weight of the copolymer (20,000 Mn), and on the mass percentage of each type of repeating unit (75 mass %, 25 mass %):

Attached data differs from chemically-insignificant text (plain text). Attached data can be exported to a molfile, stored in a molecule database, and/or used in a graphical search query in a remote molecule database.

121.5.1 Substance Group (Sgroup) Database Fields

Each piece of attached data is associated with a special kind of database field, called a Substance Group (Sgroup) field. The Sgroup field defines what the data means. The following illustration shows a polymer structure. The table shows the associated Sgroup field and the meaning of each piece of attached data:

Note: Your ISIS Administrator creates and maintains the Sgroup fields in your corporate database. Your ISIS Administrator also establishes guidelines that specify which Sgroup fields you must associate with specific types of data. In the previous example, the ISIS Administrator defines the Sgroup field POLYMER_MASS_PERCENT in your database and assigns the units "mass %" to the Sgroup field.

121.5.2 Specifying Tags For Attached Data

You can display attached data with a tag character that serves as a footnote. In searching, ISIS ignores tags. For example, the following structures are equivalent in a POLY/Exact search:

121.5.3 Attached Data in Searching

In a POLY/Exact search, you can choose whether the attached data in the structures that you retrieve must match the attached data in your query:

*	To specify that attached data must match exactly, set [image] Attached data must match in the Polymer dialog:

*	To ignore attached data, set [image] Attached data must match.

121.6 Specifying Stereochemistry

You can specify the following types of stereochemistry in polymer structures:

*	Stereoregularity of polymers.

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry in non-polymer components of polymer mixtures. You can specify tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

121.6.1 Stereoregularity in Polymers

Polymer structures that are stored in a database do not use Up and Down stereo bonds to show stereoregularity, because these bonds can cause inaccurate search results in certain types of searches, such as POLY/Both and POLY/Co. Instead, polymer structures use attached data to show stereoregularity. In the following example, attached data (associated with the Sgroup field STEREO) shows tacticity in polystyrene (Ph is an abbreviated structure that represents a phenyl group):

To retrieve the structures of your choice, specify attached data on your query, and set [image] Attached data must match. For example:

To retrieve all structures, regardless of stereoregularity, set [image] Attached data must match. For example:

For more information on attached data, see Section 121.5.

121.6.2 Geometric Stereochemistry

Your structure query must contain the exact configuration that you want to retrieve. For example, a POLY/Exact search produces the following results:

121.6.3 Tetrahedral Stereochemistry in Non-Polymer Structures

If you want to retrieve structures that contain non-polymer components that are optical stereoisomers, use Up and Down bonds with chiral flags to show stereochemistry.

Up and Down Bonds

In non-polymer structures, you can use Up and Down stereo bonds to show stereochemistry. An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

A POLY/Exact search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Chiral Flags on Molecules

If your structure contains Up and Down stereo bonds, you can create a query with a chiral flag on a molecule with at least one asymmetric center. The chiral flag ensures that you retrieve solely the absolute stereoconfiguration, and eliminates the relative stereoconfigurations. For example:

121.7 Guidelines for Revising the Query

If your POLY/Exact search retrieved no records, you might want to:

*	Conduct a POLY/Exact search on a different set of records with the same query.

*	Conduct a different search on the same set of records with the same query. For example, you might conduct one of the following searches: Polymer Search for Both Source-Based and Structure-Based Polymers (POLY/Both), Polymer Search for Copolymers (POLY/Co), and Polymer Search for Substructures (POLY/Sub). For more information on these searches, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click the search of your choice. You will see the full definition of the search and how to do it.

*	Conduct the search with options to ignore attached data and polymer end groups:

Attached data must match

Polymer end groups must match

*	Verify that search domain is set to the entire database.

*	Verify that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Add or delete the stereochemistry in your query. If you omit the stereochemistry in your query, the records retrieved will contain no stereochemistry. The records match your search query exactly.

*	Make your text/numeric queries (if any) more general, and then search the same set of records. For example, you can apply operators that partially restrict, such as > or between instead of =, or you can apply wildcards. (A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters.)

*	Delete the structure query from your form, then conduct a Search By Form (SBF) search with the text/numeric data in your query.

If your POLY/Exact search retrieved too many records, you might want to:

*	Make the text/numeric strings in your query more restrictive, and then search the same set of records. For example, you can use the operator = instead of >.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	First conduct a formula search to screen out large and complex molecules that are stored in your database, and then conduct a search on the less complex molecules. If your query is not able to map a stored molecule within a specific length of time, the molecule is added to the search results.

121.8 Searching Example 1: Structure-Based Copolymer

121.8.1 Problem

You want to find copolymers of styrene and methyl methacrylate. Your polymer database uses structure-based representation, so your query looks like this:

121.8.2 Approach

Draw the structure. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE.

Conduct a POLY/Exact search in the remote molecule database of your choice. Specify the following for attached data and polymer end groups:

Attached data must match
End Groups Must Match

121.8.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for POLY/Exact, how to/examples.

121.8.4 Results

You retrieve the following structures:

Text data attached to the copolymer brackets shows the type of copolymer. The numeric data attached to the SRU brackets specifies the mass percentage each component of the polymer.

Source-based representations such as the following are not retrieved:

To retrieve both source-based and structure-based representations, use POLY/Both search.

121.9 Searching Example 2: Source-Based Copolymer

121.9.1 Problem

You want to find copolymers of styrene and methyl methacrylate. Your polymer database uses source-based representation, so your query looks like this:

121.9.2 Approach

Draw the structure with the repeat pattern that you want to see in the molecules retrieved. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE.

Conduct a POLY/Exact search in the remote molecule database of your choice. Specify the following for attached data and polymer end groups:

Attached data must match
End Groups Must Match

121.9.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for POLY/Exact, how to/examples.

121.9.4 Results

You retrieve the following structures:

Text data attached to the copolymer brackets shows the type of copolymer. The numeric data attached to the monomer brackets specifies the mass percentage each component of the polymer.

Structure-based representations such as the following are not retrieved:

To retrieve both source-based and structure-based representations, use POLY/Both search.


Remote POLY/Both: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote POLY/Both Search	122.1

*	Specifying Text/Numeric Queries	122.2

*	Specifying Polymer Structures in Queries	122.3

*	Specifying Polymer Mixtures in Queries	122.4

*	Specifying Attached Data in Queries	122.5

*	Specifying Stereochemistry	122.6

*	Guidelines for Revising the Query	122.7

*	Searching Example: Source-Based Query	122.8

We recommend that you print this N-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote POLY/Both search, click here.

122.1 Definition of a Remote POLY/Both Search

A Polymer Search for Both Structure- and Source-Based Polymer Structures (POLY/Both) finds molecules that match both source-based and structure-based representations of your polymer query and that also match any text/numeric search criteria on your form.

In the following example, the structure-based query retrieves an identical structure-based polymer, a structure-based polymer in which the structural repeating unit (SRU) is "phase-shifted" along the polymer backbone, and two source-based representations of the polymer. The form box for number-average molecular weight (Num. Avg. Mol. Wt.) contains the text/numeric query > 20000, so all the polymers retrieved have a number-average molecular weight that is greater than 20,000:

122.2 Specifying Text/Numeric Queries

A text/numeric query is a phrase in a box or column on the form that specifies the retrieval of data. For example, to find structures with a number-average molecular weight greater than 20,000, enter the text/numeric string > 20000 into the Number-Average Molecular Weight box on the form.

Each phrase in a text/numeric query contains:

*	A search operator that specifies the type of search. For example, the search operators = (equal sign) and LIKE specify the retrieval of the exact match of your query. Use = with numeric values. Use LIKE with text values.

*	A text or numeric target value that you want to find (such as 350 for the molecular weight or ANTIBIOTIC for the activity).

Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

122.2.1 Specifying Numeric Data in Queries

Do not include the units, such as a percent sign (%) or the degrees Centigrade (C). For example, to retrieve all compounds with a molecular weight greater than 350, enter:

> 350

where the search operator is > and the target value is 350.

122.2.2 Specifying Text/Numeric Strings in Queries

Enclose queries that contain text (with or without numeric values) in double quotes and always use a wildcard, such as %. For example, to retrieve all compounds from the author Smythe, enter:

LIKE "%Smythe%"

where the search operator is LIKE and the target value is Smythe.

A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. The wildcard _ is a placeholder for solely one unspecified character. Without a wildcard, you retrieve solely those records that contain exactly the target value that you specified. For example:

Query Without a Wildcard	Example of a Record Retrieved

LIKE "antibiotic"	Antibiotic

Query With the Wildcard %	Examples of Records Retrieved

LIKE "%antibiotic%"	Antibiotic

Antibiotic activity

Resistance to extracellular products such as antibiotics

Note: If you want to retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

122.2.3 The Search Operators

<, <=, >, >=, and <>

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Search Operator	Definition	Examples

=	equal (numeric)	= 350

<	less than (numeric)	< 350

<=	less than or equal to (numeric)	= 350

>	greater than (numeric)	> 350

>=	greater than or equal to (numeric)	>= 350

<>	not equal to (text or numeric)	<> 350

<> "initiator"

LIKE

Use LIKE with text enclosed in double quotation marks. Enter your query as follows:

Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. For example:

Query	Examples of Records Retrieved

LIKE "methane"	Methane

LIKE "benzoic acid"	Benzoic Acid

LIKE "%acid"	Benzoic Acid

Acetic Acid

LIKE "%acid%"	Benzoic Acid Sodium Salt

Acetic Acid Sodium Salt

LIKE "%but_ne"	Trans 2-Butene

2-Butene

N-Butane

Butane

Butene

LIKE "_ethyl"	Methyl

Ethyl

LIKE "antibiotic"	Antibiotic

LIKE "%antibiotic%"	Antibiotic activity

Resistance to extracellular products such as antibiotics

Note: To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice. To retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

BETWEEN

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks. For example:

BETWEEN "XR11" "XZ15"

BETWEEN 95 100

EXISTS

Use EXISTS to retrieve all records in the database that contain data in a specific database field. For example:

EXISTS

Note: You can only use the EXISTS search operator for certain types of database fields. Using EXISTS with other types of fields produces an error message.

122.3 Specifying Polymer Structures in Queries

Polymer structures can be drawn as structure-based or source-based representations. The following example shows both representations of a simple homopolymer:

Your corporate database might contain structures that are drawn in the structure-based representation, the source-based representation, or both.

Note: This document assumes that your company uses MDL's recommended conventions for drawing structure-based and source-based representations of polymers. If you are not sure whether your company uses these conventions, see your ISIS Administrator.

In a POLY/Both search, the source-based and structure-based representations of certain types of polymers can find each other in the database. This applies to the following types of single-step polymerization reactions:

*	Addition to a double bond. Polymers created in this type of reaction include polystyrene, polyethylene, and poly(styrene-co-butadiene).

*	Condensation reaction with elimination of water or HCl. Polymers created in this type of reaction include polyesters and polyamides.

Use the information in this section to learn how to draw source-based and structure-based queries for your database. For more information and examples of structure-based and source-based polymers, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

122.3.1 Structural Repeating Unit (SRU) Brackets (n) in Structure-Based Polymers

Use Structural Repeating Unit (SRU) brackets to enclose the structural repeating unit of the structure-based search query:

SRU brackets imply that the structure within the brackets can repeat with itself (...AAAAA... can occur). Consequently, you should enclose the structure "A" in SRU brackets solely if the sequence ...AAAAA... can occur.

Each set of SRU brackets has one or two bonds that cross each bracket, called crossing bonds. The crossing bonds of an SRU show where the repeating units connect to each other within the polymer (connectivity).

Polymers With Two Crossing Bonds

The polymer repeat pattern shows how the repeating units are joined together. In structures with two crossing bonds, the repeat pattern of an SRU with respect to the next SRU in sequence can be head-to-tail (the default), head-to-head (hh), or either/unknown (eu).

The following table shows examples of the three repeat patterns:

Note: Use the either/unknown repeat pattern when the repeat pattern is unknown, or when both the head-to-tail and head-to-head repeat patterns might be present. In the following example, poly(1-chloroethylene/2-chloroethylene) consists of units of chloroethylene that can be joined head-to-head (1-chloroethylene) or head-to-tail (2-chloroethylene):

In a POLY/Both search, polymer repeat patterns must match exactly.

Ladder-Type Polymers

Polymers with two crossing bonds on each bracket of the SRU (ladder-type polymers) can have a repeat pattern of head-to-tail, head-to-head, or either/unknown. For the head-to tail and head-to-head repeat patterns, you must also specify how the two crossing bonds on each bracket connect to the corresponding bonds of the adjacent SRU:

*	The head-to-tail repeat pattern has the following two options for connecting the bonds in adjacent SRUs:

*	The head-to-head repeat pattern has the following two options for connecting the bonds in adjacent SRUs:

*	If the repeat pattern is either/unknown, the connections between corresponding bonds might be unknown, or the polymer might contain a mixture of units that are joined head-to-head and other units that are joined head-to-tail (either).

The following table shows examples of the five repeat patterns that are possible for polymers with two crossing bonds on each bracket:

In a POLY/Both search, polymer repeat patterns -- including flip/no flip -- must match exactly.

For the either/unknown repeat pattern, a structure that contains two brackets with four crossing bonds is equivalent to a structure that contains four brackets with one crossing bond on each bracket. For example:

Polymers With Three or More Brackets

Polymers with 3 or more brackets always have the either/unknown (eu) repeat pattern. For example:

Cyclization and "Phase Shifting"

For SRUs that contain a pair of brackets and that have the head-to-tail repeat pattern, you can define the structural repeating unit anywhere along the polymer backbone (that is, you can "phase-shift" the brackets along the polymer backbone). For example:

You can visualize the connectivity between SRUs as a cyclization of the crossing bonds:

In a POLY/Both search, the head-to-tail repeat pattern shows cyclization and "phase-shifting". For example:

The head-to-head and either/unknown repeat patterns do not show cyclization or "phase-shifting." For example:

122.3.2 Monomer Brackets (mon) and Mer Brackets (mer)

Use Monomer (mon) brackets to draw the repeating unit(s) for the source-based representation of a homopolymer:

Enclose a monomer within monomer brackets solely if the monomer molecule is homopolymerizable. If the structural repeating unit consists of one or more monomers that cannot homopolymerize, use mer brackets (mer) to enclose each of these monomers. Then, enclose the mer brackets within monomer brackets. For example:

In this polymer, enclosing the diol and diacid monomers of the polyester in mer brackets shows that these monomers do not homopolymerize to form polyperoxides and polyanhydrides.

122.3.3 Copolymer Brackets (co)

If a structure contains more than one set of SRU and/or monomer brackets, enclose the entire structure within copolymer brackets. Always use copolymer brackets when the structure requires more than one set of polymer brackets (monomer or SRU) to represent the structure. This includes both true copolymers and polymers that are modified after polymerization. For examples of structures that use copolymer brackets, see the Request-A-Document Drawing Polymers: MDL Requirements for Database Searching and Registration.

122.3.4 Additional Polymer Bracket Types

ISIS/Draw provides additional polymer and copolymer bracket types that can be used for alternative representations of certain types of polymers. Use these brackets in search queries only if you know that your company uses these alternative representations. If you are not sure whether your company uses alternative representations of polymers, see your ISIS Administrator.

The additional polymer and copolymer bracket types are as follows:

*	Copolymer bracket types: alternating (alt), block (blk), and random (ran)

*	Polymer bracket types: cross-link (xl), modified (mod), and graft (grf)

*	Mer brackets (mer) can be used to enclose a structural unit that does not repeat with itself, such as a junction unit within a block copolymer

The following are the search characteristics of the additional polymer types:

*	Polymer and copolymer types must match the query exactly. For example:

*	Unspecified copolymer brackets (co) match any type of copolymer (co, blk, ran, alt).

122.3.5 Abbreviated Structures and Multiple Groups

For complex polymers, you might want to abbreviate parts of the structure. An abbreviated structure is all or part of a molecule that has been abbreviated to a text label. Structures that you abbreviate keep their chemical significance, but the underlying structure is hidden. In this example, the phenyl ring in polystyrene is abbreviated to the text string Ph:

A POLY/Both search finds the underlying chemistry and ignores the name. For example:

For more information on abbreviated structures, click here. Alternatively, choose Help > Index, and search for abbreviated structures, definition of.

You can also use multiple groups to abbreviate structures. A multiple group is a pair of brackets that represents a fixed number of replications of the structure within the brackets. For example:

A POLY/Both search finds the underlying chemistry of a multiple group. For example:

For step-by-step instructions on creating multiple groups, click here. Alternatively, choose Help > Index, and search for multiple groups, drawing.

122.3.6 Polymer End Groups

The end groups of polymers are generally unknown. Use *atoms (star atoms) to represent unknown or unspecified end groups. For example:

In a POLY/Both search, you can choose whether polymer end groups must match:

*	To specify that polymer end groups must match in a POLY/Both search, set [image] End Groups Must Match in the Polymer dialog.

*	To ignore end groups during the search, set [image] End Groups Must Match

122.4 Specifying Polymer Mixtures in Queries

You can define both ordered and unordered mixtures in polymer queries:

*	If the order of addition of components is not important, specify an unordered mixture (mix). Unordered mixtures contain components (c) that are not numbered:

*	If the order of addition of components of the formulation is important, use an ordered mixture (f). Ordered mixtures contain components that are numbered (c1, c2, c3, and so forth):

In a POLY/Both search, all characteristics of a mixture (number of components, order of ordered components, and structures within component brackets) must match the query exactly.

For more information and examples of structures that use mixtures, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

122.5 Specifying Attached Data in Queries

Attached data is chemically-significant text that you can associate with an atom, a bond, a set of atoms and bonds, or with a bracket. Attached data differs from chemically-insignificant text (plain text). Attached data can be stored in a molecule database and/or used in a graphical search query in a remote molecule database.

For example, the following structure of a statistical copolymer contains attached data on the type of copolymer (stat), the number-average molecular weight of the copolymer (20,000 Mn), and on the mass percentage of each type of repeating unit (75 mass %, 25 mass %):

Attached data differs from chemically-insignificant text (plain text). Attached data can be exported to a molfile, stored in a molecule database, and/or used in a graphical search query in a remote molecule database.

122.5.1 Substance Group (Sgroup) Database Fields

Each piece of attached data is associated with a special kind of database field, called a Substance Group (Sgroup) field. The Sgroup field defines what the data means. The following illustration shows a polymer structure. The table shows the associated Sgroup field and the meaning of each piece of attached data:

Note: Your ISIS Administrator creates and maintains the Sgroup fields in your corporate database. Your ISIS Administrator also establishes guidelines that specify which Sgroup fields you must associate with specific types of data. In the previous example, the ISIS Administrator defines the Sgroup field POLYMER_MASS_PERCENT in your database and assigns the units "mass %" to the Sgroup field.

122.5.2 Specifying Tags For Attached Data

You can display attached data with a tag character that serves as a footnote. In searching, ISIS ignores tags. For example, the following structures are equivalent in a POLY/Both search:

122.5.3 Attached Data in Searching

In a POLY/Both search, you can choose whether the attached data in the structures that you retrieve must match the attached data in your query:

*	To specify that attached data must match exactly, set [image] Attached data must match in the Polymer dialog:

*	To ignore attached data, set [image] Attached data must match.

122.6 Specifying Stereochemistry

You can specify the following types of stereochemistry in polymer structures:

*	Stereoregularity of polymers.

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry in non-polymer components of polymer mixtures. You can specify tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

122.6.1 Stereoregularity in Polymers

Polymer structures that are stored in a database do not use Up and Down stereo bonds to show stereoregularity, because these bonds can cause inaccurate search results in certain types of searches, such as POLY/Both. Instead, polymer structures use attached data to show stereoregularity. In the following example, attached data (associated with the Sgroup field STEREO) shows tacticity in polystyrene (Ph is an abbreviated structure that represents a phenyl group):

To retrieve the structures of your choice, specify attached data on your query, and set [image] Attached data must match. For example:

To retrieve all structures, regardless of stereoregularity, set [image] Attached data must match. For example:

For more information on attached data, see Section 122.5.

122.6.2 Geometric Stereochemistry

Your structure query must contain the exact configuration that you want to retrieve. For example, a POLY/Both search produces the following results:

122.6.3 Tetrahedral Stereochemistry in Non-Polymer Structures

If you want to retrieve structures that contain non-polymer components that are optical stereoisomers, use Up and Down bonds with chiral flags to show stereochemistry.

Up and Down Bonds

In non-polymer structures, you can use Up and Down stereo bonds to show stereochemistry. An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

A POLY/Both search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Chiral Flags on Molecules

If your structure contains Up and Down stereo bonds, you can create a query with a chiral flag on a molecule with at least one asymmetric center. The chiral flag ensures that you retrieve solely the absolute stereoconfiguration, and eliminates the relative stereoconfigurations. For example:

122.7 Guidelines for Revising the Query

If your POLY/Both search retrieved no records, you might want to:

*	Conduct a POLY/Both search on a different set of records with the same query.

*	Conduct a different search on the same set of records with the same query. For example, you might conduct one of the following searches: Polymer Search for Copolymers (POLY/Co) and Polymer Search for Substructures (POLY/Sub). For more information on these searches, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click the search of your choice. You will see the full definition of the search and how to do it.

*	Conduct the search with options to ignore attached data and polymer end groups:

Attached data must match

Polymer end groups must match

*	Verify that search domain is set to the entire database.

*	Verify that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Add or delete the stereochemistry in your query. If you omit the stereochemistry in your query, the records retrieved will contain no stereochemistry. The records match your search query exactly.

*	Make your text/numeric queries (if any) more general, and then search the same set of records. For example, you can apply operators that partially restrict, such as > or between instead of =, or you can apply wildcards. (A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters.)

*	Delete the structure query from your form, then conduct a Search By Form (SBF) search with the text/numeric data in your query.

If your POLY/Both search retrieved too many records, you might want to:

*	Make the text/numeric strings in your query more restrictive, and then search the same set of records. For example, you can use the operator = instead of >.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	First conduct a formula search to screen out large and complex molecules that are stored in your database, and then conduct a search on the less complex molecules. If your query is not able to map a stored molecule within a specific length of time, the molecule is added to the search results.

122.8 Searching Example: Source-Based Query

The following searching example shows you how to use the source-based representation of a polymer to retrieve both structure-based and source-based representations of the polymer.

122.8.1 Problem

You want to find copolymers of styrene and methyl methacrylate. Your query looks like this:

122.8.2 Approach

Draw the structure. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE.

Conduct a POLY/Both search in the remote molecule database of your choice. Specify the following for attached data and polymer end groups:

Attached data must match
End Groups Must Match

122.8.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for POLY/Both, how to/examples.

122.8.4 Results

You retrieve the following structures:

Text data attached to the copolymer brackets shows the type of copolymer. The numeric data attached to the monomer brackets specifies the mass percentage each component of the polymer.

Structures that contain additional types of monomers, such as the following, are not retrieved:

To retrieve structures such as these, use a POLY/Co search.


Remote POLY/Co: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote POLY/Co Search	123.1

*	Specifying Text/Numeric Queries	123.2

*	Specifying Polymer Structures in Queries	123.3

*	Specifying Polymer Mixtures in Queries	123.4

*	Specifying Attached Data in Queries	123.5

*	Specifying Stereochemistry	123.6

*	Guidelines for Revising the Query	123.7

*	Searching Example: Copolymers of Polystyrene	123.8

We recommend that you print this N-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote POLY/Co search, click here.

123.1 Definition of a Remote POLY/Co Search

A Polymer Search for Copolymers (POLY/Co) search finds molecule records that are copolymers of your polymer query. For example:

In addition, you can combine text/numeric and graphical queries. For example, you can find structures that are copolymers of your query and have a number-average molecular weight > 20000 (> 20000 number-average molecular weight).

A remote search is a search over a database that typically exists on a mainframe.

123.2 Specifying Text/Numeric Queries

A text/numeric query is a phrase in a box or column on the form that specifies the retrieval of data. For example, to find structures with a number-average molecular weight greater than 20,000, enter the text/numeric string > 20000 into the Number-Average Molecular Weight box on the form.

Each phrase in a text/numeric query contains:

*	A search operator that specifies the type of search. For example, the search operators = (equal sign) and LIKE specify the retrieval of the exact match of your query. Use = with numeric values. Use LIKE with text values.

*	A text or numeric target value that you want to find (such as 350 for the molecular weight or ANTIBIOTIC for the activity).

Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

123.2.1 Specifying Numeric Data in Queries

Do not include the units, such as a percent sign (%) or the degrees Centigrade (C). For example, to retrieve all compounds with a molecular weight greater than 350, enter:

> 350

where the search operator is > and the target value is 350.

123.2.2 Specifying Text/Numeric Strings in Queries

Enclose queries that contain text (with or without numeric values) in double quotes and always use a wildcard, such as %. For example, to retrieve all compounds from the author Smythe, enter:

LIKE "%Smythe%"

where the search operator is LIKE and the target value is Smythe.

A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. The wildcard _ is a placeholder for solely one unspecified character. Without a wildcard, you retrieve solely those records that contain exactly the target value that you specified. For example:

Query Without a Wildcard	Example of a Record Retrieved

LIKE "antibiotic"	Antibiotic

Query With the Wildcard %	Examples of Records Retrieved

LIKE "%antibiotic%"	Antibiotic

Antibiotic activity

Resistance to extracellular products such as antibiotics

Note: If you want to retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

123.2.3 The Search Operators

<, <=, >, >=, and <>

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Search Operator	Definition	Examples

=	equal (numeric)	= 350

<	less than (numeric)	< 350

<=	less than or equal to (numeric)	= 350

>	greater than (numeric)	> 350

>=	greater than or equal to (numeric)	>= 350

<>	not equal to (text or numeric)	<> 350

<> "initiator"

LIKE

Use LIKE with text enclosed in double quotation marks. Enter your query as follows:

Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. For example:

Query	Examples of Records Retrieved

LIKE "methane"	Methane

LIKE "benzoic acid"	Benzoic Acid

LIKE "%acid"	Benzoic Acid

Acetic Acid

LIKE "%acid%"	Benzoic Acid Sodium Salt

Acetic Acid Sodium Salt

LIKE "%but_ne"	Trans 2-Butene

2-Butene

N-Butane

Butane

Butene

LIKE "_ethyl"	Methyl

Ethyl

LIKE "antibiotic"	Antibiotic

LIKE "%antibiotic%"	Antibiotic activity

Resistance to extracellular products such as antibiotics

Note: To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice. To retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

BETWEEN

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks. For example:

BETWEEN "XR11" "XZ15"

BETWEEN 95 100

EXISTS

Use EXISTS to retrieve all records in the database that contain data in a specific database field. For example:

EXISTS

Note: You can only use the EXISTS search operator for certain types of database fields. Using EXISTS with other types of fields produces an error message.

123.3 Specifying Polymer Structures in Queries

Polymer structures can be drawn as structure-based or source-based representations. The following example shows both representations of a simple homopolymer:

Your corporate database might contain structures that are drawn in the structure-based representation, the source-based representation, or both.

Note: This document assumes that your company uses MDL's recommended conventions for drawing structure-based and source-based representations of polymers. If you are not sure whether your company uses these conventions, see your ISIS Administrator.

In a POLY/Co search, the source-based and structure-based representations of certain types of polymers can find each other in the database. This applies to the following types of single-step polymerization reactions:

*	Addition to a double bond. Polymers created in this type of reaction include polystyrene, polyethylene, and poly(styrene-co-butadiene).

*	Condensation reaction with elimination of water or HCl. Polymers created in this type of reaction include polyesters and polyamides.

Use the information in this section to learn how to draw source-based and structure-based queries for your database. For more information and examples of structure-based and source-based polymers, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

123.3.1 Structural Repeating Unit (SRU) Brackets (n) in Structure-Based Polymers

Use Structural Repeating Unit (SRU) brackets to enclose the structural repeating unit of the structure-based search query:

SRU brackets imply that the structure within the brackets can repeat with itself (...AAAAA... can occur). Consequently, you should enclose the structure "A" in SRU brackets solely if the sequence ...AAAAA... can occur.

Each set of SRU brackets has one or two bonds that cross each bracket, called crossing bonds. The crossing bonds of an SRU show where the repeating units connect to each other within the polymer (connectivity).

Polymers With Two Crossing Bonds

The polymer repeat pattern shows how the repeating units are joined together. In structures with two crossing bonds, the repeat pattern of an SRU with respect to the next SRU in sequence can be head-to-tail (the default), head-to-head (hh), or either/unknown (eu).

The following table shows examples of the three repeat patterns:

Note: Use the either/unknown repeat pattern when the repeat pattern is unknown, or when both the head-to-tail and head-to-head repeat patterns might be present. In the following example, poly(1-chloroethylene/2-chloroethylene) consists of units of chloroethylene that can be joined head-to-head (1-chloroethylene) or head-to-tail (2-chloroethylene):

In a POLY/Co search, polymer repeat patterns must match exactly.

Ladder-Type Polymers

Polymers with two crossing bonds on each bracket of the SRU (ladder-type polymers) can have a repeat pattern of head-to-tail, head-to-head, or either/unknown. For the head-to tail and head-to-head repeat patterns, you must also specify how the two crossing bonds on each bracket connect to the corresponding bonds of the adjacent SRU:

*	The head-to-tail repeat pattern has the following two options for connecting the bonds in adjacent SRUs:

*	The head-to-head repeat pattern has the following two options for connecting the bonds in adjacent SRUs:

*	If the repeat pattern is either/unknown, the connections between corresponding bonds might be unknown, or the polymer might contain a mixture of units that are joined head-to-head and other units that are joined head-to-tail (either).

The following table shows examples of the five repeat patterns that are possible for polymers with two crossing bonds on each bracket:

In a POLY/Co search, polymer repeat patterns -- including flip/no flip -- must match exactly.

For the either/unknown repeat pattern, a structure that contains two brackets with four crossing bonds is equivalent to a structure that contains four brackets with one crossing bond on each bracket. For example:

Polymers With Three or More Brackets

Polymers with 3 or more brackets always have the either/unknown (eu) repeat pattern. For example:

Cyclization and "Phase Shifting"

For SRUs that contain a pair of brackets and that have the head-to-tail repeat pattern, you can define the structural repeating unit anywhere along the polymer backbone (that is, you can "phase-shift" the brackets along the polymer backbone). For example:

You can visualize the connectivity between SRUs as a cyclization of the crossing bonds:

In a POLY/Co search, the head-to-tail repeat pattern shows cyclization and "phase-shifting". For example:

The head-to-head and either/unknown repeat patterns do not show cyclization or "phase-shifting." For example:

123.3.2 Monomer Brackets (mon) and Mer Brackets (mer)

Use Monomer (mon) brackets to draw the repeating unit(s) for the source-based representation of a homopolymer:

Enclose a monomer within monomer brackets solely if the monomer molecule is homopolymerizable. If the structural repeating unit consists of one or more monomers that cannot homopolymerize, use mer brackets (mer) to enclose each of these monomers. Then, enclose the mer brackets within monomer brackets. For example:

In this polymer, enclosing the diol and diacid monomers of the polyester in mer brackets shows that these monomers do not homopolymerize to form polyperoxides and polyanhydrides.

123.3.3 Copolymer Brackets (co)

If a structure contains more than one set of SRU and/or monomer brackets, enclose the entire structure within copolymer brackets. Always use copolymer brackets when the structure requires more than one set of polymer brackets (monomer or SRU) to represent the structure. This includes both true copolymers and polymers that are modified after polymerization. For examples of structures that use copolymer brackets, see the Request-A-Document Drawing Polymers: MDL Requirements for Database Searching and Registration.

123.3.4 Additional Polymer Bracket Types

ISIS/Draw provides additional polymer and copolymer bracket types that can be used for alternative representations of certain types of polymers. Use these brackets in search queries only if you know that your company uses these alternative representations. If you are not sure whether your company uses alternative representations of polymers, see your ISIS Administrator.

The additional polymer and copolymer bracket types are as follows:

*	Copolymer bracket types: alternating (alt), block (blk), and random (ran)

*	Polymer bracket types: cross-link (xl), modified (mod), and graft (grf)

*	Mer brackets (mer) can be used to enclose a structural unit that does not repeat with itself, such as a junction unit within a block copolymer

The following are the search characteristics of the additional polymer types:

*	Polymer and copolymer types must match the query exactly. For example:

*	Unspecified copolymer brackets (co) match any type of copolymer (co, blk, ran, alt).

123.3.5 Abbreviated Structures and Multiple Groups

For complex polymers, you might want to abbreviate parts of the structure. An abbreviated structure is all or part of a molecule that has been abbreviated to a text label. Structures that you abbreviate keep their chemical significance, but the underlying structure is hidden. In this example, the phenyl ring in polystyrene is abbreviated to the text string Ph:

A POLY/Co search finds the underlying chemistry and ignores the name. For example:

For more information on abbreviated structures, click here. Alternatively, choose Help > Index, and search for abbreviated structures, definition of.

You can also use multiple groups to abbreviate structures. A multiple group is a pair of brackets that represents a fixed number of replications of the structure within the brackets. For example:

A POLY/Co search finds the underlying chemistry of a multiple group. For example:

For step-by-step instructions on creating multiple groups, click here. Alternatively, choose Help > Index, and search for multiple groups, drawing.

123.3.6 Polymer End Groups

The end groups of polymers are generally unknown. Use *atoms (star atoms) to represent unknown or unspecified end groups. For example:

In a POLY/Co search, you can choose whether polymer end groups must match:

*	To specify that polymer end groups must match in a POLY/Co search, set [image] End Groups Must Match in the Polymer dialog.

*	To ignore end groups during the search, set [image] End Groups Must Match

123.4 Specifying Polymer Mixtures in Queries

You can define both ordered and unordered mixtures in polymer queries:

*	If the order of addition of components is not important, specify an unordered mixture (mix). Unordered mixtures contain components (c) that are not numbered:

*	If the order of addition of components of the formulation is important, use an ordered mixture (f). Ordered mixtures contain components that are numbered (c1, c2, c3, and so forth):

In a POLY/Co search, all characteristics of a mixture (number of components, order of ordered components, and structures within component brackets) must match the query exactly.

For more information and examples of structures that use mixtures, see the Request-A-Document Drawing Polymers: MDL Requirements for Database Searching and Registration.

123.5 Specifying Attached Data in Queries

Attached data is chemically-significant text that you can associate with an atom, a bond, a set of atoms and bonds, or with a bracket. Attached data differs from chemically-insignificant text (plain text). Attached data can be stored in a molecule database and/or used in a graphical search query in a remote molecule database.

For example, the following structure of a statistical copolymer contains attached data on the type of copolymer (stat), the number-average molecular weight of the copolymer (20,000 Mn), and on the mass percentage of each type of repeating unit (75 mass %, 25 mass %):

Attached data differs from chemically-insignificant text (plain text). Attached data can be exported to a molfile, stored in a molecule database, and/or used in a graphical search query in a remote molecule database.

123.5.1 Substance Group (Sgroup) Database Fields

Each piece of attached data is associated with a special kind of database field, called a Substance Group (Sgroup) field. The Sgroup field defines what the data means. The following illustration shows a polymer structure. The table shows the associated Sgroup field and the meaning of each piece of attached data:

Note: Your ISIS Administrator creates and maintains the Sgroup fields in your corporate database. Your ISIS Administrator also establishes guidelines that specify which Sgroup fields you must associate with specific types of data. In the previous example, the ISIS Administrator defines the Sgroup field POLYMER_MASS_PERCENT in your database and assigns the units "mass %" to the Sgroup field.

123.5.2 Specifying Tags For Attached Data

You can display attached data with a tag character that serves as a footnote. In searching, ISIS ignores tags. For example, the following structures are equivalent in a POLY/Co search:

123.5.3 Attached Data in Searching

In a POLY/Co search, you can choose whether the attached data in the structures that you retrieve must match the attached data in your query:

*	To specify that attached data must match exactly, set [image] Attached data must match in the Polymer dialog:

*	To ignore attached data, set [image] Attached data must match.

123.6 Specifying Stereochemistry

You can specify the following types of stereochemistry in polymer structures:

*	Stereoregularity of polymers.

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry in non-polymer components of polymer mixtures. You can specify tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

123.6.1 Stereoregularity in Polymers

Polymer structures that are stored in a database do not use Up and Down stereo bonds to show stereoregularity, because these bonds can cause inaccurate search results in certain types of searches, such as POLY/Both and POLY/Co. Instead, polymer structures use attached data to show stereoregularity. In the following example, attached data (associated with the Sgroup field STEREO) shows tacticity in polystyrene (Ph is an abbreviated structure that represents a phenyl group):

To retrieve the structures of your choice, specify attached data on your query, and set [image] Attached data must match. For example:

To retrieve all structures, regardless of stereoregularity, set [image] Attached data must match. For example:

For more information on attached data, see Section 123.5.

123.6.2 Geometric Stereochemistry

Your structure query must contain the exact configuration that you want to retrieve. For example, a POLY/Co search produces the following results:

123.6.3 Tetrahedral Stereochemistry in Non-Polymer Structures

If you want to retrieve structures that contain non-polymer components that are optical stereoisomers, use Up and Down bonds with chiral flags to show stereochemistry.

Up and Down Bonds

In non-polymer structures, you can use Up and Down stereo bonds to show stereochemistry. An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

A POLY/Co search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Chiral Flags on Molecules

If your structure contains Up and Down stereo bonds, you can create a query with a chiral flag on a molecule with at least one asymmetric center. The chiral flag ensures that you retrieve solely the absolute stereoconfiguration, and eliminates the relative stereoconfigurations. For example:

123.7 Guidelines for Revising the Query

If your POLY/Co search retrieved no records, you might want to:

*	Conduct a POLY/Co search on a different set of records with the same query.

*	Conduct a different search on the same set of records with the same query. For example, you might conduct a Polymer Search for Substructures (POLY/Sub). For more information on this search, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click the search of your choice. You will see the full definition of the search and how to do it.

*	Conduct the search with options to ignore attached data and polymer end groups:

Attached data must match

Polymer end groups must match

*	Verify that search domain is set to the entire database.

*	Verify that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Add or delete the stereochemistry in your query. If you omit the stereochemistry in your query, the records retrieved will contain no stereochemistry. The records match your search query exactly.

*	Make your text/numeric queries (if any) more general, and then search the same set of records. For example, you can apply operators that partially restrict, such as > or between instead of =, or you can apply wildcards. (A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters.)

*	Delete the structure query from your form, then conduct a Search By Form (SBF) search with the text/numeric data in your query.

If your POLY/Co search retrieved too many records, you might want to:

*	Make the text/numeric strings in your query more restrictive, and then search the same set of records. For example, you can use the operator = instead of >.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	First conduct a formula search to screen out large and complex molecules that are stored in your database, and then conduct a search on the less complex molecules. If your query is not able to map a stored molecule within a specific length of time, the molecule is added to the search results.

*	If you are interested in additional properties of the polymers that you want to find, add a text/numeric query to a box on your form (for example, number-average molecular weight > 30000).

123.8 Searching Example: Copolymers of Polystyrene

The following searching example shows you how to retrieve copolymers of polystyrene.

123.8.1 Problem

You want to retrieve copolymers of polystyrene. You can use either of the following structures as your query:

Note: You must enclose the styrene monomer or SRU brackets within copolymer brackets. If you do not draw the copolymer brackets, you retrieve styrene homopolymers only.

123.8.2 Approach

Draw the structure. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE.

Conduct a POLY/Co search in the remote molecule database of your choice. Specify the following for attached data and polymer end groups:

Attached data must match
End Groups Must Match

123.8.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for POLY/Co, how to/examples.

123.8.4 Results

You retrieve all structures that are copolymers of styrene. The structures include both source-based and structure-based representations:

The following structures are not retrieved:


Remote POLY/Sub: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote POLY/Sub Search	124.1

*	Specifying Text/Numeric Queries	124.2

*	Specifying Polymers in Graphical Queries	124.3

*	Specifying Mixtures in Graphical Queries	124.4

*	Specifying Attached Data in Graphical Queries	124.5

*	Specifying Atom and Bond Query Features	124.6

*	Specifying Rgroup Query Features	124.7

*	Specifying Stereochemistry	124.8

*	Guidelines for Revising the Query	124.9

*	Searching Example 1: Allowing Specific Bond Types 	124.10

*	Searching Example 2: Variable Chain Length	124.11

*	Searching Example 3: Polymer Mixture	124.12

We recommend that you print this N-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote POLY/Sub search, click here.

124.1 Definition of a Remote POLY/Sub Search

A Polymer Substructure (POLY/Sub) search finds molecule records that contain your polymer query as a substructure wholly within another molecule:

In addition, you can combine text/numeric and graphical queries. For example, you can find structures that contain your query as a substructure and have a number-average molecular weight > 20000 (> 20000 number-average molecular weight).

You can also increase the power of a POLY/Sub search by the addition of specific restrictions (called query features) on atoms and bonds. In the following example, the ISIS bond query feature S/D finds both single and double bonds. In addition, the anypolymer (anyp) polymer brackets specify the retrieval of any polymer type (mon, SRU, co, and so forth) that contains the substructure:

124.2 Specifying Text/Numeric Queries

A text/numeric query is a phrase in a box or column on the form that specifies the retrieval of data. For example, to find structures with a number-average molecular weight greater than 20,000, enter the text/numeric string > 20000 into the Number-Average Molecular Weight box on the form.

Each phrase in a text/numeric query contains:

*	A search operator that specifies the type of search. For example, the search operators = (equal sign) and LIKE specify the retrieval of the exact match of your query. Use = when you want to retrieve data with numeric values. Use LIKE when you want to retrieve data with text.

*	A text or numeric target value that you want to find (such as 350 for the molecular weight or ANTIBIOTIC for the activity).

Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

124.2.1 Specifying Numeric Data in Queries

Do not include the units, such as a percent sign (%) or the degrees Centigrade (C). For example, to retrieve all compounds with a molecular weight greater than 350, enter:

> 350

where the search operator is > and the target value is 350.

124.2.2 Specifying Text/Numeric Data in Queries

Enclose queries that contain text (with or without numeric values) in double quotes and always use a wildcard, such as %. For example, to retrieve all compounds from the author Smythe, enter:

LIKE "%Smythe%"

where the search operator is LIKE and the target value is Smythe.

A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. The wildcard _ is a placeholder for solely one unspecified character. Without a wildcard, you retrieve solely those records that contain exactly the target value that you specified. For example:

Query Without a Wildcard	Example of a Record Retrieved

LIKE "antibiotic"	Antibiotic

Query With the Wildcard %	Examples of Records Retrieved

LIKE "%antibiotic%"	Antibiotic

Antibiotic activity

Resistance to extracellular products such as antibiotics

Note: If you want to retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

124.2.3 The Search Operators

<, <=, >, >=, and <>

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Search Operator	Definition	Examples

=	equal (numeric)	= 350

<	less than (numeric)	< 350

<=	less than or equal to (numeric)	= 350

>	greater than (numeric)	> 350

>=	greater than or equal to (numeric)	>= 350

<>	not equal to (text or numeric)	<> 350

<> "initiator"

To specify an exact formula query, specify the target value for the formula. The target value must include all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required. The equals operator (=) and quotes are optional. For example:

LIKE

Use LIKE with text enclosed in double quotation marks. Enter your query as follows:

Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. For example:

Query	Examples of Records Retrieved

LIKE "methane"	Methane

LIKE "benzoic acid"	Benzoic Acid

LIKE "%acid"	Benzoic Acid

Acetic Acid

LIKE "%acid%"	Benzoic Acid Sodium Salt

Acetic Acid Sodium Salt

LIKE "%but_ne"	Trans 2-Butene

2-Butene

N-Butane

Butane

Butene

LIKE "_ethyl"	Methyl

Ethyl

LIKE "antibiotic"	Antibiotic

LIKE "%antibiotic%"	Antibiotic activity

Resistance to extracellular products such as antibiotics

Note: To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice. To retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

BETWEEN

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks. For example:

BETWEEN "XR11" "XZ15"

BETWEEN 95 100

EXISTS

Use EXISTS to retrieve all records in the database that contain data in a specific database field. For example:

EXISTS

Note: You can only use the EXISTS search operator for certain types of database fields. Using EXISTS with other types of fields produces an error message.

124.2.4 Specifying a Molecular Formula as a Query

To search the data in Formula box (that is, a box that is connected to a MOLFORMULA field), you can specify the following text/numeric queries:

*	An exact formula. Use an exact formula query to find records that contain solely the exact atoms that you specify.

*	A subformula. Use a subformula query to find records that contain the specific atoms that you specify, and any additional atoms.

Exact Formula Query

To specify an exact formula query, specify the target value for the formula. The target value must include all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required. The equals operator (=) and quotes are optional. For example:

Exact Formula Query	Examples of Records Retrieved

c6 h6 O	Phenol

c6h6o

C20 H12 Na2 O4	Sodium salt of phenolphthalein

C20H12Na2O4

= C20 H12 Na2 O4

= C20H12Na2O4

= "C20 H12 Na2 O4"

= "C20H12Na2O4"

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Exact Formula Query	Examples of Records Retrieved

C17 H19 N 03	Piperine

C17H19N 03	Piperine

C17H19N103	Piperine

C17H19N03	No molecules retrieved. ISIS interprets "NO3" as 3 Nobelium atoms.

Subformula Query

To specify a subformula query, use the LIKE operator with a target value for the subformula. The target value can include a range of atom counts, and typically excludes the hydrogens. To exclude specific atoms from the molecules that you retrieve, specify zero for that atom. You can use a single space to separate atoms. Capital letters are not required. Quotes are optional.

Subformula Query	Examples of Records Retrieved

LIKE Na	All sodium salts

LIKE c12 Br(1-2) S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE "C12Br(1-2)S2"	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE c6 h6	All molecules that contain six carbon atoms, six hydrogen atoms, and any number of other atoms

LIKE C5 H10 N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

LIKE C5H10N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Subformula Query	Examples of Records Retrieved

LIKE C12 Br S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12Br1S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12BrS2	No molecules retrieved. ISIS interprets "BrS" as an atom symbol, and gives an error message.

124.3 Specifying Polymers in Graphical Queries

Polymer queries can be drawn as structure-based or source-based representations. The following example shows both representations of a simple homopolymer:

Your corporate database might contain structures that are drawn in the structure-based representation, the source-based representation, or both.

Note: Conventions for drawing structure-based and source-based representations of polymers are provided in the Request-A-Document Drawing Polymers: MDL Requirements for Database Searching and Registration.

Study the following sections to learn how to use the different types of polymer brackets to create structure-based and source-based queries.

124.3.1 Structural Repeating Unit (SRU) Brackets (n)

Use Structural Repeating Unit (SRU) brackets to enclose the structural repeating unit of the structure-based search query:

SRU brackets imply that the structure within the brackets can repeat with itself (...AAAAA... can occur). Consequently, you should enclose the structure "A" in SRU brackets solely if the sequence ...AAAAA... can occur.

Each set of SRU brackets has one or two bonds that cross each bracket, called crossing bonds. The crossing bonds of an SRU show where the repeating units connect to each other within the polymer (connectivity).

Polymers With Two Crossing Bonds

The polymer repeat pattern shows how the repeating units are joined together. In structures with two crossing bonds, the repeat pattern of an SRU with respect to the next SRU in sequence can be head-to-tail (the default), head-to-head (hh), or either/unknown (eu).

The following table shows examples of the three repeat patterns:

Note: Use the either/unknown repeat pattern when the repeat pattern is unknown, or when both the head-to-tail and head-to-head repeat patterns might be present. In the following example, poly(1-chloroethylene/2-chloroethylene) consists of units of chloroethylene that can be joined head-to-head (1-chloroethylene) or head-to-tail (2-chloroethylene):

In searching, a polymer with the either/unknown repeat pattern finds all other repeat patterns. Other polymer repeat patterns must match exactly. The following table summarizes the search characteristics of repeat patterns for polymers with two crossing bonds:

Ladder-Type Polymers

Polymers with two crossing bonds on each bracket of the SRU (ladder-type polymers) can have a repeat pattern of head-to-tail, head-to-head, or either/unknown. For the head-to tail and head-to-head repeat patterns, you must also specify how the two crossing bonds on each bracket connect to the corresponding bonds of the adjacent SRU:

*	The head-to-tail repeat pattern has the following two options for connecting the bonds in adjacent SRUs:

*	The head-to-head repeat pattern has the following two options for connecting the bonds in adjacent SRUs:

*	If the repeat pattern is either/unknown, the connections between corresponding bonds might be unknown, or the polymer might contain a mixture of units that are joined head-to-head and other units that are joined head-to-tail (either).

The following table shows examples of the five repeat patterns that are possible for polymers with two crossing bonds on each bracket:

In searching, a polymer with the either/unknown repeat pattern finds all other repeat patterns. Other polymer repeat patterns must match exactly. The following table summarizes the search characteristics of repeat patterns for ladder-type polymers:

For the either/unknown repeat pattern, a structure that contains two brackets with four crossing bonds is equivalent to a structure that contains four brackets with one crossing bond on each bracket. For example, the following structures represent the same polymer:

Polymers With Three or More Brackets

Polymers with 3 or more brackets always have the either/unknown (eu) repeat pattern. The following are additional representations of polymer structures:

Cyclization and "Phase Shifting"

For SRUs that contain a pair of brackets and that have the head-to-tail repeat pattern, you can define the structural repeating unit anywhere along the polymer backbone (that is, you can "phase-shift" the brackets along the polymer backbone). For example:

You can visualize the connectivity between SRUs as a cyclization of the crossing bonds:

The head-to-tail repeat pattern (the default) shows cyclization and "phase-shifting". For example:

The head-to-head repeat pattern does not show cyclization or "phase shifting." For example:

The either/unknown repeat pattern finds structures that have the following:

*	Identical SRUs and any repeat pattern (head-to-tail, head-to-head, or either/unknown):

*	"Phase-shifted" SRUs with the head-to-tail repeat pattern:

124.3.2 Monomer Brackets (mon) and Mer Brackets (mer)

Use Monomer (mon) brackets to draw the repeating unit(s) for the source-based representation of a homopolymer:

Enclose a monomer within monomer brackets solely if the monomer molecule is homopolymerizable.

124.3.3 Copolymer Brackets (co)

If a structure contains more than one set of SRU and/or monomer brackets, enclose the entire structure within copolymer brackets. Copolymer brackets can have crossing bonds, cyclization, and phase-shifting. The following figure shows cyclization of a structure-based copolymer query:

If the sequence of the repeating units is known (for example, a block copolymer that consists of regular blocks), draw the structure-based representation with connecting bonds between the SRUs. If the sequence repeats, draw the structure so that bonds cross the copolymer brackets:

However, if the sequence of the repeating units is unknown or unspecified (for example, an irregular block copolymer, or a random copolymer), draw the structure-based representation with no connecting bonds between the SRUs:

In searching, copolymers in which the sequence of SRUs is unspecified match structures in which the sequence is specified. The following table summarizes the search characteristics of copolymer structures that contain SRUs:

Note: Always use copolymer brackets when the structure requires more than one set of polymer brackets (monomer or SRU) to represent the structure. For example, polymers that are chemically modified after polymerization are represented as copolymers. For examples of structures that use copolymer brackets, see the Request-A-Document Drawing Polymers: MDL Requirements for Database Searching and Registration.

124.3.4 Mer Brackets (mer)

For source-based polymers only, use Mer brackets (mer) to enclose a monomer that can not repeat with itself. For example, the diol and diacid monomers of the following polyester do not homopolymerize to form polyperoxides and polyanhydrides:

124.3.5 Additional Polymer Bracket Types

The additional polymer and copolymer bracket types are as follows:

*	Copolymer bracket types: alternating (alt), block (blk), and random (ran)

*	Polymer bracket types: cross-link (xl), modified (mod), and graft (grf)

*	Mer brackets (mer) can be used to enclose a structural unit that does not repeat with itself, such as a junction unit within a block copolymer

The following are the search characteristics of the additional polymer types:

*	Polymer and copolymer types must match the query exactly. For example:

*	Unspecified copolymer brackets (co) match any type of copolymer (co, blk, ran, alt).

124.3.6 Anypolymer Brackets (anyp)

Use Anypolymer (anyp) brackets when you want your search query to find any polymer that contains your query embedded within it. For example, you might use atom and bond query features to create a generic polymer query that finds both the structure-based and source-based representations of an addition polymer:

In this example, the bond query feature S/D finds both single and double bonds. The anyp brackets allow ISIS to retrieve structures with either monomer (mon) or SRU (n) brackets.

For more information on atom and bond query features, see Section 124.5

124.3.7 Abbreviated Structures and Multiple Groups

For complex polymers, you might want to abbreviate parts of the structure. An abbreviated structure is all or part of a molecule that has been abbreviated to a text label. Structures that you abbreviate keep their chemical significance, but the underlying structure is hidden. In this example, the phenyl ring in polystyrene is abbreviated to the text string Ph:

A POLY/Sub search finds the underlying chemistry and ignores the name. For example:

For more information on abbreviated structures, click here. Alternatively, choose Help > Index, and search for abbreviated structures, definition of.

You can also use multiple groups to abbreviate structures. A multiple group is a pair of brackets that represents a fixed number of replications of the structure within the brackets. For example:

A POLY/Sub search finds the underlying chemistry of a multiple group. For example:

For step-by-step instructions on creating multiple groups, click here. Alternatively, choose Help > Index, and search for multiple groups, drawing.

124.4 Specifying Mixtures in Graphical Queries

You can define both ordered and unordered mixtures in search queries:

*	If the order of addition of components is not important, specify an unordered mixture (mix). Unordered mixtures contain components (c) that are not numbered:

*	If the order of addition of components of the formulation is important, use an ordered mixture (f). Ordered mixtures contain components that are numbered (c1, c2, c3, and so forth):

A query that contains ordered components finds structures that contain ordered components with the same relative (not necessarily sequential) order. For example:

To find both unordered and ordered mixtures that contain specified components, use an unordered component without brackets. For example:

For an example of a polymer mixture as a search query, see Section 124.11.

124.5 Specifying Attached Data in Graphical Queries

Attached data is chemically-significant text that you can associate with an atom, a bond, a set of atoms and bonds, or with a bracket. Attached data differs from chemically-insignificant text (plain text). Attached data can be exported to a molfile, stored in a molecule database, and/or used in a graphical search query in a remote molecule database.

For example, the following structure of a statistical copolymer contains attached data on the type of copolymer (stat), the number-average molecular weight of the copolymer (20,000 Mn), and on the mass percentage of each type of repeating unit (75 mass %, 25 mass %):

124.5.1 Substance Group (Sgroup) Database Fields

Each piece of attached data is associated with a special kind of database field, called a Substance Group (Sgroup) field. The Sgroup field defines what the data means. The following table shows the associated Sgroup field and the meaning of each piece of attached data in the polymer structure in the previous example:

Caution: Your ISIS Administrator defines the Sgroup fields that you can use to specify attached data. When you draw a structure for registration or searching, you must specify the correct Sgroup fields for the data that you attach to the structure. If you do not specify the correct Sgroup fields, you might not be able to retrieve the structures that you want. For more information on the Sgroup fields that are available at your site, see your ISIS Administrator.

124.5.2 Specifying Attached Data in a Query

You can specify a text/numeric query (search operator with conditions) for attached data, a target value (specific data) of attached data, or no attached data. The following sections show the search results that you obtain for each type of query.

Text/Numeric Query (Search Operator and Target Value)

A query that contains a text/numeric query retrieves structures in which the attached data meets the conditions that are specified by the text/numeric query. A text/numeric query contains a search operator (such as <) and a text or numeric target value (such as 25% mole fraction) that you want to find. For example, to find copolymers that contain less than 25% polystyrene, attach the text/numeric query < 25 to the monomer brackets of polystyrene:

For an example of a text/numeric query in attached data, see Section 99.11.

Target Value (Specific Data)

A query that contains a target value (specific data) retrieves structures in which the attached data matches exactly. For example:

No Attached Data

A query that contains no attached data retrieves structures that contain any attached data. For example:

For more information on search operators for text/numeric queries, see Section 99.4.3.

124.5.3 Search Operators for Text/Numeric Queries in Attached Data

Text/numeric queries generally use the same search operators and syntax as text/numeric queries that you enter on a form.

*	The EXISTS operator is not available.

*	An additional operator for text data, CONTAINS, is available.

CONTAINS

Use CONTAINS with text. You retrieve all values that contain the text string that you specify embedded within them. For example:

Query	Examples of Records Retrieved

CONTAINS tactic	Isotactic

Syndiotactic

Tacticity

Note: The CONTAINS operator is a special case of the LIKE operator. For example, the query like "%tactic%" is equivalent to the query contains tactic. ISIS automatically supplies the quotes and wildcard for the target value of the CONTAINS operator.

124.6 Specifying Atom and Bond Query Features

A query feature on an atom and/or a bond in a molecule is a restriction that specifies the retrieval of certain types of molecule records from an ISIS/Base database.

If you do not use query features, the molecules retrieved contain solely your exact substructure query embedded wholly within them. For example:

You can also define Rgroups that specify a root structure with defined Rgroup substituents attached to it at specific positions. For more information on Rgroups, see Section 99.6.

124.6.1 Definition of Aromaticity

For remote databases: ISIS interprets the following ring systems as aromatic:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:

Note: The bonds of six-membered aromatic ring systems and the perimeter bonds of azulenes are stored as aromatic bonds in the database. The bonds of five-membered aromatic rings, however, are stored as single and double bonds and interpreted as aromatic during a search. The differences between five-membered rings and other types of aromatic rings can cause different search results for five- and six-membered rings/azulenes when you use the following bonds in queries: Single, Double, and Single/Double query bonds. For more information on the Single/Double query bond, see Section 124.6.8.

124.6.2 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except implicit or explicit hydrogens:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

124.6.3 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of implicit hydrogens. For example:

124.6.4 Allowing an Unsaturated Atom

Use an atom query feature to specify that an atom is unsaturated, or attached to at least one multiple bond: double, triple, or aromatic.

Atom Query Feature: Unsaturated Atom (u)

Specifies that the atom of your choice is unsaturated. For example, the following query specifies both an unsaturated atom and single or double bonds (the double dashed lines).

124.6.5 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

Use explicit hydrogens to block non-hydrogen attachments on atoms. For example:

Atom Query Feature: Substitution Count of Zero, s0

Specifies that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of an isolated atom.

Atom Query Feature: Substitution Count of One, s1

Specifies that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Two, s2

Specifies that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Three, s3

Specifies that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Four, s4

Specifies that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Five, s5

Specifies that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of at Least Six, s6

Specifies that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count as Drawn, s*

Specifies that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:

124.6.6 Allowing a Specific Number of Ring Bond Attachments

Use atom query features to specify the number of ring bond attachments.

Atom Query Feature: Ring Bond Count of Zero, r0

Specifies that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:

Atom Query Feature: Ring Bond Count of Two, r2

Specifies that the records retrieved have solely two ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of Three, r3

Specifies that the records retrieved have solely three ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of at Least Four, r4

Specifies that the records retrieved have at least four ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count as Drawn, r*

Specifies that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:

124.6.7 Allowing Additional Atoms and/or Bonds in a Chain or a Ring

Use a query feature that is for either atoms or bonds to specify the addition of atoms and/or bonds in a chain or a ring.

Atom or Bond Query Feature: Link Node

Use a link node to specify the addition of variable numbers repeating units (atoms and/or bonds) to a ring or chain. A repeating unit must be attached to two adjacent bonds. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the link node [L1-3]:

Or, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the link node [L1-3]:

124.6.8 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Note: An aromatic query bond hits any bond in all types of aromatic rings: 6-membered ring bonds, 5-membered ring bonds, and azulene perimeter bonds. For more information on the structures that ISIS interprets as aromatic, see Section 124.6.1.

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

Note: A Single/Double query bond does not hit bonds in 6-membered aromatic rings, or perimeter bonds of azulenes, because bonds in these structures are stored in the database as aromatic bonds. However, a Single/Double query bond does hit bonds in 5-membered rings that ISIS interprets as aromatic. For more information on the structures that ISIS interprets as aromatic, see Section 124.6.1.

Bond Query Feature: Single/Aromatic Bond

Specifies either a single or an aromatic bond at that position:

Bond Query Feature: Double/Aromatic Bond

Specifies either a double or an aromatic bond at that position:

124.6.9 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is attached to a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

124.6.10 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is attached to a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

124.7 Specifying Rgroup Query Features

An Rgroup query finds structures that contain your query as a root structure with defined Rgroup substituents attached to it at specific positions. Your query can contain restrictions on the Rgroup substituents, called Rgroup conditions: You can specify the number of Rgroup sites that must be occupied in the records retrieved, specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site, or specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

Your Rgroup query can also contain restrictions on atoms and bonds of the root structure and Rgroup substituents. For example, you can use the atom query feature H(0) to prohibit the attachment of implicit hydrogens on a specific atom in the structures retrieved.

An example of an Rgroup query is as follows:

124.7.1 The Root Structure

The root structure contains the portion of the structure that does not vary among the structures retrieved. For example, if you want to find 2, 5-Dihydroxypyridine in which the substituent at position 2 can be COOH, CN, or Ph, and the substituent at position 5 can be OH or CH3, the root structure is 2, 5-Dihydroxypyridine with Rgroups (such as R1 and R2):

Rgroups

On the root structure, Rgroups (R1 through R32) are placeholders that designate where the lists of functional groups and atoms that can attach to the root structure. In the example above, the Rgroup R1 designates that the members of the list R1 (the Rgroup substituents) are allowed at position 5 on the root structure. The Rgroup R2 designates that the members of the list R2 (the Rgroup substituents) are allowed at position 2 on the root structure.

Multiple Rgroups at One Position

You can specify multiple Rgroups at a single site on the root structure. For example:

One Rgroup at Multiple Positions

You can specify a single Rgroup (such as R1) at multiple positions on the root structure. For example:

Note: See the section 124.6.3 Rgroup Conditions to restrict the number of Rgroups that must be occupied in the records retrieved. A molecule might not have to satisfy all the Rgroup sites on the root structure to be retrieved. For example, the Rgroup condition R1 > 0 specifies that any molecule in which at least one of the R1 sites is filled by an R1 member will be retrieved. In addition, the Rgroup condition RestH determines whether the unsatisfied sites must be filled with hydrogen atoms or if other molecule fragments are allowed to be attached if they are not on the list.

124.7.2 Rgroup Substituents

Rgroup substituents are the members of the list of Rgroups. You define the Rgroup substituents that you will allow to be found at specified positions in the molecules retrieved. Rgroup substituents can be any structural fragment, including functional groups and single atoms.

In the example below, the Rgroup substituents COOH, CN, or Ph are allowed at position 5 (R1) on the root structure and the Rgroup substituents OH or CH3 are allowed at position 2 (R2) on the root structure:

Attachment Points

An attachment point (marked with an arrow and an asterisk) designates the atom on the Rgroup substituent that is attached to the root structure:

You must designate an attachment point on an Rgroup substituent for each bond that is attached to the substituent. If an Rgroup is attached to two bonds on the root structure, you must designate two attachment points. The bond on the root structure that is marked with double quotes corresponds to the attachment point on the Rgroup substituent that is marked with double quotes. The other attachment point on the Rgroup substituent is marked with a single quote:

Nested Rgroups

A nested Rgroup is an Rgroup that is a placeholder within another Rgroup rather than within the root structure. (You cannot nest an Rgroup any lower than this level.) In the following example, Rgroup R2 is nested within the Rgroup R1:

Nested Rgroups are equivalent to the following structures:

124.7.3 Rgroup Conditions

You can apply restrictions to each Rgroup in your query after you assemble all the Rgroups. The set of restrictions is called the Rgroup conditions.

If you do not apply Rgroup conditions, ISIS assigns the default conditions: Occurrence > 0 and RestH off for each Rgroup.

Occurrence

With the Rgroup condition Occurrence, you can specify the number of Rgroup sites that must be occupied in the records retrieved. For example, the occurrence designation R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved. Type one of the following values in the Occurrence range text box:

Value	Explanation

0	All members of the Rgroup are excluded from the Rgroup site (such as R1). To allow any other Rgroup substituent at the Rgroup site, set RestH to off.

> 0	At least one Rgroup must be satisfied. If RestH is off, any other substituent can attach to unsatisfied sites. If RestH is on, unsatisfied sites must be filled solely by hydrogens.

n	Exactly n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

< n	Less than n number of sites (including zero) must be satisfied. RestH controls substitution at unsatisfied sites.

m - n	Any number of sites falling within the range of m to n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

m,n,...	Any combination of the above expressions, separated by commas. For example: 1, 3-5, 9, >12.

For example, the Rgroup condition R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved.

In another example, the Rgroup condition R1 > 0 and R2 > 0 specifies that an Rgroup substituent from the R1 list AND an Rgroup substituent from the R2 list must occupy at least one site on the root structure in the records retrieved.

Finally, the Rgroup conditions R1 = 1, 3-5, 9, >12 specify that either 1, 3, 4, 5, 9, or more than 12 sites must be satisfied:

RestH

With the Rgroup condition RestH, you can specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site.

An unsatisfied Rgroup site is an Rgroup site on the root structure that does not have an Rgroup member attached: If RestH is off, any functional group or atom may be attached at unsatisfied Rgroup sites on the root structure. If RestH is on, solely hydrogens are allowed to be attached at unsatisfied Rgroup sites on the root structure.

If/Then

With the Rgroup condition If/then, you can specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

For example, If R1 then R2 specifies that if the conditions for R1 are satisfied, then the conditions for R2 must also be satisfied. (If the conditions for R1 are not satisfied, then the conditions for R2 are ignored.) The If/then condition implies that a molecule may be retrieved even though R1 is not satisfied.

In the following query, R1 contains a nitro group and a sulfonic acid group. R2 contains a chlorine atom. The condition If R1 then R2 specifies that if a nitro group or a sulfonic acid group is attached at R1 on the root structure, then a chlorine must also be attached at R2. However, if the R1 site on the root structure does not have either the nitro or the sulfonic acid group (R1 is unsatisfied), then R2 can have any substituent (R2 is ignored):

124.8 Specifying Stereochemistry in Graphical Queries

You can specify the following types of stereochemistry:

*	Stereoregularity in polymers.

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond). Use this for non-polymer components of your query.

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

124.8.1 Stereoregularity in Polymers

Polymer structures that are stored in a database do not use Up and Down stereo bonds to show stereoregularity, because these bonds can cause inaccurate search results in certain types of searches, such as POLY/Both and POLY/Co. Instead, polymer structures use attached data to show stereoregularity. In the following example, attached data (associated with the Sgroup field STEREO) shows tacticity in polystyrene:

Use attached data on your query to retrieve the structures of your choice. For example:

To retrieve all structures, regardless of stereoregularity, use a query without attached data:

For more information on attached data, see Section 124.5.

124.8.2 Geometric Stereochemistry

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve molecules with matching cis or trans stereochemistry. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

A POLY/Sub search produces the following results:

A Double Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain cis and trans isomers at the specified position.

124.8.3 Tetrahedral Stereochemistry in Non-Polymer Structures

If you want to retrieve structures that contain non-polymer components that are optical stereoisomers, use Up and Down bonds with chiral flags to show stereochemistry.

Up and Down Bonds

In non-polymer structures, you can use Up and Down stereo bonds to show stereochemistry. An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

A POLY/Sub search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Chiral Flags on Molecules

If your structure contains Up and Down stereo bonds, you can create a query with a chiral flag on a molecule with at least one asymmetric center. The chiral flag ensures that you retrieve solely the absolute stereoconfiguration, and eliminates the relative. stereoconfigurations. (In a local database, the chiral flag is ignored.) For example:

124.9 Guidelines for Revising the Query

If your POLY/Sub search retrieved no records or too few records, you might want to:

*	Conduct an POLY/Sub search on a different set of records with the same query.

*	Verify that your search domain is set to the entire database.

*	Verify that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, remove substituent limits, remove stereochemical requirements, or specify anypolymer (anyp) for all polymer brackets.

*	Remove the attached data from your query, and then search the same set of records. For example, if your query contains the attached data value 0.7 attached to polymer brackets, you can delete the attached data.

*	Make the Rgroup conditions in your query more general, and then search the same set of records. For example, you can decrease the number of Rgroup sites that must be satisfied or allow unsatisfied Rgroup sites to be filled with non-Rgroup substituents (instead of with hydrogens solely).

If your POLY/Sub search retrieved too many records, you might want to:

*	Refine your query by specifying atom and bond query features that limit the types of structures that you retrieve, and then search the same set of records. For example, you can limit substitution at specific positions, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Refine your query by adding restrictions to the attached data in the structures that you retrieve. For example, if your query contains no attached data, you can attach a target value or a text/numeric query (such as < 90) to your query structure.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	Make the Rgroup conditions in your query more specific, and then search the same set of records. For example, you can increase the number of Rgroup sites that must be satisfied or restrict unsatisfied Rgroup sites to be filled solely with hydrogens.

*	If you are interested in additional properties of the polymers that you want to find, add a text/numeric query to a box on your form (for example, number-average molecular weight > 30000).

124.10 Searching Example 1: Allowing Specific Bond Types

To retrieve a general class of compounds, draw a substructure query that contains the minimum structural features that define the class of compounds. If you draw too many specific features, you might unintentionally eliminate some molecules.

124.10.1 Problem

You want to retrieve all polymers that contain 1-methyl-4-vinylpyridinium.

124.10.2 Approach

Conduct an POLY/Sub search with a query that consists of:

*	1-methyl-4-vinylpryidinium within anypolymer (anyp) brackets

*	A single/double query bond in the vinyl group. This allows your query to match the bonds in both structure-based (SRU) and source-based (mon) polymer representations.

124.10.3 Query

The anyp polymer bracket specifies any polymer type.

The bond query feature S/D specifies a single or double bond.

124.10.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for POLY/Sub, how to/examples.

124.10.5 Results

The search retrieves the following structures:

*	The source-based and structure-based representations of poly(1-methyl-4-vinylpyridinium chloride):

*	An N-methylated modification of poly(4-vinyl-pyridine):

*	Three block copolymers of 4-vinylpryidine and 1-methyl-4-pyridinium chloride with varying information on how the repeating units are linked together (connectivity):

*	A random copolymer of 4-vinylpyridine and 1-methyl-4-pyridinium chloride:

124.11 Searching Example 2: Variable Chain Length

To retrieve a general class of compounds, draw a substructure query that contains the minimum structural features that define the class of compounds. If you draw too many specific features, you might unintentionally eliminate some molecules.

124.11.1 Problem

You want to retrieve all polyamides that contain alkylamines.

124.11.2 Approach

Conduct an POLY/Sub search using a polymer query that contains:

*	An amide, N-substituted with a link node [L1-9] that specifies 1 to 9 units. (The link atom must be long enough to find any alkylamine substructures that are likely to be in the database.)

*	A Ring bond count of zero (r0) on the amide nitrogen. The r0 excludes cyclic amides.

*	Anypolymer brackets (anyp)

124.11.3 Query

The ring atom query feature r0 excludes cyclic alkylamines.

The atom and/or bond query feature link node [L1-9] allows alkylamine chains of from 2 to 10 carbons.

The polymer repeat pattern head-to-tail allows the repeating unit to be defined anywhere along the polymer backbone ("phase-shifting" the repeating unit).

124.11.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for SSS, how to/examples.

124.11.5 Results

Molecules Retrieved

Some of the molecules that might be retrieved from the remote molecule database of your choice are as follows:

*	Three versions of Nylon 3 (poly(3-aminopropionic acid)):

These three structures represent the same polymer, but the repeating unit is defined at different points along the backbone of the polymer. These structures were retrieved because the query has a polymer repeat pattern of head-to-tail.

*	Other polyamides of varying chain length, such as poly(caprolactam):

Molecules Not Retrieved

The following structures are not retrieved:

*	The ring atom query feature r0 excludes cyclic alkylamines, such as this lactam version of Nylon 3:

*	The head-to-tail repeat pattern on the query excludes the following structure, because polymers with the either/unknown (eu) repeat pattern are not checked for phase-shifting:

124.12 Searching Example 3: Polymer Mixture

To retrieve a general class of compounds, draw a substructure query that contains the minimum structural features that define the class of compounds. If you draw too many specific features, you might unintentionally eliminate some molecules.

124.10.11 Problem

Find all polymer mixtures that contain up to 20% poly(ethylene oxide).

124.12.2 Approach

Perform an POLY/Sub search using a query that consists of the following:

*	Poly(ethylene oxide) as a component in an unordered mixture.

*	Attached data that specifies a poly(ethylene oxide) concentration range of 0-20%.

124.12.3 Query

The unordered mixture (mix) contains a single component, poly(ethylene oxide). The mixtures that you retrieve can contain additional components.

The attached data (between 0 20) specifies the concentration range.

124.12.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for POLY/Sub, how to/examples.

124.12.5 Results

Some of the molecules that might be retrieved from the remote molecule database of your choice are as follows:


Remote QB in a Molecule Database: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote QB Search in a Molecule Database	49.1

*	Specifying a QB Query	49.2

*	Specifying Flexmatch Parameters	49.3

*	Definition of Aromaticity	49.4

*	Specifying Query Features on Atoms and Bonds in Structures	49.5

*	Specifying Rgroup Query Features	49.6

*	Specifying Stereochemistry	49.7

*	Guidelines for Revising the Query	49.8

*	Searching Example 1: Combining Text/Numeric Queries	49.9

*	Searching Example 2: Combining Text/Numeric and Graphical Queries	49.10

We recommend that you print this 37-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote QB search in a molecule database, click here.

49.1 Definition of a Remote QB Search in a Molecule Database

You can use the remote Query Builder (QB) search to create any of the other remote searches in ISIS. However, you must use an all-text search query. Thus, we recommend that you use another type of search where possible!

A QB search does have one unique feature: You can combine AND, OR and NOT boolean operators in a search query. For example:

To find all molecules that contain benzaldehyde AND all molecules with a melting point greater than 220 degrees, enter:

To find all molecules that contain both indole and a molecular weight greater than 200 but NOT those molecules with a melting point below 190, enter:

To find all molecules that do NOT contain benzaldehyde embedded wholly within them, enter:

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

49.2 Specifying a QB Query

Each QB query contains:

*	The database field that you want to search.

For example, to search the melting point field, enter either the full path name, MOL>MELTING.POINT>MELTING.POINT, or the minimum tree name that uniquely identifies the field, namely MELTING.POINT. To search the structure field, enter either the full path name MOL>MOLSTRUCTURE, or the minimum tree name that uniquely identifies the field, namely MOLSTRUCTURE.

*	A search operator that specifies the type of search (such as a greater than sign, >, to specify a search that finds solely the target text in the query).

*	The text or numeric target value (specific data) that you want to find. (In addition, your target value can be a file name that corresponds to a structure that you want to retrieve.)

A text or numeric target value can contain wildcards. A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. For example, you can specify the query LIKE "%ALD%" (instead of the query LIKE "BENZALDEHYDE"). The wildcard _ is a placeholder for solely one unspecified character. For example, you can specify the query LIKE "_CHLOROBENZENE" (instead of the query LIKE "2-CHLOROBENZENE"). Target values that contain text or wildcards require double quotation marks.

Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

For example, to find records that contain structures with a melting point that is greater than 220, enter:

MOL>MELTING.POINT>MELTING.POINT > 220

Note 1: You can combine statements in a single text/numeric string with one of the logical operators AND, OR, and NOT. When you use the NOT operator, enclose the text/numeric string in parentheses. For example, enter:

NOT (MOL>MELTING.POINT>MELTING.POINT > 220)

49.2.1 The Search Operators

<, <=, >, >=, and <>

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Search Operator	Definition	Examples

=	equal (numeric)	MOLECULAR.WEIGHT = 350

<	less than (numeric)	MOLECULAR.WEIGHT < 350

<=	less than or equal to (numeric)	MOLECULAR.WEIGHT <= 350

>	greater than (numeric)	MOLECULAR.WEIGHT > 350

>=	greater than or equal to (numeric)	MOLECULAR.WEIGHT >= 350

<>	not equal to (text or numeric)	MOLECULAR.WEIGHT <> 350

ACTIVITY <> "inhibitor"

For a MOLFORMULA field, an exact formula query retrieves records that contain solely the exact atoms that you specify. To create an exact formula query, specify the target value for the formula. The target value must include all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required. The equals operator (=) and quotes are optional. For example:

Exact Formula Query	Examples of Records Retrieved

c6 h6 O	Phenol

c6h6o

C20 H12 Na2 O4	Sodium salt of phenolphthalein

C20H12Na2O4

= C20 H12 Na2 O4

= C20H12Na2O4

= "C20 H12 Na2 O4"

= "C20H12Na2O4"

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Exact Formula Query	Examples of Records Retrieved

C17 H19 N 03	Piperine

C17H19N 03	Piperine

C17H19N103	Piperine

C17H19N03	No molecules retrieved. ISIS interprets "NO3" as 3 Nobelium atoms.

LIKE

Use LIKE with text enclosed in double quotation marks. Enter your query as follows:

Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. For example:

Query	Examples of Records Retrieved

COMPOUND.NAME LIKE "methane"	Methane

COMPOUND.NAME LIKE "benzoic acid"	Benzoic Acid

COMPOUND.NAME LIKE "%acid"	Benzoic Acid

Acetic Acid

COMPOUND.NAME LIKE "%acid%"	Benzoic Acid Sodium Salt

Acetic Acid Sodium Salt

COMPOUND.NAME LIKE "%but_ne"	Trans 2-Butene

2-Butene

N-Butane

Butane

Butene

COMPOUND.NAME LIKE "_ethyl"	Methyl

Ethyl

ACTIVITY LIKE "antibiotic"	Antibiotic

ACTIVITY LIKE "%antibiotic%"	Antibiotic activity

Resistance to antibiotics

Note: To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice. To retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: ACTIVITY LIKE "aa""a" or ACTIVITY LIKE"%aa""a%".

For a MOLFORMULA field, a subformula query retrieves records that contain the specific atoms that you specify, and any additional atoms. To create a subformula query, use the LIKE operator with a target value. The target value can include a range of atom counts, and typically excludes the hydrogens. To exclude specific atoms from the molecules that you retrieve, specify zero for that atom. You can use a single space to separate atoms. Capital letters are not required. Quotes are optional.

Subformula Query	Examples of Records Retrieved

LIKE Na	All sodium salts

LIKE c12 Br(1-2) S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE "C12Br(1-2)S2"	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE c6 h6	All molecules that contain six carbon atoms, six hydrogen atoms, and any number of other atoms

LIKE C5 H10 N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

LIKE C5H10N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Subformula Query	Examples of Records Retrieved

LIKE C12 Br S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12Br1S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12BrS2	No molecules retrieved. ISIS interprets "BrS" as an atom symbol, and gives an error message.

BETWEEN

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks. For example:

CORPORATE.ID BETWEEN "XR11" "XZ15"

CORPORATE.ID BETWEEN 95 100

EXISTS

Use EXISTS to retrieve all records in the database that contain data in a specific database field. For example:

MOL>MOLSTRUCTURE EXISTS

To retrieve all records in the database that contain no data in a specific database field, use NOT in your query:

NOT (MOL>MOLSTRUCTURE EXISTS)

Note: You can only use the EXISTS search operator for certain types of database fields. Using EXISTS with other types of fields produces an error message.

=

Use = to retrieve database structures that contain a SEMA match to your graphical query. For example (query is the file name of your graphical query):

MOL>MOLSTRUCTURE = query

Note1: The SEMA name is an encoded identifier that uniquely defines a molecule with respect to its atoms, their connectivity, stereochemistry, charge, and isotopic properties. The SEMA name does not contain information on attached data, polymers, or mixtures. These features are ignored when you search by SEMA name. If you want to match attached data, polymers, and mixtures, use the FLEXMATCH operator.

Note2: For information on attached data, polymers, and mixtures, see Drawing Polymers: MDL Requirements for Database Searching and Registration. For information on attached data and mixtures in non-polymer structures, see Drawing Mixtures: MDL Requirements for Database Searching and Registration.

ISOMER

Use ISOMER to retrieve 2D structures that contain a SEMA match of your graphical query and its geometric isomers and/or optical stereoisomer. For example (query is the file name of your graphical query):

MOL>MOLSTRUCTURE ISOMER query

TAUTOMER

Use TAUTOMER to retrieve 2D structures that contain a SEMA match of your graphical query and its tautomers. For example:

MOL>MOLSTRUCTURE TAUTOMER query

PARENT

Use PARENT to retrieve 2D structures that are the parent molecules of an exact SEMA match of your salt query. For example (query is the file name of your graphical query):

MOL>MOLSTRUCTURE PARENT query

SSS

Use SSS to retrieve database structures that contain your graphical query as a substructure embedded wholly within them. For example (query is the file name of your graphical query):

MOL>MOLSTRUCTURE SSS query

FLEXMATCH

Use FLEXMATCH to find 2D structures that are an exact match of your query, except in the ways that you specify with any of the flexmatch parameters. You specify features of retrieved structures that must match your query. This allows you to find structures that:

*	Contain features such as chemically-significant text (attached data) and chemically-significant brackets (for example, polymers and mixtures)

*	Have different counterions than the salt in your query.

*	Match your query, but have different isotopic labels.

*	Match your query, but might be represented differently in the database. For example, the pi-metal bonds in ferrocene can be represented in different ways:

For example, to specify the loosest possible definition of exact match, you specify the FLEXMATCH operator without flexmatch parameters:

MOL>MOLSTRUCTURE FLEXMATCH steroid ""

To specify that all bond types must match (BON, in single or double quotes) for a graphical query that you named steroid, enter:

MOL>MOLSTRUCTURE FLEXMATCH steroid "BON"

To specify that all bond types must match (BON) and that all metal bonds must match (MET), enter:

MOL>MOLSTRUCTURE FLEXMATCH steroid "BON/MET"

When you specify multiple flexmatch parameters, separate them with a forward slash, /. In addition, enclose all flexmatch parameters within the same set in single or double quotes. For more information and examples of flexmatch parameters, see Section 49.1.3.

MSIMILAR

Use MSIMILAR to retrieve 2D structures that are structurally similar to your graphical query. With this search operator, you can define the degree of similarity in your query to be an arbitrary value between 0 and 100 (these are not actual units). The higher the value, the more similarity. For example, to specify a structural similarity value of 10 (in single or double quotes) for a 2D graphical query that you named steroid, enter:

MOL>MOLSTRUCTURE MSIMILAR steroid '10'

You can also specify that the retrieved records contain the same structural complexity as your query (enter NORMAL), more structural complexity than your query (enter SUB), or less structural complexity than your query (enter SUPER). For example, to specify that the retrieved records contain more structural complexity than your query, enter:

MOL>MOLSTRUCTURE MSIMILAR steroid 'SUB 10'

49.2.2 Specifying a Structure in a QB Query

To include a graphical (structural) component in your QB query, you must enter the following in the Query Builder text box in the order shown:

*	The name of the database field that will hold your graphical search results. For a molecule record, enter MOL>MOLSTRUCTURE.

*	The search operator. For example, enter SSS to specify that the structures retrieved contain your graphical query embedded wholly within them. OR, enter the equal sign (=) to specify that the structures retrieved contain your graphical query exactly as drawn.

*	The file name (not the structure) of the structure. For example, enter the file name BENZALD for the 2D structure (the two-dimensional representation of a molecule) of Benzaldehyde:

Or, enter the file name BENZFRAG for any of these 2D substructures (any portion of a 2D structure) of Benzaldehyde:

Entering the File Name of a Structure

You can enter the file name of the structure in several ways:

*	To enter a structure that is on the form in ISIS/Base, double-click Query (or Mquery, if present) in the Structures box.

*	To enter a structure that was saved in the database, double-click the name of the structure in the Structures box.

*	To enter a structure that was saved as a molfile, click Read Structure, enter the name of the structure in the Files text box, click OK, and then double-click the name of the structure in the Structures box. (A molfile is a file in CTfile (chemical table files) format that contains either a single molecular structure or disjointed structural fragments.)

You see the structure in the box at the bottom-right corner of the Query Builder.

49.2.3 Searching Top-Level and Lower Level Records

When you combine two or more queries of any type into a single QB search, the search results that you obtain depend on both the specifications and accuracy of your query and the way that information is stored in your database.

Information in a database is stored either in a single level (called a flat database) or in multiple levels (called a hierarchical database). Storage in a hierarchical database is more efficient, but it requires you to enter your queries in the correct location on the form to obtain the search results that you want. For example, the following hierarchical database stores data for multiple decomposition tests that are conducted under different atmospheric conditions:

In this database, structures are stored at the top (or root) level, and the percentage of oxygen and the number of peaks are stored at a lower level, under the parent field Decomposition. A parent field is a branch in the hierarchy that contains a set of child fields, such as percent O2 and number of peaks.

You want specific decomposition data from different tests. Your multiple query in a single QB search specifies that you want all compounds within a single test that contain: Query 1, greater than 65% O2; Query 2, less than three peaks. To obtain search results that match either one query or the other (Query 1 OR Query 2), enter:

ROOT>DECOMPOSITION>Percent_O2 > 65 OR ROOT>DECOMPOSITION > Peaks < 3

This search gives you all compounds within a single test that meet either requirement in your query (but not necessarily both requirements). To obtain search results that match all queries (Query 1 AND Query 2), specify the hierarchy level that you want to search at the beginning of the search syntax. Then enclose the remainder of the query in double parentheses (If you do not specify a hierarchy level that you want to search, ISIS searches the top-level records in the database.):

ROOT>DECOMPOSITION ((ROOT>DECOMPOSITION>Percent_O2 > 65 AND ROOT>DECOMPOSITION > Peaks < 3))

This search does gives you all compounds within a single test that meet both requirements in your query.

Note: When you filter your search results, you see solely those lower-level records that meet your search requirements.

49.2.4 Specifying Searchable Keys as a Query

If your database contains the database field MOLSKEYS, you can use numbered keys to retrieve specific substructures or chemical representations. You must separate multiple keys with a comma (do not include spaces):

*	Use parentheses to specify the retrieval of all the keys in your query. Example: To specify the retrieval of molecules that contain 6-membered rings and bromine, enter the following into the Query Builder text box:

MOL>MOLSKEYS = "(163,46)"

*	Use square brackets to specify the retrieval of one ore more keys in your query. Example: To specify the retrieval of molecules that contain 6-membered rings or bromine, enter the following into the Query Builder text box:

MOL>MOLSKEYS = "[163,46]"

*	Use angle brackets to specify the retrieval of none of the keys in your query. Example: To specify the retrieval of molecules that do not contain 6-membered rings or bromine, enter the following into the Query Builder text box:

MOL>MOLSKEYS = "<163,46>"

*	Use braces to specify the retrieval of solely one of the keys in your query but not any others in your query. Example: To specify the retrieval of molecules that contain either 6-membered rings or bromine but not both 6-membered rings and bromine, enter the following into the Query Builder text box:

MOL>MOLSKEYS = "{163,46}"

*	Use no restrictors to specify the retrieval of one and/or any other keys in your query. Example: To specify the retrieval of molecules that contain 6-membered rings and/or bromine, enter the following into the Query Builder text box:

MOL>MOLSKEYS = "163,46"

Additional Examples

The query MOL>MOLSKEYS = "161,[11,96]" specifies the retrieval of N and a 4- or 5-membered ring.

The query MOL>MOLSKEYS = "[(161,96),(164,163)]" specifies the retrieval of N and a 5-membered ring or O and a 6-membered ring. Both sets of molecules can be retrieved.

The query MOL>MOLSKEYS = "[42,46,103],<27>" specifies the retrieval of at least one halogen, which cannot be iodine.

The List of Searchable Keys

If you search a MACCS-II database, there are 166 numbered keys that you can use. If you do not recognize the words for a specific key, the words might be in a special type of language called query language. The list of searchable keys is as follows:

Key	Description	Key	Description

1	ISOTOPE	84	NH2

2	103 < ATOMIC NO. < 256	85	CN(C)C

3	GROUP IVA,VA,VIA PERIODS 4-6 (GE..)	86	CH2QCH2

4	ACTINIDE	87	X!A$A

5	GROUP IIIB,IVB (SC..)	88	S

6	LANTHANIDE	89	OAAAO

7	GROUP VB,VIB,VIIB (V..)	90	QHAACH2A

8	QAAA@1	91	QHAAACH2A

9	GROUP VIII (FE..)	92	OC(N)C

10	GROUP IIA (ALKALINE EARTH)	93	QCH3

11	4M RING	94	QN

12	GROUP IB,IIB (CU..)	95	NAAO

13	ON(C)C	96	5M RING

14	S-S	97	NAAAO

15	OC(O)O	98	QAAAAA@1

16	QAA@1	99	C=C

17	CTC	100	ACH2N

18	GROUP IIIA (B..)	101	8M RING OR LARGER

19	7M RING	102	QO

20	Si	103	CL

21	C=C(Q)Q	104	QHACH2A

22	3M RING	105	A$A($A)$A

23	NC(O)O	106	QA(Q)Q

24	N-O	107	XA(A)A

25	NC(N)N	108	CH3AAACH2A

26	C$=C($A)$A	109	ACH2O

27	I	110	NCO

28	QCH2Q	111	NACH2A

29	P	112	AA(A)(A)A

30	CQ(C)(C)A	113	Onot%A%A

31	QX	114	CH3CH2A

32	CSN	115	CH3ACH2A

33	NS	116	CH3AACH2A

34	CH2=A	117	NAO

35	GROUP IA (ALKALI METAL)	118	ACH2CH2A>1

36	S HETEROCYCLE	119	N=A

37	NC(O)N	120	HETEROCYCLIC ATOM>1 (&..)

38	NC(C)N	121	N HETEROCYCLE

39	OS(O)O	122	AN(A)A

40	S-O	123	OCO

41	CTN	124	QQ

42	F	125	AROMATIC RING>1

43	QHAQH	126	A!O!A

44	OTHER	127	A$A!O>1 (&..)

45	C=CN	128	ACH2AAACH2A

46	BR	129	ACH2AACH2A

47	SAN	130	QQ>1 (&..)

48	OQ(O)O	131	QH>1

49	CHARGE	132	OACH2A

50	C=C(C)C	133	A$A!N

51	CSO	134	X (HALOGEN)

52	NN	135	Nnot%A%A

53	QHAAAQH	136	O=A.1

54	QHAAQH	137	HETEROCYCLE

55	OSO	138	QCH2A>1 (&..)

56	ON(O)C	139	OH

57	O HETEROCYCLE	140	O>3 (&..)

58	QSQ	141	CH3>2 (&..)

59	Snot%A%A	142	N>1

60	S=O	143	A$A!O

61	AS(A)A	144	Anot%A%Anot%A

62	A$A!A$A	145	6M RING>1

63	N=O	146	O>2

64	A$A!S	147	ACH2CH2A

65	C%N	148	AQ(A)A

66	CC(C)(C)A	149	CH3>1

67	QS	150	A!A$A!A

68	QHQH (&..)	151	NH

69	QQH	152	OC(C)C

70	QNQ	153	QCH2A

71	NO	154	C=O

72	OAAO	155	A!CH2!A

73	S=A	156	NA(A)A

74	CH3ACH3	157	C-O

75	A!N$A	158	C-N

76	C=C(A)A	159	O>1

77	NAN	160	CH3

78	C=N	161	N

79	NAAN	162	AROMATIC

80	NAAAN	163	6M RING

81	SA(A)A	164	O

82	ACH2QH	165	RING

83	QAAAA@1	166	FRAGMENTS

Where (&..) is equivalent to "and other rare features;" and Key 166 Key 166 corresponds to molecules that consist of more than one fragment. (A molecule has more than one fragment if its structure cannot be drawn in one connected set of bonds.)

Some of the keys that you see are encoded in a substructure-search query language, such as QAAAA@1 for Key 83. This language allows atoms to be expressed as follows:

*	Unbracketed for C, N, O, P, and S; but bracketed for all other single element symbols, such as [CL] for chlorine, or multiple element symbols in lists, such as [N,O] for nitrogen and oxygen, or [F,CL,BR,I] for halogens.

*	A for any atom except hydrogen, and Q for any atom except carbon or hydrogen.

*	Substituted with a specific number of hydrogens: H0 on an atom prohibits hydrogens at that position, such as CH0; and Hn allows at least that number (n) of hydrogens, such as CH2 (methyl or methylene).

*	Charged: A plus sign (+) on an atom is a positive charge, such as +, +2, or +3; a single quote (') is a monoradical; a double quote (") is a negative charge; and an asterisk (*) is a neutral atom.

*	Variable in mass: The isotopic label M+n indicates a difference of n from the standard mass, such as CM+1 to indicate the isotope carbon 13, or OM-1 to indicate the isotope oxygen 15.

*	Variable in atom number: The notation @n at the end of the atom to which it refers indicates that atom number (n) is attached here. Atoms (except hydrogen) are numbered from left to right, such as C-C-C-@1 (but not @3-C-C-C) to indicate a three-membered ring, or CH3-C-C-C-@2 to indicate (methyl or methylene).

*	Branched: The parentheses around an atom or group indicates that the atom or group branches from the atom at its left (but not its right) in the string. For example, C-C-C-C is butane, while C-C(C)-C-C is 2-methyl butane. N+(-C)(-C)(-C)(-C) is a quaternary ammonium salt.

This language allows bonds to be expressed as follows:

*	Variable bond type: A hyphen (-) is a single bond; an equal sign (=) is a double bond; a (T) is a triple bond; a percent sign (%) is an aromatic bond; a tilde (~) is either a single or a double bond; and an unspecified bond type is the omission a bond marker. For example, the two carbon chain CC contains any type of bond.

*	Variable numbers of fragments: A space between strings indicates that there is no connection between the groups. For example, C=O C-OH retrieves a carbonyl and a hydroxyl, but the groups cannot be centered on the same carbon (the fragments cannot overlap).

*	Part of a ring: A dollar sign ($) that precedes a bond indicates that the bond is part of a ring.

*	Part of a chain: An exclamation sign (!) that precedes a bond indicates that the bond is part of a chain.

49.3 Specifying Flexmatch Parameters

This section contains information on the parameters that you specify with the FLEXMATCH search operator.

49.3.1 Flexmatch Parameters

A Flexmatch (FLEX) search finds records that are an exact match of your query, except in the ways that you specify with any of the flexmatch parameters. You specify features of retrieved structures that must match your query. If you specify flexmatch parameters, you tighten the definition of an exact match. This allows you to find structures that:

*	Have different counterions than the salt in your query.

*	Match your query, but have different isotopic labels.

*	Match your query, but might be represented differently in the database. For example, the pi-metal bonds in ferrocene can be represented in different ways.

Flexmatch parameters define the features of retrieved 2D structures that must match your query molecule. When you specify flexmatch parameters, you tighten the definition of an exact match. (If you do not specify flexmatch parameters, you retrieve the loosest possible match that is possible for an exact match.) The flexmatch parameters are as follows:

Bond Type (BON)

BON specifies that all bond types must match.

Tautomer (TAU)

TAU specifies that tautomer groups must contain the same number of hydrogens in the tautomeric region, within a tolerance limit. The tolerance limit is the sum of the absolute values of charges plus the sum of the number of radicals plus the number of metal bonds. Diradicals count as two radicals. (If you specify TAU and also specify HYD, the tolerance limit is zero.)

A tautomer is a group of atoms with any of the following patterns:

Where	Q = O, N, S, Se, or Te

X = C, O, N, S, Se, or Te

Y = C, I, P, As, Sb, Cl, or Br

You can have multiple tautomeric groups in a single molecule. For example:

In addition, any bonds in the tautomeric region can be aromatic. For example:

Atom charges (CHA)

CHA specifies that the charge on each atom must match those in your query. This automatically ensures that the sum of the charges on each fragment must match.

Ion charges (ION)

ION specifies that the total charge for each fragment in the query must match.

Fragments (FRA)

FRA specifies that all fragments must match your query, and that no additional fragments are allowed.

For monomer and structural repeating unit (SRU) brackets, the settings of POL and TYP influence how ISIS perceives fragments. For example, ISIS perceives the following source-based representation of a polymer as a single fragment when you specify both POL and TYP in the query, but perceives two fragments when you do not specify POL and TYP:

With POL and TYP specified, ISIS sees the polymer as a single chemical species, and therefore as a single fragment.

Hydrogen (HYD)

HYD specifies that hydrogen count must match for each fragment in your query.

If you do not specify HYD, the hydrogen count within a tolerance limit for each of the fragments must match. The tolerance limit is the sum of the absolute values of charges plus the sum of the number of radicals plus the number of metal bonds. Diradicals count as two radicals.

If you specify TAU and HYD, the hydrogen count must match exactly in both the tautomeric regions and in the individual atoms of non-tautomeric regions.

If you specify TAU, but do not specify HYD, the hydrogen count must match within the tolerance limit in both the tautomeric regions and in the individual atoms of non-tautomeric regions.

Isotopes (MAS)

MAS specifies that the isotopic labels on each atom must match those in your query. (Isotopic labels include H, D, and T.)

If you do not specify MAS, you retrieve molecules in the database that have different isotopic labels, and H, D, and T are equivalent to each other.

Metal (MET)

MET specifies that the connectivity of all metals must match your query. A metal is any atom other than H, D, T, He, B through Ne, Si through Ar, As through Kr, Te, I, Xe, At, and Rn.

If you do not specify MET, you can retrieve all the different representations of your query. For example, to retrieve all representations of ferrocene even though the pi-metal bonds are represented in different ways in your database, do not specify MET.

If you do not specify MET, and also do not specify SAL, any counterions that are attached to the metal are removed.

Radicals (RAD)

RAD specifies that the radical value on each atom must match those in your query.

Salts (SAL)

SAL specifies that the counterions in the structures retrieved must match the counterion in your query. A counterion is any fragment or single atom in the SALTS.DAT file (or equivalent). This file is customizable. For more information, see your ISIS Administrator.

If you do not specify SAL, you retrieve molecules with different counterions than those in your salt query.

If you do not specify SAL, and also specify FRA, you retrieve solely the parent structures of salts.

Stereoconfiguration (STE)

You can specify that the configuration of stereo centers (in geometric and optical stereoisomers) must match. You can only use this feature if you also specify BON.

If your query contains unspecified stereo centers, you retrieve solely those structures with unspecified stereo centers. An unspecified stereo center is the asymmetric center of atoms C, N, O, P, S, or Si, that is connected to one of the following:

*	No stereo bonds

*	An EITHER query bond (specifies either the Up or Down stereoconfiguration)

*	A DOUBLE EITHER bond that (specifies either the cis or trans stereoconfiguration)

Valence (VAL)

VAL specifies that the valence on each atom must match those in your query.

Notes: (1) If no valence is specified, an implicit valence is calculated from the structure. A query with an unspecified valence (with a calculated implicit valence) might retrieve a structure that contains the matching explicit valence. Or, a query with an explicit valence might retrieve a structure that does not contain an explicit valence (that contains a calculated implicit valence). (2) Some valences are illegal. For transition metals, a valence is illegal if it is smaller than the number of bonds to the atom. For other real atom types, an illegal valence is ignored in a FLEX search and the query retrieves any valence.

Polymer End Groups (END)

END specifies that polymer end groups must match those in your query. A polymer end group is a connected set of atom and bonds that:

*	is connected to the rest of the structure by just one crossing bond (a crossing bond is a bond that crosses a bracket)

*	contains no brackets.

END depends on POL. END can be on solely when POL is also on.

Attached Data (DAT)

DAT specifies that attached data must match the attached data in your query. For example:

Mixtures (MIX)

MIX specifies that the type of mixture (ordered or unordered), and the order of components in an ordered mixture, must match the corresponding structures in your query.

Monomer/SRU Uniqueness (MSU)

MSU specifies that the source-based and structure-based representations of the same polymer are considered distinct structures. When MSU is OFF (not specified), the source-based and structure-based representations of a polymer find each other. For example:

MSU depends on both POL and TYP. POL and TYP must be on for MSU to function.

When MSU is off (not specified), ISIS ignores the settings of BON and HYD for structures within monomer and SRU brackets.

Polymers (POL)

POL specifies that all polymer definitions must match. (The polymer definition is the set of atoms and bonds that is associated with a set of polymer brackets).

The TYP, END, and MSU switches depend on POL. That is, turning off POL automatically turns off TYP, END, and MSU. For monomer and SRU brackets, the setting of POL also determines how ISIS perceives fragments within the polymer. For more information, see FRA.

Polymer Type (TYP)

TYP specifies that the polymer bracket type (for example, monomer, SRU, crosslink, block copolymer, and other bracket types) and polymer connectivity must match your query.

TYP depends upon the setting of POL. That is, POL must be on for TYP to be on. MSU also depends on TYP; TYP must be on for MSU to be on. For monomer and SRU brackets, the setting of TYP also influences how ISIS perceives fragments in the polymer. For more information, see FRA.

49.3.2 Combinations of Flexmatch Parameters

The Most Restricted Flexmatch Parameters

To retrieve the most restricted exact match of your FLEX query from the database, specify all flexmatch parameters. For example:

MODEL>MOL>MOLSTRUCTURE FLEXMATCH query "FRA/HYD/MAS/MET/RAD/SAL/STE/VAL/BON/TAU/ION/CHA"

The Least Restricted Flexmatch Parameters

To retrieve the least restricted exact match of your FLEX query from the database, specify no flexmatch parameters. For example:

MODEL>MOL>MOLSTRUCTURE FLEXMATCH query ""

Source-Based and Structure-Based Polymers

To retrieve polymer structures in which the source-based representation of a polymer must match the corresponding structure-based representation, specify the following flexmatch parameters:

MOL>MOLSTRUCTURE FLEXMATCH query "FRA/HYD/MAS/MET/RAD/SAL/STE/VAL/BON/TAU/ION/CHA/MIX/POL
/TYP"

To retrieve polymer structures in which the source-based representation of a polymer must match the corresponding structure-based representation, and in which polymer end groups and attached data must match exactly, specify the following flexmatch parameters:

MOL>MOLSTRUCTURE FLEXMATCH query "FRA/HYD/MAS/MET/RAD/SAL/STE/VAL/BON/TAU/ION/CHA/MIX/DAT/END/POL
/TYP"

49.3.3 Examples of the Interactivity of Flexmatch Parameters

The flexmatch parameters are typically interactive. To obtain the correct results, you need to know which flexmatch parameters require other flexmatch parameters to function correctly. With the correct interactive settings, you can retrieve closely related structures that are represented in a variety of ways in your database. For example:

*	MDL depicts sulfones with undisplayed charges in which two of the four bonds on the sulfur atom are double bonds. In your database, these compounds might be displayed with charges instead:

You need to consider both charges and bond types. To retrieve all representations of a specific sulfone, use the following query:

MOL>MOLSTRUCTURE FLEXMATCH query ""

Note: You can specify other flexmatch parameters to tighten the definition of exact match. However, you must not specify TAU or ION.

*	MDL depicts sulfoxides with undisplayed charges in which there is a double bond on the sulfur atom. In your database, these compounds might be displayed with charges instead:

You need to consider both charges and bond types. To retrieve all representations of a specific sulfoxide, use the following query:

MOL>MOLSTRUCTURE FLEXMATCH query "TAU/ION"

Note: You can specify other flexmatch parameters to tighten the definition of exact match. However, you must not specify CHA or BON.

*	MDL depicts thiocarboxylic acid salts with undisplayed charges in which there is a bond from the ion to the counterion. In your database, these compounds might be displayed with charges instead:

You need to consider charges, bond types, and metal bonds. To retrieve all representations of a specific salt, use the following query:

MOL>MOLSTRUCTURE FLEXMATCH query "BON/TAU"

Note: You can specify other flexmatch parameters to tighten the definition of exact match. However, you must not specify MET, CHA, SAL, FRA, or ION.

*	MDL depicts π ligands in organometallic complexes with radicals or with covalent bonds. You need to consider charges, bond types, metal bonds, and radicals. To retrieve all representations of a specific organometallic complex, use the following query:

MOL>MOLSTRUCTURE FLEXMATCH query "TAU"

Note 1: You can specify other flexmatch parameters to tighten the definition of exact match. However, you must not specify BON, CHA, ION, MET, or RAD.

Note 2: You can also retrieve specific organometallic complexes with an exact formula query in an FMLA search.

49.4 Definition of Aromaticity

For remote databases: ISIS interprets the following ring systems as aromatic:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:

Note: The bonds of six-membered aromatic ring systems and the perimeter bonds of azulenes are stored as aromatic bonds in the database. The bonds of five-membered aromatic rings, however, are stored as single and double bonds and interpreted as aromatic during a search. The differences between five-membered rings and other types of aromatic rings can cause different search results for five- and six-membered rings/azulenes when you use the following bonds in queries: Single, Double, and Single/Double query bonds. For more information on the Single/Double query bond, see Section 49.5.7.

49.5 Specifying Query Features on Atoms and Bonds in Structures

A query feature on an atom and/or a bond in a molecule is a restriction that specifies the retrieval of certain types of molecule records from an ISIS/Base database.

If you do not use query features, the molecules retrieved contain solely your exact substructure query embedded wholly within them. For example:

49.5.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

49.5.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of hydrogens. For example:

49.5.3 Allowing an Unsaturated Atom

Use an atom query feature to specify that an atom is attached to at least one multiple bond (double, triple, or aromatic).

Atom Query Feature: Unsaturated Atom (u)

Specifies that the atom of your choice is attached to at least one multiple bond (double, triple, or aromatic). For example, the following query specifies both an unsaturated atom (u) and single or double bonds (the double dashed lines).

49.5.4 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

Atom Query Feature: Substitution Count of Zero, s0

Specifies that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of a single atom with attached hydrogens (if any).

Atom Query Feature: Substitution Count of One, s1

Specifies that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Two, s2

Specifies that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Three, s3

Specifies that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Four, s4

Specifies that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Five, s5

Specifies that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of at Least Six, s6

Specifies that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count as Drawn, s*

Specifies that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:

49.5.5 Allowing a Specific Number of Ring Bond Attachments

Use atom query features to specify the number of ring bond attachments.

Atom Query Feature: Ring Bond Count of Zero, r0

Specifies that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:

Atom Query Feature: Ring Bond Count of Two, r2

Specifies that the records retrieved have solely two ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of Three, r3

Specifies that the records retrieved have solely three ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of at Least Four, r4

Specifies that the records retrieved have at least four ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count as Drawn, r*

Specifies that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:

49.5.6 Allowing Additional Atoms and/or Bonds in a Chain or a Ring

Use a query feature that is for either atoms or bonds to specify the addition of atoms and/or bonds in a chain or a ring.

Atom or Bond Query Feature: Link Node

Use a link node to specify the addition of variable numbers repeating units (atoms and/or bonds) to a ring or chain. A repeating unit must be attached to two adjacent bonds. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the link node [L1-3]:

Or, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the link node [L1-3]:

49.5.7 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Note: An aromatic query bond hits any bond in all types of aromatic rings: 6-membered ring bonds, 5-membered ring bonds, and azulene perimeter bonds. For more information on the structures that ISIS interprets as aromatic, see Section 49.2.

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

Note: A Single/Double query bond does not hit bonds in 6-membered aromatic rings, or perimeter bonds of azulenes, because bonds in these structures are stored in the database as aromatic bonds. However, a Single/Double query bond does hit bonds in 5-membered rings that ISIS interprets as aromatic. For more information on the structures that ISIS interprets as aromatic, see Section 49.2.

Bond Query Feature: Single/Aromatic Bond

Specifies either a single or an aromatic bond at that position:

Bond Query Feature: Double/Aromatic Bond

Specifies either a double or an aromatic bond at that position:

49.5.8 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

49.5.9 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

49.6 Specifying Rgroup Query Features

An Rgroup query finds structures that contain your query as a root structure with defined Rgroup substituents attached to it at specific positions. Your query can contain restrictions on the Rgroup substituents, called Rgroup conditions: You can specify the number of Rgroup sites that must be occupied in the records retrieved, specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site, or specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

Your Rgroup query can also contain restrictions on atoms and bonds of the root structure and Rgroup substituents. For example, you can use the atom query feature H(0) to prohibit the attachment of implicit hydrogens on a specific atom in the structures retrieved.

An example of an Rgroup query is as follows:

49.6.1 The Root Structure

The root structure contains the portion of the structure that does not vary among the structures retrieved. For example, if you want to find 2, 5-Dihydroxypyridine in which the substituent at position 2 can be COOH, CN, or Ph, and the substituent at position 5 can be OH or CH3, the root structure is 2, 5-Dihydroxypyridine with Rgroups (such as R1 and R2):

Rgroups

On the root structure, Rgroups (R1 through R32) are placeholders that designate where the lists of functional groups and atoms that can attach to the root structure. In the example above, the Rgroup R1 designates that the members of the list R1 (the Rgroup substituents) are allowed at position 5 on the root structure. The Rgroup R2 designates that the members of the list R2 (the Rgroup substituents) are allowed at position 2 on the root structure.

Multiple Rgroups at One Position

You can specify multiple Rgroups at a single site on the root structure. For example:

One Rgroup at Multiple Positions

You can specify a single Rgroup (such as R1) at multiple positions on the root structure. For example:

Note: For information on how to restrict the number of Rgroups that must be occupied in the records retrieved, See Section 49.6.3, "Rgroup Conditions." A molecule need not satisfy all the Rgroup sites on the root structure to be retrieved. For example, the Rgroup condition R1 > 0 specifies that any molecule in which at least one of the R1 sites is filled by an R1 member will be retrieved. In addition, the Rgroup condition RestH determines whether the unsatisfied sites must be filled with hydrogen atoms or if other molecule fragments are allowed to be attached if they are not on the list.

49.6.2 Rgroup Substituents

Rgroup substituents are the members of the list of Rgroups. You define the Rgroup substituents that you will allow to be found at specified positions in the molecules retrieved. Rgroup substituents can be any structural fragment, including functional groups and single atoms.

In the example below, the Rgroup substituents COOH, CN, or Ph are allowed at position 5 (R1) on the root structure and the Rgroup substituents OH or CH3 are allowed at position 2 (R2) on the root structure:

Attachment Points

An attachment point (marked with an arrow and an asterisk) designates the atom on the Rgroup substituent that is attached to the root structure:

You must designate an attachment point on an Rgroup substituent for each bond that is attached to the substituent. If an Rgroup is attached to two bonds on the root structure, you must designate two attachment points. The bond on the root structure that is marked with double quotes corresponds to the attachment point on the Rgroup substituent that is marked with double quotes. The other attachment point on the Rgroup substituent is marked with a single quote:

Nested Rgroups

A nested Rgroup is an Rgroup that is a placeholder within another Rgroup rather than within the root structure. (You cannot nest an Rgroup any lower than this level.) In the following example, Rgroup R2 is nested within the Rgroup R1:

Nested Rgroups are equivalent to the following structures:

49.6.3 Rgroup Conditions

You can apply restrictions to each Rgroup in your query after you assemble all the Rgroups. The set of restrictions is called the Rgroup conditions.

If you do not apply Rgroup conditions, ISIS assigns the default conditions: Occurrence > 0 and RestH off for each Rgroup.

Occurrence

With the Rgroup condition Occurrence, you can specify the number of Rgroup sites that must be occupied in the records retrieved. For example, the occurrence designation R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved. Type one of the following values in the Occurrence range text box:

Value	Explanation

0	All members of the Rgroup are excluded from the Rgroup site (such as R1). To allow any other Rgroup substituent at the Rgroup site, set RestH to off.

> 0	At least one Rgroup must be satisfied. If RestH is off, any other substituent can attach to unsatisfied sites. If RestH is on, unsatisfied sites must be filled solely by hydrogens.

n	Exactly n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

< n	Less than n number of sites (including zero) must be satisfied. RestH controls substitution at unsatisfied sites.

m - n	Any number of sites falling within the range of m to n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

m,n,...	Any combination of the above expressions, separated by commas. For example: 1, 3-5, 9, >12.

For example, the Rgroup condition R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved.

In another example, the Rgroup condition R1 > 0 and R2 > 0 specifies that an Rgroup substituent from the R1 list AND an Rgroup substituent from the R2 list must occupy at least one site on the root structure in the records retrieved.

Finally, the Rgroup conditions R1 = 1, 3-5, 9, >12 specify that either 1, 3, 4, 5, 9, or more than 12 sites must be satisfied:

RestH

With the Rgroup condition RestH, you can specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site.

An unsatisfied Rgroup site is an Rgroup site on the root structure that does not have an Rgroup member attached: If RestH is off, any functional group or atom may be attached at unsatisfied Rgroup sites on the root structure. If RestH is on, solely hydrogens are allowed to be attached at unsatisfied Rgroup sites on the root structure.

If/Then

With the Rgroup condition If/then, you can specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

For example, If R1 then R2 specifies that if the conditions for R1 are satisfied, then the conditions for R2 must also be satisfied. (If the conditions for R1 are not satisfied, then the conditions for R2 are ignored.) The If/then condition implies that a molecule may be retrieved even though R1 is not satisfied.

In the following query, R1 contains a nitro group and a sulfonic acid group. R2 contains a chlorine atom. The condition If R1 then R2 specifies that if a nitro group or a sulfonic acid group is attached at R1 on the root structure, then a chlorine must also be attached at R2. However, if the R1 site on the root structure does not have either the nitro or the sulfonic acid group (R1 is unsatisfied), then R2 can have any substituent (R2 is ignored):

49.7 Specifying Stereochemistry

For remote databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

An SSS search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve molecules with matching cis or trans stereochemistry. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An SSS search produces the following results:

Chiral Flags on Molecules

In a remote database, you can create a query with a chiral flag on a molecule with at least one asymmetric center or on a molecule that is asymmetric to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

49.8 Guidelines for Revising the Query

If your QB search retrieved no records or too few records, you might want to:

*	Conduct a QB search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the structural constraints in your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, remove substituent limits, or remove stereochemical requirements.

*	Make the text/numeric strings in your query more general, and then search the same set of records. For example, you can apply operators that partially restrict, such as > or between instead of =, or you can apply wildcards. (A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters.)

If your QB search retrieved too many records, you might want to:

*	Refine the structural constraints in your query, and then search the same set of records. For example, you can limit substitution at specific positions, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Make the text/numeric string in your query more restrictive, and then search the same set of records. For example, you can use the operator = instead of >.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	First conduct a formula search to screen out large and complex molecules that are stored in your database, and then conduct a search on the less complex molecules. If your query is not able to map a stored molecule within a specific length of time, the molecule is added to the search results.

*	Filter your search results so that you view solely the lower-level records. (This assumes that you are viewing both upper- and lower-level records.)

49.9 Searching Example 1: Combining Text/Numeric Queries

This searching example shows you how to conduct a single QB search with a query that contains two text/numeric string components.

49.9.1 Problem

You want to retrieve all molecules that meet both of the following requirements:

*	Have a molecular weight greater than 250

*	Contain two or three oxygen atoms

49.9.2 Approach

In the Query Builder text box in ISIS/Base:

1.	Enter the database field MOL>MOLECULAR.WEIGHT.

2.	(Optional) Enter a space.

3.	Enter the search operator >.

4.	(Optional) Enter a space.

5.	Enter the target value 250.

6.	(Optional) Enter a space.

7.	Enter the boolean algebraic operator AND. (Alternatively, to find records that meet either requirement, enter OR.)

8.	(Optional) Enter a space.

9.	Enter the database field MOL>MOLFORMULA.

10. (Optional) Enter a space.

11. Enter the search operator LIKE. You use the search operator LIKE instead of the search operator = with target values that contain text. In this example, the o (for oxygen) is text.

12. (Optional) Enter a space.

13. Enter the target value "o(2-3)". Enter all target values with the search operator LIKE in double quotation marks, where o is either in upper- or lower-case characters.

14. Conduct a QB search in the remote molecule database of you choice, such as the ISISMX demo database.

49.9.3 Query

In the Query Builder text box, you see the following query:

49.9.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for QB, how to/examples.

49.9.5 Results

You retrieve records with molecules that have a molecular weight greater than 250 and that contain two or three oxygens.

49.10 Searching Example 2: Combining Text/Numeric and Graphical Queries

This searching example shows you how to conduct a single QB search with a query that contains a text/numeric string query component and a graphical query component.

49.10.1 Problem

You want to retrieve all molecules that meet both of the following requirements:

*	Contain a steroid substructure embedded wholly within them

*	Have a melting point that is greater than 220 degrees Centigrade

49.10.2 Approach

Note: This example assumes that you have previously created a graphical structure with the file name STEROID.MOL (Mac = STEROID) that you stored with the database.

To find results that match the text/numeric string query component or the graphical query component, in the Query Builder text box in ISIS/Base:

1.	Enter the database field MOL>MELTING.POINT>MELTING.POINT.

2.	(Optional) Enter a space.

3.	Enter the search operator >. This portion of your query executes a search that retrieves all molecules that are greater than your target value.

4.	(Optional) Enter a space.

5.	Enter the target value 220.

6.	(Optional) Enter a space.

7.	Enter the boolean algebraic operator AND. (Alternatively, to find records that meet either requirement, enter OR.)

8.	(Optional) Enter a space.

9.	Enter the database field MOL>MOLSTRUCTURE.

10. (Optional) Enter a space.

11. Enter the search operator SSS. This portion of your query executes a molecule substructure search (SSS) that retrieves all molecules that contain your target value (in this case, your graphical substructure) embedded wholly within them.

12. (Optional) Enter a space.

13. Enter the target value that is the file name of the graphical substructure that you want to use. For example, enter the file name STEROID.MOL (Mac = STEROID). Alternatively, if you want to use the graphical query that you see on the form in ISIS/Base, you can enter the temporary file name QUERY. If you cannot remember the file name of the stored query that you want to use, you are prompted to browse specific directories and to read in the file name that you want.

14. Conduct a QB search in the remote molecule database of you choice, such as the ISISMX demo database.

49.10.3 Query

In the Query Builder text box, you see the following query:

49.10.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for QB, how to/examples.

49.10.5 Results

You retrieve records with molecules that have a melting point greater than 220 and that contain the steroid substructure in your query.


Local QB in a Molecule Database: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Local QB Search in a Molecule Database	50.1

*	Specifying a QB Query	50.2

*	Definition of Aromaticity	50.3

*	Specifying Query Features on Atoms and Bonds in Structures	50.4

*	Specifying Stereochemistry	50.5

*	Guidelines for Revising the Query	50.6

*	Searching Example 1: Combining Text/Numeric Queries	50.7

*	Searching Example 2: Combining Text/Numeric and Graphical Queries	50.8

We recommend that you print this 14-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a local QB search in a molecule database, click here.

50.1 Definition of a Local QB Search in a Molecule Database

You can use the local Query Builder (QB) search to create any of the other remote searches in ISIS. However, you must use an all-text search query. Thus, we recommend that you use another type of search where possible!

A QB search does have one unique feature: You can combine AND, OR and NOT boolean operators in a search query. For example:

To find all molecules that contain benzaldehyde AND all molecules with a melting point greater than 220 degrees, enter:

To find all molecules that contain both indole and a molecular weight greater than 200 but NOT those molecules with a melting point below 190, enter:

To find all molecules that do NOT contain benzaldehyde embedded wholly within them, enter:

A local search is a search over a database that typically exists on your hard disk. To do a local search on your hard disk, you do not need to input network information.

Note: To do a local search that is accessed from a shared network, you need to input network information.

50.2 Specifying a QB Query

Each QB query contains:

*	The database field that you want to search.

For example, to search the melting point field, enter either the full path name, MOL>MELTING.POINT>MELTING.POINT, or the minimum tree name that uniquely identifies the field, namely MELTING.POINT. To search the structure field, enter either the full path name MOL>MOLSTRUCTURE, or the minimum tree name that uniquely identifies the field, namely MOLSTRUCTURE.

*	A search operator that specifies the type of search (such as a greater than sign, >, to specify a search that finds solely the target text in the query).

*	The text or numeric target value (specific data) that you want to find. (In addition, your target value can be a file name that corresponds to a structure that you want to retrieve.)

A text or numeric target value can contain wildcards. A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. For example, you can specify the query LIKE "%ALD%" (instead of the query LIKE "BENZALDEHYDE"). The wildcard _ is a placeholder for solely one unspecified character. For example, you can specify the query LIKE "_CHLOROBENZENE" (instead of the query LIKE "2-CHLOROBENZENE"). Target values that contain text or wildcards require double quotation marks.

Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

For example, to find records that contain structures with a melting point that is greater than 220, enter:

MOL>MELTING.POINT>MELTING.POINT > 220

Note: You can combine statements in a single text/numeric string with one of the logical operators AND, OR, and NOT. When you use the NOT operator, enclose the text/numeric string in parentheses. For example, enter:

NOT (MOL>MELTING.POINT>MELTING.POINT > 220)

50.2.1 The Search Operators

<, <=, >, >=, and <>

Use one of the following search operators with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005): <, <=, >, >=, and <>. With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Search Operator	Definition	Examples

=	equal (numeric)	MOLECULAR.WEIGHT = 350

<	less than (numeric)	MOLECULAR.WEIGHT < 350

<=	less than or equal to (numeric)	MOLECULAR.WEIGHT <= 350

>	greater than (numeric)	MOLECULAR.WEIGHT > 350

>=	greater than or equal to (numeric)	MOLECULAR.WEIGHT >= 350

<>	not equal to (text or numeric)	MOLECULAR.WEIGHT <> 350

ACTIVITY <> "inhibitor"

For a MOLFORMULA field, an exact formula query retrieves records that contain solely the exact atoms that you specify. To create an exact formula query, specify the target value for the formula. The target value must include all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required. The equals operator (=) and quotes are optional. For example:

Exact Formula Query	Examples of Records Retrieved

c6 h6 O	Phenol

c6h6o

C20 H12 Na2 O4	Sodium salt of phenolphthalein

C20H12Na2O4

= C20 H12 Na2 O4

= C20H12Na2O4

= "C20 H12 Na2 O4"

= "C20H12Na2O4"

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Exact Formula Query	Examples of Records Retrieved

C17 H19 N 03	Piperine

C17H19N 03	Piperine

C17H19N103	Piperine

C17H19N03	No molecules retrieved. ISIS interprets "NO3" as 3 Nobelium atoms.

LIKE

Use LIKE with text enclosed in double quotation marks. Enter your query as follows:

Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. For example:

Query	Examples of Records Retrieved

COMPOUND.NAME LIKE "methane"	Methane

COMPOUND.NAME LIKE "benzoic acid"	Benzoic Acid

COMPOUND.NAME LIKE "%acid"	Benzoic Acid

Acetic Acid

COMPOUND.NAME LIKE "%acid%"	Benzoic Acid Sodium Salt

Acetic Acid Sodium Salt

COMPOUND.NAME LIKE "%but_ne"	Trans 2-Butene

2-Butene

N-Butane

Butane

Butene

COMPOUND.NAME LIKE "_ethyl"	Methyl

Ethyl

ACTIVITY LIKE "antibiotic"	Antibiotic

ACTIVITY LIKE "%antibiotic%"	Antibiotic activity

Resistance to antibiotics

Note: To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice. To retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: ACTIVITY LIKE "aa""a" or ACTIVITY LIKE"%aa""a%".

For a MOLFORMULA field, a subformula query retrieves records that contain the specific atoms that you specify, and any additional atoms. To create a subformula query, use the LIKE operator with a target value. The target value can include a range of atom counts, and typically excludes the hydrogens. To exclude specific atoms from the molecules that you retrieve, specify zero for that atom. You can use a single space to separate atoms. Capital letters are not required. Quotes are optional.

Subformula Query	Examples of Records Retrieved

LIKE Na	All sodium salts

LIKE c12 Br(1-2) S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE "C12Br(1-2)S2"	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE c6 h6	All molecules that contain six carbon atoms, six hydrogen atoms, and any number of other atoms

LIKE C5 H10 N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

LIKE C5H10N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Subformula Query	Examples of Records Retrieved

LIKE C12 Br S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12Br1S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12BrS2	No molecules retrieved. ISIS interprets "BrS" as an atom symbol, and gives an error message.

BETWEEN

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks. For example:

CORPORATE.ID BETWEEN "XR11" "XZ15"

CORPORATE.ID BETWEEN 95 100

EXISTS

Use EXISTS to retrieve all records in the database that contain data in a specific database field. For example:

MOL>MOLSTRUCTURE EXISTS

To retrieve all records in the database that contain no data in a specific database field, use NOT in your query:

NOT (MOL>MOLSTRUCTURE EXISTS)

Note: You can only use the EXISTS search operator for certain types of database fields. Using EXISTS with other types of fields produces an error message.

SSS

Use SSS to retrieve database structures that contain your graphical query as a substructure embedded wholly within them. For example (query is the file name of your graphical query):

MOL>MOLSTRUCTURE SSS query

50.2.2 Specifying a Structure in a QB Query

To include a graphical (structural) component in your QB query, you must enter the following in the Query Builder text box in the order shown:

*	The name of the database field that will hold your graphical search results. For a molecule record, enter MOL>MOLSTRUCTURE.

*	The search operator. For example, enter SSS to specify that the structures retrieved contain your graphical query embedded wholly within them. OR, enter the equal sign (=) to specify that the structures retrieved contain your graphical query exactly as drawn.

*	The file name (not the structure) of the structure. For example, enter the file name BENZALD for the 2D structure (the two-dimensional representation of a molecule) of Benzaldehyde:

Or, enter the file name BENZFRAG for any of these 2D substructures (any portion of a 2D structure) of Benzaldehyde:

Entering the File Name of a Structure

You can enter the file name of the structure in several ways:

*	To enter a structure that is on the form in ISIS/Base, double-click query (or mquery) in the Structures box.

*	To enter a structure that was saved in the database, double-click the name of the structure in the Structures box.

*	To enter a structure that was saved as a molfile, click Read Structure, enter the name of the structure in the Files text box, click OK, and then double-click the name of the structure in the Structures box. (A molfile is a file in CTfile (chemical table files) format that contains either a single molecular structure or disjointed structural fragments.)

You see the structure in the box at the bottom-right corner of the Query Builder.

50.2.3 Searching Top-Level and Lower Level Records

When you combine two or more queries of any type into a single QB search, the search results that you obtain depend on both the specifications and accuracy of your query and the way that information is stored in your database.

Information in a database is stored either in a single level (called a flat database) or in multiple levels (called a hierarchical database). Storage in a hierarchical database is more efficient, but it requires you to enter your queries in the correct location on the form to obtain the search results that you want. For example, the following hierarchical database stores data for multiple decomposition tests that are conducted under different atmospheric conditions:

In this database, structures are stored at the top (or root) level, and the percentage of oxygen and the number of peaks are stored at a lower level, under the parent field Decomposition. A parent field is a branch in the hierarchy that contains a set of child fields, such as percent O2 and number of peaks.

You want specific decomposition data from different tests. Your multiple query in a single QB search specifies that you want all compounds within a single test that contain: Query 1, greater than 65% O2; Query 2, less than three peaks. To obtain search results that match either one query or the other (Query 1 OR Query 2), enter:

ROOT>DECOMPOSITION>Percent_O2 > 65 OR ROOT>DECOMPOSITION > Peaks < 3

This search gives you all compounds within a single test that meet either requirement in your query (but not necessarily both requirements). To obtain search results that match all queries (Query 1 AND Query 2), specify the hierarchy level that you want to search at the beginning of the search syntax. Then enclose the remainder of the query in double parentheses (If you do not specify a hierarchy level that you want to search, ISIS searches the top-level records in the database.):

ROOT>DECOMPOSITION ((ROOT>DECOMPOSITION>Percent_O2 > 65 AND ROOT>DECOMPOSITION > Peaks < 3))

This search does gives you all compounds within a single test that meet both requirements in your query.

Note: When you filter your search results, you see solely those lower-level records that meet your search requirements.

50.3 Definition of Aromaticity

For local databases: A bond is aromatic if it is in a six-membered ring with alternating double and single bonds, such as benzene.

Note: Aromaticity is not perceived for fused rings in which the double bonds are arranged in a way that cannot be defined as aromatic.

50.4 Specifying Query Features on Atoms and Bonds in Structures

A query feature on an atom and/or a bond in a molecule is a restriction that specifies the retrieval of certain types of molecule records from an ISIS/Base database.

If you do not use query features, the molecules retrieved contain solely your exact substructure query embedded wholly within them. For example:

50.4.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

50.4.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of hydrogens. For example:

50.4.3 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

50.4.4 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

50.4.5 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

50.4.6 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

50.5 Specifying Stereochemistry

For local databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

An SSS search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve molecules with matching cis or trans stereochemistry. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An SSS search produces the following results:

50.6 Guidelines for Revising the Query

If your QB search retrieved no records or too few records, you might want to:

*	Conduct a QB search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the structural constraints in your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, or remove stereochemical requirements.

*	Make the text/numeric strings in your query more general, and then search the same set of records. For example, you can apply operators that partially restrict, such as > or between instead of =, or you can apply wildcards. (A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters.)

If your QB search retrieved too many records, you might want to:

*	Refine the structural constraints in your query, and then search the same set of records. For example, you can limit substitution at specific positions with explicit hydrogens, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Make the text/numeric string in your query more restrictive, and then search the same set of records. For example, you can use the operator = instead of >.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	First conduct a formula search to screen out large and complex molecules that are stored in your database, and then conduct a search on the less complex molecules. If your query is not able to map a stored molecule within a specific length of time, the molecule is added to the search results.

*	Filter your search results so that you view solely the lower-level records. (This assumes that you are viewing both upper- and lower-level records.)

50.7 Searching Example 1: Combining Text/Numeric Queries

This searching example shows you how to conduct a single QB search with a query that contains two text/numeric strings.

50.7.1 Problem

You want to retrieve all molecules that meet both of the following requirements:

*	Have a molecular weight greater than 250

*	Contain two or three oxygen atoms

50.7.2 Approach

In the Query Builder text box in ISIS/Base:

1.	Enter the database field MOL>MOLECULAR.WEIGHT.

2.	(Optional) Enter a space.

3.	Enter the search operator >.

4.	(Optional) Enter a space.

5.	Enter the target value 250.

6.	(Optional) Enter a space.

7.	Enter the boolean algebraic operator AND. (Alternatively, to find records that meet either requirement, enter OR.)

8.	(Optional) Enter a space.

9.	Enter the database field MOL>MOLFORMULA.

10. (Optional) Enter a space.

11. Enter the search operator LIKE. You use the search operator LIKE instead of the search operator = with target values that contain text. In this example, the o (for oxygen) is text.

12. (Optional) Enter a space.

13. Enter the target value "o(2-3)". Enter all target values with the search operator LIKE in double quotation marks, where o is either in upper- or lower-case characters.

14. Conduct a QB search in the local molecule database of you choice, such as the LOCALMX demo database.

50.7.3 Query

In the Query Builder text box, you see the following query:

50.7.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for QB, how to/examples.

50.7.5 Results

You retrieve records with molecules that have a molecular weight greater than 250 and that contain two or three oxygens.

50.8 Searching Example 2: Combining Text/Numeric and Graphical Queries

This searching example shows you how to conduct a single QB search with a query that contains a text/numeric string query component and a graphical query component.

50.8.1 Problem

You want to retrieve all molecules that meet both of the following requirements:

*	Contain a steroid substructure embedded wholly within them

*	Have a melting point that is greater than 220 degrees Centigrade

50.8.2 Approach

Note: This example assumes that you have previously created a graphical structure with the file name STEROID.MOL (Mac = STEROID) that you stored with the database.

To find results that match the text/numeric string query component or the graphical query component, in the Query Builder text box in ISIS/Base:

1.	Enter the database field MOL>MELTING.POINT>MELTING.POINT.

2.	(Optional) Enter a space.

3.	Enter the search operator >. This portion of your query executes a search that retrieves all molecules that are greater than your target value.

4.	(Optional) Enter a space.

5.	Enter the target value 220.

6.	(Optional) Enter a space.

7.	Enter the boolean algebraic operator AND. (Alternatively, to find records that meet either requirement, enter OR.)

8.	(Optional) Enter a space.

9.	Enter the database field MOL>MOLSTRUCTURE.

10. (Optional) Enter a space.

11. Enter the search operator SSS. This portion of your query executes a molecule substructure search (SSS) that retrieves all molecules that contain your target value (in this case, your graphical substructure) embedded wholly within them.

12. (Optional) Enter a space.

13. Enter the target value that is the file name of the graphical substructure that you want to use. For example, enter the file name STEROID.MOL (Mac = STEROID). Alternatively, if you want to use the graphical query that you see on the form in ISIS/Base, you can enter the temporary file name QUERY. If you cannot remember the file name of the stored query that you want to use, you are prompted to browse specific directories and to read in the file name that you want.

14. Conduct a QB search in the local molecule database of you choice, such as the LOCALMX demo database.

50.8.3 Query

In the Query Builder text box, you see the following query:

50.8.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for QB, how to/examples.

50.8.5 Results

You retrieve records with molecules that have a melting point greater than 220 and that contain the steroid substructure in your query.


Remote QB in a Reaction Database: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote QB Search in a Reaction Database	51.1

*	Specifying a QB Query	51.2

*	Definition of Aromaticity	51.3

*	Specifying Query Features on Atoms and Bonds in Structures	51.4

*	Specifying Rgroup Query Features	51.5

*	Specifying Stereochemistry	51.6

*	Specifying Query Features on a Reaction	51.7

*	Specifying an Atom-Atom Map on a Reaction	51.8

*	Guidelines for Revising the Query	51.9

*	Searching Example 1: Combining Text/Numeric Queries	51.10

*	Searching Example 2: Combining Text/Numeric and Graphical Queries	51.11

We recommend that you print this 39-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote QB search in a reaction database, click here.

51.1 Definition of a Remote QB Search in a Reaction Database

You can use the remote Query Builder (QB) search to create any of the other remote searches in ISIS. However, you must use an all-text search query. Thus, we recommend that you use another type of search where possible!

A QB search does have one unique feature: You can combine AND, OR and NOT boolean operators in a search query. For example:

To find all reactants that contain benzaldehyde AND all reactants with a melting point greater than 220 degrees, enter:

To find all reactants that contain both indole and a molecular weight greater than 200 but NOT those reactants with a melting point below 190, enter:

To find all reactants that do NOT contain benzaldehyde embedded wholly within them, enter:

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

Note: If your query retrieves data that you perceive to be in the wrong place on the form, see your ISIS Administrator. (This might be the result of specifying the same name for multiple database fields on your form or in the Hview.)

51.2 Specifying a QB Query

Each QB query contains:

*	The database field that you want to search.

For example, to search the melting point field of a reactant, enter either the full path name, RXN>reactant_link>MELTING.POINT>MELTING.POINT, or the minimum tree name that uniquely identifies the field, namely MELTING.POINT. To search the reactant structure field, enter either the full path name RXN>reactant_link>MOL>MOLSTRUCTURE.

*	A search operator that specifies the type of search (such as a greater than sign, >, to specify a search that finds solely the target text in the query).

*	The text or numeric target value (specific data) that you want to find. (In addition, your target value can be a file name that corresponds to a structure that you want to retrieve.)

A text or numeric target value can contain wildcards. A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. For example, you can specify the query LIKE "%ALD%" (instead of the query LIKE "BENZALDEHYDE"). The wildcard _ is a placeholder for solely one unspecified character. For example, you can specify the query LIKE "_CHLOROBENZENE" (instead of the query LIKE "2-CHLOROBENZENE"). Target values that contain text or wildcards require double quotation marks.

Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

Note: You cannot use the query LIKE "_" if you search a REACCS database.

For example, to find records that contain reactant structures with a melting point that is greater than 220, enter:

RXN>reactant_link>MELTING.POINT>MELTING.POINT>MELTING.POINT > 220

Note: You can combine statements in a single text/numeric string with one of the logical operators AND, OR, and NOT. When you use the NOT operator, enclose the text/numeric string in parentheses. For example, enter:

NOT (RXN>reactant_link>MELTING.POINT>MELTING.POINT>MELTING.POINT > 220)

51.2.2 The Search Operators

=, <, <=, >, =>, <>

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Search Operator	Definition	Examples

=	equal (numeric)	MOLECULAR.WEIGHT = 350

<	less than (numeric)	MOLECULAR.WEIGHT < 350

<=	less than or equal to (numeric)	MOLECULAR.WEIGHT <= 350

>	greater than (numeric)	MOLECULAR.WEIGHT > 350

>=	greater than or equal to (numeric)	MOLECULAR.WEIGHT >= 350

<>	not equal to (text or numeric)	MOLECULAR.WEIGHT <> 350

ACTIVITY <> "inhibitor"

For a MOLFORMULA field, an exact formula query retrieves records that contain solely the exact atoms that you specify. To create an exact formula query, specify the target value for the formula. The target value must include all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required. The equals operator (=) and quotes are optional. For example:

Exact Formula Query	Examples of Records Retrieved

c6 h6 O	Phenol

c6h6o

C20 H12 Na2 O4	Sodium salt of phenolphthalein

C20H12Na2O4

= C20 H12 Na2 O4

= C20H12Na2O4

= "C20 H12 Na2 O4"

= "C20H12Na2O4"

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Exact Formula Query	Examples of Records Retrieved

C17 H19 N 03	Piperine

C17H19N 03	Piperine

C17H19N103	Piperine

C17H19N03	No molecules retrieved. ISIS interprets "NO3" as 3 Nobelium atoms.

LIKE

Use LIKE with text enclosed in double quotation marks. Enter your query as follows:

Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. For example:

Query	Examples of Records Retrieved

COMPOUND.NAME LIKE "methane"	Methane

COMPOUND.NAME LIKE "benzoic acid"	Benzoic Acid

COMPOUND.NAME LIKE "%acid"	Benzoic Acid

Acetic Acid

COMPOUND.NAME LIKE "%acid%"	Benzoic Acid Sodium Salt

Acetic Acid Sodium Salt

COMPOUND.NAME LIKE "%but_ne"	Trans 2-Butene

2-Butene

N-Butane

Butane

Butene

COMPOUND.NAME LIKE "_ethyl"	Methyl

Ethyl

ACTIVITY LIKE "antibiotic"	Antibiotic

ACTIVITY LIKE "%antibiotic%"	Antibiotic activity

Resistance to antibiotics

Note: To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice. To retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: ACTIVITY LIKE "aa""a" or ACTIVITY LIKE"%aa""a%".

For a MOLFORMULA field, a subformula query retrieves records that contain the specific atoms that you specify, and any additional atoms. To create a subformula query, use the LIKE operator with a target value. The target value can include a range of atom counts, and typically excludes the hydrogens. To exclude specific atoms from the molecules that you retrieve, specify zero for that atom. You can use a single space to separate atoms. Capital letters are not required. Quotes are optional.

Subformula Query	Examples of Records Retrieved

LIKE Na	All sodium salts

LIKE c12 Br(1-2) S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE "C12Br(1-2)S2"	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE c6 h6	All molecules that contain six carbon atoms, six hydrogen atoms, and any number of other atoms

LIKE C5 H10 N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

LIKE C5H10N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Subformula Query	Examples of Records Retrieved

LIKE C12 Br S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12Br1S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12BrS2	No molecules retrieved. ISIS interprets "BrS" as an atom symbol, and gives an error message.

BETWEEN

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks. For example:

CORPORATE.ID BETWEEN "XR11" "XZ15"

CORPORATE.ID BETWEEN 95 100

EXISTS

Use EXISTS to retrieve all records in the database that contain data in a specific database field. For example:

RXN>reactant_link>MOL>MOLSTRUCTURE EXISTS

To retrieve all records in the database that contain no data in a specific database field, use NOT in your query:

NOT (RXN>reactant_link>MOL>MOLSTRUCTURE EXISTS)

Note: You can only use the EXISTS search operator for certain types of database fields. Using EXISTS with other types of fields produces an error message.

SSS

Use SSS to retrieve database structures that contain your graphical query as a reactant substructure (without a reaction arrow) or a product substructure (without a reaction arrow) embedded wholly within them. For example (query is the file name of your graphical query):

RXN>reactant_link>MOL>MOLSTRUCTURE SSS query

ISOMER

Use ISOMER to retrieve database structures that contain your graphical query as a geometric isomer or a stereoisomer. For example (query is the file name of your graphical query):

RXN>reactant_link>MOL>MOLSTRUCTURE ISOMER query

TAUTOMER

Use TAUTOMER to retrieve database structures that contain your graphical query as a tautomer. For example (query is the file name of your graphical query):

RXN>reactant_link>MOL>MOLSTRUCTURE TAUTOMER query

PARENT

Use PARENT to retrieve database structures that contain your graphical query as a parent structure of a salt. For example (query is the file name of your graphical query):

RXN>reactant_link>MOL>MOLSTRUCTURE PARENT query

FLEXMATCH

Use FLEXMATCH to retrieve database structures that contain your graphical query as a loosely fitting exact match. With this search operator, you define the default exact match parameters or specify your own (called flexmatch parameters). For example, to specify that all bond types must match (BON, in single or double quotes) for a graphical reactant query that you named steroid, enter:

RXN>reactant_link>MOL>MOLSTRUCTURE FLEXMATCH steroid 'BON'

To specify that all bond types must match (BON) and that all metal bonds must match (MET), enter:

RXN>reactant_link>MOL>MOLSTRUCTURE FLEXMATCH steroid 'BON/MET'

When you specify multiple flexmatch parameters, separate them with a forward slash, /. In addition, enclose all flexmatch parameters within the same set in single or double quotes. To specify any other flexmatch parameters, see Section 51.2.3.

MSIMILAR

Use MSIMILAR to retrieve database structures (such as reactants or products, without reaction arrows) that are structurally similar to your graphical query. With this search operator, you can define the degree of similarity in your query to be an arbitrary value between 0 and 100 (these are not actual units). The higher the value, the more similarity. For example, to specify a structural similarity value of 10 (in single or double quotes) for a graphical reactant query that you named steroid, enter:

RXN>reactant_link>MOL>MOLSTRUCTURE MSIMILAR steroid '10'

You can also specify that the retrieved records contain the same structural complexity as your query (enter NORMAL), more structural complexity than your query (enter SUB), or less structural complexity than your query (enter SUPER). For example, to specify that the retrieved records contain more structural complexity than your query, enter:

RXN>reactant_link>MOL>MOLSTRUCTURE MSIMILAR steroid 'SUB 10'

RSS

Use RSS to retrieve database structures that contain your graphical query as a reaction substructure, a reactant substructure (with a reaction arrow), or a product substructure (with a reaction arrow) embedded wholly within them. For example (query is the file name of your graphical query):

RXN>RXNSTRUCTURE RSS query

SUBSET

Use SUBSET to retrieve database structures that contain your graphical query as the exact match of a reactant with a reaction arrow or a product with a reaction arrow. This is equivalent to the REXACT/Comp search that you might see elsewhere in this version of ISIS. For example (query is the file name of your graphical query):

RXN>RXNSTRUCTURE SUBSET query

RSIMILAR

Use RSIMILAR to retrieve database structures that are structurally similar and or transformationally similar to your graphical query (that is a reaction). With this search operator, you can define the degree of structural or transformational similarities in your query to be arbitrary values between 0 and 100 (these are not actual units). In each case, the higher the value, the more similarity. For example, to specify a structural similarity value of 10 (in single or double quotes) for a graphical query that you named query, enter:

RXN>RXNSTRUCTURE RSIMILAR query '10'

To specify a structural similarity value of 10 and a transformational similarity value of 65, enter the QB query (with a comma and a single space between both values in single or double quotes):

RXN>RXNSTRUCTURE RSIMILAR query '65, 10'

You can also specify that the retrieved records contain more structural complexity than your query (enter SUB), or less structural complexity than your query (enter SUPER). For example, to specify that the retrieved records contain more structural complexity than your query, enter:

RXN>RXNSTRUCTURE RSIMILAR query 'SUB 10'

51.2.3 Specifying Flexmatch Parameters

A Flexmatch (FLEX) search finds records that are an exact match of your query, except in the ways that you specify with any of the flexmatch parameters. You specify features of retrieved structures that must match your query. If you specify flexmatch parameters, you tighten the definition of an exact match. This allows you to find structures that:

*	Have different counterions than the salt in your query.

*	Match your query, but have different isotopic labels.

*	Match your query, but might be represented differently in the database. For example, the pi-metal bonds in ferrocene can be represented in different ways.

Flexmatch parameters define the features of retrieved molecules that must match your query molecule. When you specify flexmatch parameters, you tighten the definition of an exact match. (If you do not specify flexmatch parameters, you retrieve the loosest possible match that is possible for an exact match.) The flexmatch parameters are as follows:

Bond Type (BON)

BON specifies that all bond types must match.

Tautomer (TAU)

TAU specifies that tautomer groups must contain the same number of hydrogens in the tautomeric region, within a tolerance limit. The tolerance limit is the sum of the absolute values of charges plus the sum of the number of radicals plus the number of metal bonds. Diradicals count as two radicals. (If you specify TAU and also specify HYD, the tolerance limit is zero.)

A tautomer is a group of atoms with any of the following patterns:

Where	Q = O, N, S, Se, or Te

X = C, O, N, S, Se, or Te

Y = C, I, P, As, Sb, Cl, or Br

You can have multiple tautomeric groups in a single molecule. For example:

In addition, any bonds in the tautomeric region can be aromatic. For example:

Atom charges (CHA)

CHA specifies that the charge on each atom must match those in your query. This automatically ensures that the sum of the charges on each fragment must match.

Ion charges (ION)

ION specifies that the total charge for each fragment in the query must match.

Fragments (FRA)

FRA specifies that all fragments must match your query, and that no additional fragments are allowed.

For example, a single query that contains solely fragments A and B retrieves molecules that contain solely fragments A and B. However, the same query does not retrieve molecules that contain solely fragment A, solely fragment B, or fragments A, B, and C (where C is any fragment that is not in the query).

Note: Salt queries that contain fragment B as the counterion retrieve solely Fragment A, where A is the parent of the salt.

Hydrogen (HYD)

HYD specifies that hydrogen count must match for each fragment in your query.

If you do not specify HYD, the hydrogen count within a tolerance limit for each of the fragments must match. The tolerance limit is the sum of the absolute values of charges plus the sum of the number of radicals plus the number of metal bonds. Diradicals count as two radicals.

If you specify TAU and HYD, the hydrogen count must match exactly in both the tautomeric regions and in the individual atoms of non-tautomeric regions.

If you specify TAU, but do not specify HYD, the hydrogen count must match within the tolerance limit in both the tautomeric regions and in the individual atoms of non-tautomeric regions.

Isotopes (MAS)

MAS specifies that the isotopic labels on each atom must match those in your query. (Isotopic labels include H, D, and T.)

If you do not specify MAS, you retrieve molecules in the database that have different isotopic labels, and H, D, and T are equivalent to each other.

Metal (MET)

MET specifies that the connectivity of all metals must match your query. A metal is any atom other than H, D, T, He, B through Ne, Si through Ar, As through Kr, Te, I, Xe, At, and Rn.

If you do not specify MET, you can retrieve all the different representations of your query. For example, to retrieve all representations of ferrocene even though the pi-metal bonds are represented in different ways in your database, do not specify MET.

If you do not specify MET, and also do not specify SAL, any counterions that are attached to the metal are removed.

Radicals (RAD)

RAD specifies that the radical value on each atom must match those in your query.

Salts (SAL)

SAL specifies that the counterions in the structures retrieved must match the counterion in your query. A counterion is any fragment or single atom in the SALTS.DAT file (or equivalent). This file is customizable. For more information, see your ISIS Administrator.

If you do not specify SAL, you retrieve molecules with different counterions than those in your salt query.

If you do not specify SAL, and also specify FRA, you retrieve solely the parent structures of salts.

Stereoconfiguration (STE)

You can specify that the configuration of stereo centers (in geometric and optical stereoisomers) must match. You can only use this feature if you also specify BON.

If your query contains unspecified stereo centers, you retrieve solely those structures with unspecified stereo centers. An unspecified stereo center is the asymmetric center of atoms C, N, O, P, S, or Si, that is connected to one of the following:

*	No stereo bonds

*	An EITHER query bond (specifies either the Up or Down stereoconfiguration)

*	A DOUBLE EITHER bond that (specifies either the cis or trans stereoconfiguration)

Valence (VAL)

VAL specifies that the valence on each atom must match those in your query.

Notes: (1) If no valence is specified, an implicit valence is calculated from the structure. A query with an unspecified valence (with a calculated implicit valence) might retrieve a structure that contains the matching explicit valence. Or, a query with an explicit valence might retrieve a structure that does not contain an explicit valence (that contains a calculated implicit valence). (2) Some valences are illegal. For transition metals, a valence is illegal if it is smaller than the number of bonds to the atom. For other real atom types, an illegal valence is ignored in a FLEX search and the query retrieves any valence.

The Most Restricted Flexmatch Parameters

To retrieve the most restricted exact match of your FLEX query from the database, specify all flexmatch parameters. For example:

RXN>reactant_link>MOL>MOLSTRUCTURE FLEXMATCH query "FRA/HYD/MAS/MET/RAD/SAL/STE/VAL/BON/TAU/ION/CHA"

The Least Restricted Flexmatch Parameters

To retrieve the least restricted exact match of your FLEX query from the database, specify no flexmatch parameters. For example:

RXN>reactant_link>MOL>MOLSTRUCTURE FLEXMATCH query ""

Examples of the Interactivity of Flexmatch Parameters

The flexmatch parameters are typically interactive. To obtain the correct results, you need to know which flexmatch parameters require other flexmatch parameters to function correctly. With the correct interactive settings, you can retrieve closely related structures that are represented in a variety of ways in your database. For example:

*	MDL depicts sulfones with undisplayed charges in which two of the four bonds on the sulfur atom are double bonds. In your database, these compounds might be displayed with charges instead:

You need to consider both charges and bond types. To retrieve all representations of a specific sulfone, use the following query:

RXN>reactant_link>MOL>MOLSTRUCTURE FLEXMATCH query ""

Note: You can specify other flexmatch parameters to tighten the definition of exact match. However, you must not specify TAU or ION.

*	MDL depicts sulfoxides with undisplayed charges in which there is a double bond on the sulfur atom. In your database, these compounds might be displayed with charges instead:

You need to consider both charges and bond types. To retrieve all representations of a specific sulfoxide, use the following query:

RXN>reactant_link>MOL>MOLSTRUCTURE FLEXMATCH query "TAU/ION"

Note: You can specify other flexmatch parameters to tighten the definition of exact match. However, you must not specify CHA or BON.

*	MDL depicts thiocarboxylic acid salts with undisplayed charges in which there is a bond from the ion to the counterion. In your database, these compounds might be displayed with charges instead:

You need to consider charges, bond types, and metal bonds. To retrieve all representations of a specific salt, use the following query:

RXN>reactant_link>MOL>MOLSTRUCTURE FLEXMATCH query "BON/TAU"

Note: You can specify other flexmatch parameters to tighten the definition of exact match. However, you must not specify MET, CHA, SAL, FRA, or ION.

*	MDL depicts π ligands in organometallic complexes with radicals or with covalent bonds. You need to consider charges, bond types, metal bonds, and radicals. To retrieve all representations of a specific organometallic complex, use the following query:

RXN>reactant_link>MOL>MOLSTRUCTURE FLEXMATCH query "TAU"

Note 1: You can specify other flexmatch parameters to tighten the definition of exact match. However, you must not specify BON, CHA, ION, MET, or RAD.

Note 2: You can also retrieve specific organometallic complexes with an exact formula query in an FMLA search.

51.1.3 Specifying a Structure in a QB Query

To include a structure (a graphical component) in your QB query, such as a reactant, a product, or a reaction, you need to do the following in the Query Builder text box:

*	Enter the name of the database field that will hold your graphical search results. For a reactant record, enter RXN>reactant_link>MOL>MOLSTRUCTURE. For a product record, enter RXN>product_link>MOL>MOLSTRUCTURE. For a reaction record, enter RXN>RXNSTRUCTURE.

*	Enter the search operator, such as SSS, the equal sign (to specify that the structures retrieved contain your graphical query as a substructure embedded wholly within them).

Note: You can only use SSS as a search operator if your query is a structure without a reaction arrow. If your structure contains a reaction arrow, use RSS instead.

*	Enter the file name (not the structure) of the structure. For example, you might enter the file name BENZALD for the 2D structure (the two-dimensional representation of a molecule) of Benzaldehyde:

Or, you might enter the file name BENZFRAG for any of these 2D substructures (any portion of a 2D structure) of Benzaldehyde:

Entering the File Name of a Structure

You can enter the file name of the structure in several ways:

*	To enter a structure that is on the form in ISIS/Base, double-click query (or mquery) in the Structures box.

*	To enter a structure that was saved in the database, double-click the name of the structure in the Structures box.

*	To enter a structure that was saved as a molfile (without a reaction arrow), click Read Structure, enter the name of the structure in the Files text box, click OK, and then double-click the name of the structure in the Structures box. A molfile is a file in CTfile (chemical table files) format that contains either a single molecular structure or disjointed structural fragments.

*	To enter a reaction component (with a reaction arrow) or an entire reaction that was saved as a rxnfile, click Read Structure, enter the name of the reaction in the Files text box, click OK, and then double-click the name of the reaction in the Structures box. A rxnfile is a file in CTfile (chemical table files) format that contains the structural information for the reactants and products of a single reaction.

You see the structure in the box at the bottom-right corner of the Query Builder.

51.2.4 Searching Top-Level and Lower Level Records

When you combine two or more queries of any type into a single QB search, the search results that you obtain depend on both the specifications and accuracy of your query and the way that information is stored in your database.

How Information Can Be Stored

Information in a database is stored either in a single level (called a flat database) or in multiple levels (called a hierarchical database). Storage in a hierarchical database is more efficient, but it requires you to enter your queries in the correct location on the form to obtain the search results that you want.

A typical hierarchical database is as follows:

The top (or root) level in the hierarchy stores the reaction structure and ID number for each reaction record, and the lower level in the hierarchy stores the literature references and variations for each reaction structure. LITREF is the parent field for the database fields journal and author, and VARIATION is the parent field for the database fields variation number (varno), solvent, and yield. Each reaction record might have multiple literature references and multiple variation subrecords associated with it.

Obtaining the Correct Search Results From a Hierarchical Database

If you search a hierarchical database for lower level records with multiple text/numeric strings in a single QB search, how you enter your query into the Query Builder text box is significant.

For example, the following hierarchical database stores data for multiple decomposition tests that are conducted under different atmospheric conditions:

(In this database, structures are stored at the top (or root) level, and the percentage of oxygen and the number of peaks are stored at a lower level, under the parent field Decomposition. A parent field is a branch in the hierarchy that contains a set of child fields, such as percent O2 and number of peaks.)

You want specific decomposition data from different tests. Your multiple query in a single QB search specifies that you want all compounds within a single test that contain: Query 1, greater than 65% O2; Query 2, less than three peaks.

To obtain search results that match either one query or the other (Query 1 OR Query 2), enter:

ROOT>DECOMPOSITION>Percent_O2 > 65 OR ROOT>DECOMPOSITION > Peaks < 3

This search gives you all compounds within a single test that meet either requirement in your query (but not necessarily both requirements).

To obtain search results that match all queries (Query 1 AND Query 2), specify the hierarchy level that you want to search at the beginning of the search syntax. Then enclose the remainder of the query in double parentheses (If you do not specify a hierarchy level that you want to search, ISIS searches the top-level records in the database.):

ROOT>DECOMPOSITION ((ROOT>DECOMPOSITION>Percent_O2 > 65 AND ROOT>DECOMPOSITION > Peaks < 3))

This search does gives you all compounds within a single test that meet both requirements in your query.

When you filter your search results, you see solely those lower-level records that meet your search requirements.

51.3 Definition of Aromaticity

For remote databases: ISIS interprets the following ring systems as aromatic:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:

Note: The bonds of six-membered aromatic ring systems and the perimeter bonds of azulenes are stored as aromatic bonds in the database. The bonds of five-membered aromatic rings, however, are stored as single and double bonds and interpreted as aromatic during a search. The differences between five-membered rings and other types of aromatic rings can cause different search results for five- and six-membered rings/azulenes when you use the following bonds in queries: Single, Double, and Single/Double query bonds. For more information on the Single/Double query bond, see Section 51.4.7.

51.4 Specifying Query Features on Atoms and Bonds in Structures

A query feature on an atom and/or a bond in a reaction component is a restriction that specifies the retrieval of certain types of reaction records from an ISIS/Base database.

If you do not use query features, the records retrieved contain solely your exact substructure query embedded wholly within them. For example:

51.4.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

51.4.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of hydrogens. For example:

51.4.3 Allowing an Unsaturated Atom

Use an atom query feature to specify that an atom is attached to at least one multiple bond (double, triple, or aromatic).

Atom Query Feature: Unsaturated Atom (u)

Specifies that the atom of your choice is attached to at least one multiple bond (double, triple, or aromatic). For example, the following query specifies both an unsaturated atom (u) and single or double bonds (the double dashed lines).

51.4.4 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

Atom Query Feature: Substitution Count of Zero, s0

Specifies that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of a single atom with attached hydrogens (if any).

Atom Query Feature: Substitution Count of One, s1

Specifies that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Two, s2

Specifies that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Three, s3

Specifies that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Four, s4

Specifies that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Five, s5

Specifies that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of at Least Six, s6

Specifies that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count as Drawn, s*

Specifies that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:

51.4.5 Allowing a Specific Number of Ring Bond Attachments

Use atom query features to specify the number of ring bond attachments.

Atom Query Feature: Ring Bond Count of Zero, r0

Specifies that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:

Atom Query Feature: Ring Bond Count of Two, r2

Specifies that the records retrieved have solely two ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of Three, r3

Specifies that the records retrieved have solely three ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of at Least Four, r4

Specifies that the records retrieved have at least four ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count as Drawn, r*

Specifies that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:

51.4.6 Allowing Additional Atoms and/or Bonds in a Chain or a Ring

Use a query feature that is for either atoms or bonds to specify the addition of atoms and/or bonds in a chain or a ring.

Atom or Bond Query Feature: Link Node

Use a link node to specify the addition of variable numbers repeating units (atoms and/or bonds) to a ring or chain. A repeating unit must be attached to two adjacent bonds. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the link node [L1-3]:

Or, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the link node [L1-3]:

51.4.7 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Note: An aromatic query bond hits any bond in all types of aromatic rings: 6-membered ring bonds, 5-membered ring bonds, and azulene perimeter bonds. For more information on the structures that ISIS interprets as aromatic, see Section 51.3.

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

Note: A Single/Double query bond does not hit bonds in 6-membered aromatic rings, or perimeter bonds of azulenes, because bonds in these structures are stored in the database as aromatic bonds. However, a Single/Double query bond does hit bonds in 5-membered rings that ISIS interprets as aromatic. For more information on the structures that ISIS interprets as aromatic, see Section 51.3.

Bond Query Feature: Single/Aromatic Bond

Specifies either a single or an aromatic bond at that position:

Bond Query Feature: Double/Aromatic Bond

Specifies either a double or an aromatic bond at that position:

51.4.8 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

51.4.9 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

51.5 Specifying Rgroup Query Features

An Rgroup query finds structures that contain your query as a root structure with defined Rgroup substituents attached to it at specific positions. Your query can contain restrictions on the Rgroup substituents, called Rgroup conditions: You can specify the number of Rgroup sites that must be occupied in the records retrieved, specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site, or specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

Your Rgroup query can also contain restrictions on atoms and bonds of the root structure and Rgroup substituents. For example, you can use the atom query feature H(0) to prohibit the attachment of implicit hydrogens on a specific atom in the structures retrieved.

An example of an Rgroup query is as follows:

51.5.1 The Root Structure

The root structure contains the portion of the structure that does not vary among the structures retrieved. For example, if you want to find 2, 5-Dihydroxypyridine in which the substituent at position 2 can be COOH, CN, or Ph, and the substituent at position 5 can be OH or CH3, the root structure is 2, 5-Dihydroxypyridine with Rgroups (such as R1 and R2):

Rgroups

On the root structure, Rgroups (R1 through R32) are placeholders that designate where the lists of functional groups and atoms that can attach to the root structure. In the example above, the Rgroup R1 designates that the members of the list R1 (the Rgroup substituents) are allowed at position 5 on the root structure. The Rgroup R2 designates that the members of the list R2 (the Rgroup substituents) are allowed at position 2 on the root structure.

Multiple Rgroups at One Position

You can specify multiple Rgroups at a single site on the root structure. For example:

One Rgroup at Multiple Positions

You can specify a single Rgroup (such as R1) at multiple positions on the root structure. For example:

Note: For information on how to restrict the number of Rgroups that must be occupied in the records retrieved, See Section 51.5.3, "Rgroup Conditions." A molecule need not satisfy all the Rgroup sites on the root structure to be retrieved. For example, the Rgroup condition R1 > 0 specifies that any molecule in which at least one of the R1 sites is filled by an R1 member will be retrieved. In addition, the Rgroup condition RestH determines whether the unsatisfied sites must be filled with hydrogen atoms or if other molecule fragments are allowed to be attached if they are not on the list.

51.5.2 Rgroup Substituents

Rgroup substituents are the members of the list of Rgroups. You define the Rgroup substituents that you will allow to be found at specified positions in the molecules retrieved. Rgroup substituents can be any structural fragment, including functional groups and single atoms.

In the example below, the Rgroup substituents COOH, CN, or Ph are allowed at position 5 (R1) on the root structure and the Rgroup substituents OH or CH3 are allowed at position 2 (R2) on the root structure:

Attachment Points

An attachment point (marked with an arrow and an asterisk) designates the atom on the Rgroup substituent that is attached to the root structure:

You must designate an attachment point on an Rgroup substituent for each bond that is attached to the substituent. If an Rgroup is attached to two bonds on the root structure, you must designate two attachment points. The bond on the root structure that is marked with double quotes corresponds to the attachment point on the Rgroup substituent that is marked with double quotes. The other attachment point on the Rgroup substituent is marked with a single quote:

Nested Rgroups

A nested Rgroup is an Rgroup that is a placeholder within another Rgroup rather than within the root structure. (You cannot nest an Rgroup any lower than this level.) In the following example, Rgroup R2 is nested within the Rgroup R1:

Nested Rgroups are equivalent to the following structures:

51.5.3 Rgroup Conditions

You can apply restrictions to each Rgroup in your query after you assemble all the Rgroups. The set of restrictions is called the Rgroup conditions.

If you do not apply Rgroup conditions, ISIS assigns the default conditions: Occurrence > 0 and RestH off for each Rgroup.

Occurrence

With the Rgroup condition Occurrence, you can specify the number of Rgroup sites that must be occupied in the records retrieved. For example, the occurrence designation R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved. Type one of the following values in the Occurrence range text box:

Value	Explanation

0	All members of the Rgroup are excluded from the Rgroup site (such as R1). To allow any other Rgroup substituent at the Rgroup site, set RestH to off.

> 0	At least one Rgroup must be satisfied. If RestH is off, any other substituent can attach to unsatisfied sites. If RestH is on, unsatisfied sites must be filled solely by hydrogens.

n	Exactly n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

< n	Less than n number of sites (including zero) must be satisfied. RestH controls substitution at unsatisfied sites.

m - n	Any number of sites falling within the range of m to n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

m,n,...	Any combination of the above expressions, separated by commas. For example: 1, 3-5, 9, >12.

For example, the Rgroup condition R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved.

In another example, the Rgroup condition R1 > 0 and R2 > 0 specifies that an Rgroup substituent from the R1 list AND an Rgroup substituent from the R2 list must occupy at least one site on the root structure in the records retrieved.

Finally, the Rgroup conditions R1 = 1, 3-5, 9, >12 specify that either 1, 3, 4, 5, 9, or more than 12 sites must be satisfied:

RestH

With the Rgroup condition RestH, you can specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site.

An unsatisfied Rgroup site is an Rgroup site on the root structure that does not have an Rgroup member attached: If RestH is off, any functional group or atom may be attached at unsatisfied Rgroup sites on the root structure. If RestH is on, solely hydrogens are allowed to be attached at unsatisfied Rgroup sites on the root structure.

If/Then

With the Rgroup condition If/then, you can specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

For example, If R1 then R2 specifies that if the conditions for R1 are satisfied, then the conditions for R2 must also be satisfied. (If the conditions for R1 are not satisfied, then the conditions for R2 are ignored.) The If/then condition implies that a molecule may be retrieved even though R1 is not satisfied.

In the following query, R1 contains a nitro group and a sulfonic acid group. R2 contains a chlorine atom. The condition If R1 then R2 specifies that if a nitro group or a sulfonic acid group is attached at R1 on the root structure, then a chlorine must also be attached at R2. However, if the R1 site on the root structure does not have either the nitro or the sulfonic acid group (R1 is unsatisfied), then R2 can have any substituent (R2 is ignored):

51.6 Specifying Stereochemistry

For remote databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve reactions with matching stereochemistry on the reaction components. For example:

An SSS search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve reactions with matching cis or trans stereochemistry on the reaction components. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An SSS search produces the following results:

Chiral Flags on Reaction Components

In a remote database, you can create a query with a chiral flag on a reaction component with at least one asymmetric center or on a reaction component that is asymmetric to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

51.7 Specifying Query Features on a Reaction

A query feature on a reaction is a restriction on reacting-center bonds that specifies the retrieval of certain types of reaction records from an ISIS/Base database.

You can restrict a reacting center bond to form, break, change its bond type, or change in an unspecified way or you can restrict a stereo bond to invert or retain its stereochemistry.

You can restrict an atom in a reaction to change exactly to your specifications.

51.7.1 Specifying Query Features on a Reacting Center

Use query features to specify whether a bond in a reacting center changes at all, changes in an unspecified way, or whether the bond specifically forms, breaks, or changes its bond type.

If you do not use a query feature on a reacting center, the transformations retrieved contain solely your exact substructure query embedded wholly within them, without regard to the chemistry that is involved in the reacting center.

For example, you want to retrieve solely indoles. Without a query feature on a reacting center, you might retrieve additional, unwanted transformations:

Reacting Center Query Feature: Not Center (X)

Specifies that a bond must not change in the records retrieved. For example, to specify the reduction of a carbonyl to an alcohol, the adjacent double bonds must not change as a result of the transformation:

Reacting Center Query Feature: Center (#)

Specifies that a bond changes in an unspecified way (can form, break, or change its bond type) in the records retrieved. For example, to specify the reduction of a nitrile to a primary amine:

Reacting Center Query Feature: Change (/)

Specifies that a bond changes solely its bond type in the records retrieved. For example, to change the bond type of all bonds in a cyclohexane reactant:

Reacting Center Query Feature: Make/Break (//)

Specifies that a bond is either formed or broken in the records retrieved. For example, to specify the formation of indoles (without also retrieving additional, unwanted results that are not indoles):

Reacting Center Query Feature: Make & Change (///)

Specifies that a bond is either formed or broken and that it changes its bond type in the records retrieved.

51.7.2 Specifying Query Features on a Stereo Bond

A stereo bond is an Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of any of the following atoms: C, N, O, P, S, or Si. Use query features on a stereo bond in the reactants and products of a transformation to specify whether the stereo bond inverts or retains its position.

If you do not use a query feature on a stereo bond, the transformations retrieved contain your exact substructure query embedded wholly within them.

Stereo Bond Query Feature: .Inv.

Specifies that the stereo bond is inverted in the records retrieved. For example:

Stereo Bond Query Feature: .Ret.

Specifies that the stereo is retained (does not invert) in the records retrieved. For example:

51.7.3 Specifying Exact Changes on an Atom in the Reaction

Atom Query Feature: .Ext.

Specifies that an atom changes exactly as you specify it in the reactants and products. (Mark at least one reactant and at least one product with this query feature.) No other changes may occur.

You must specify any changes in the number of hydrogens that are attached to this atom. For example, to show the chlorination of an ethyl group, draw a chlorine in the product that replaces an explicit hydrogen in the reactant. (Either draw the explicit hydrogen or specify a hydrogen count on the reactant at the site of chlorination.)

Note: You must apply atom-atom maps to the reaction before you use this query feature. (If you do not atom-atom map your reaction, this query feature is ignored during the search.

51.8 Specifying an Atom-Atom Map on a Reaction

An atom-atom map on the reaction components in a query specifies exactly which atoms in the reactants correspond to the atoms in the products. You can specify the atoms that must (or must not) change in the transformations that you retrieve.

For example, the following query allows you to see exactly which C-O bond is cleaved to form the product:

An atom-atom map eliminates additional, unwanted results. In this example, the atom-atom map eliminates transformations that produce an alcohol group that is not the result of the demethylation process.

51.8.1 Atom-Atom Map Automatically or Manually

To obtain the correct search results, you need to atom-atom map a reaction query. In ISIS, you can map either automatically or manually.

Automapping a Reaction Query (in ISIS/Base)

If you atom-atom map a reaction automatically, you execute the automap process in ISIS/Base. This process both maps your reaction query and adds any relevant reacting centers and any relevant stereo bond inversion and/or retention marks automatically.

Mapping a Reaction Query Manually (in ISIS/Draw)

If you atom-atom map a reaction manually (in ISIS/Draw), you can choose your own correspondence between the atoms in the reactants and the atoms in the products. However, the reacting centers (and stereo bond inversion and/or retention marks) are not added to your query automatically.

Note: After you atom-atom map a reaction query manually, if you want to add the reacting centers and/or stereo bond markings, you can either add them manually or you can automap the reaction query.

Guidelines for Mapping a Reaction Query

Use the following guidelines to help you to atom-atom map your query correctly:

Always atom-atom map a query that contains an entire reaction (at least a reactant and a product). Do not attempt to atom-atom map a query that contains solely a reaction component and a reaction arrow.

Note: We strongly recommend that you draw solely the reacting fragments (and use query features where relevant) rather than draw each reactant and product in detail.

Only map those specific atoms that you see in both the reactants and the products. For example, do not map the oxygen atom that you see only in the product:

To simplify the atom-atom mapping process, map your query automatically with the automap feature. However, there are specific times when you need to map a portion of your query manually, and then apply the automap feature to finish the task. For example, map a portion of your query manually if it is unbalanced or if it is mapped incorrectly with the automap feature.

An unbalanced reaction query is a reaction query that contains multiple mappings of a single atom. You need to manually map enough of the atoms to allow the automap feature to map your query correctly. Then select the entire query and automap it. For example:

*	Select a reactant atom and a product atom that you want to specify as Atom 1 and map them manually.

*	Select the same atom in the reactant and another atom in the product that you want to specify as Atom 1 (a multiple mapping of Atom 1) and map them manually. For example, you see the following:

*	Select the entire query and automap it.

Inspect the atom-atom maps on a reaction query before you use the query to conduct a search. If you notice that a map is incorrect, delete it entirely. You need to manually map enough of the atoms to allow the automap feature to map your query correctly. Then select the entire query and re-automap it.

Always atom-atom map a reaction query last, after you add all other structures, stereochemistry, and/or query features to your query.

51.9 Guidelines for Revising the Query

If your QB search retrieved no records or too few records, you might want to:

*	Conduct a QB search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the structural constraints in your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, remove substituent limits, or remove stereochemical requirements.

*	Make the text/numeric strings in your query more general, and then search the same set of records. For example, you can apply operators that partially restrict, such as > or between instead of =, or you can apply wildcards. (A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters.)

Notes: (1) To retrieve structures that contain Inversion (.Inv.), Retention (.Ret.), Exact Changes (.Ext.), and atom-atom maps, the structures in your database must contain these query features. (2) For REXACT or MEXACT searches in REACCS databases (Version 8.3 or higher) only: If your database is set up to allow duplicate reaction components to be retrieved in different orientations and you use a reaction as your query, you will not retrieve duplicate reaction components that were registered in a different orientation to those in your query. To retrieve all the duplicate reaction components with your reaction query, conduct an RSim search with a structural similarity value of 100 and a transformational similarity value of 100.

If your QB search retrieved too many records, you might want to:

*	Refine the structural constraints in your query, and then search the same set of records. For example, you can limit substitution at specific positions, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Mark the reacting centers in your query, and then search the same set of records.

*	Make the text/numeric string in your query more restrictive, and then search the same set of records. For example, you can use the operator = instead of >.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	Filter your search results so that you view solely the lower-level records. (This assumes that you are viewing both upper- and lower-level records.)

If your QB search retrieved incorrect records and your graphical query contained a transformation with atom-atom maps, you might want to:

*	Remap the atoms in your reaction substructure query.

51.10 Searching Example 1: Combining Text/Numeric Queries

This searching example shows you how to conduct a single QB search with a query that contains two text/numeric string query components.

51.10.1 Problem

You want to retrieve all reaction records that meet both of the following requirements:

*	Use the catalyst Na

*	Give product yields that are greater than 90%

51.10.2 Approach

To find results that match one or the other of the text/numeric query components, in the Query Builder text box in ISIS/Base:

1.	Enter the database field:

RXN>VARIATION>catalyst_link>MOL>*fmla_MOLSTRUCTURE

2.	(Optional) Enter a space.

3.	Enter the search operator LIKE.

4.	(Optional) Enter a space.

5.	Enter the target value "Na". Enter all target values with the search operator LIKE in double quotation marks.

6.	(Optional) Enter a space.

7.	Enter the boolean algebraic operator AND.

8.	(Optional) Enter a space.

9.	Enter the database field RXN>VARIATION>PRODUCT>YIELD.

10. (Optional) Enter a space.

11. Enter the search operator >.

12. (Optional) Enter a space.

13. Enter the target value 90. In the Query Builder text box, you see the following QB query:

RXN>VARIATION>catalyst_link>MOL>*fmla_MOLSTRUCTURE LIKE "Na" AND RXN>VARIATION>PRODUCT>YIELD > 90

This query does not specify which level in the database to search. By default, ISIS searches the top level of the database for reaction records.

14. Do one of the following:

*	To specify that both data requirements must be met within the same variation subrecord, enter your query in the following way in the Query Builder text box:

VARIATION(RXN>VARIATION>catalyst_link>MOL>*fmla_MOLSTRUCTURE LIKE "Na" AND RXN>VARIATION>PRODUCT>YIELD > 90)

ISIS must search the database for lower-level variation subrecords instead of top-level reaction records.

*	To find records that match one or the other text/numeric query components, in the Query Builder text box in ISIS/Base, enter:

VARIATION(RXN>VARIATION>catalyst_link>MOL>*fmla_MOLSTRUCTURE LIKE "Na" OR RXN>VARIATION>PRODUCT>YIELD > 90)

15. Conduct a QB search in the remote reaction database of you choice, such as the ISISRX demo database.

51.10.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for QB, how to/examples.

51.10.4 Results

If you joined the query components by AND, you retrieve records that match both text/numeric string query components.

Note: If you joined the query components by OR, you retrieve records that match one text/numeric string query component or the other (but not necessarily both).

If you filter your search results, you see solely those lower-level records that meet your search requirements.

51.11 Searching Example 2: Combining Text/Numeric and Graphical Queries

This searching example shows you how to conduct a single QB search with a query that contains a text/numeric string query component and a graphical (structure) query component.

51.11.1 Problem

You want to retrieve all reaction records that meet both of the following requirements:

*	Contain reactants that have a molecular weight greater than 250

*	Contain reactants that contain a steroid substructure embedded wholly within them

51.11.2 Approach

Note: This example assumes that you have previously created a graphical structure with the file name STEROID.MOL (Mac = STEROID) that you stored with the database.

To find results that match either the text/numeric string query component or the graphical query component, in the Query Builder text box in ISIS/Base:

1.	Enter the database field RXN>reactant_link>MOL>MOLECULAR.WEIGHT.

2.	(Optional) Enter a space.

3.	Enter the search operator >. This portion of your query executes a search that retrieves all reaction records with reactants that are greater than your target value.

4.	(Optional) Enter a space.

5.	Enter the target value 250.

6.	(Optional) Enter a space.

7.	Enter the boolean algebraic operator AND.

8.	(Optional) Enter a space.

9.	Enter the database field RXN>reactant_link>MOL>MOLSTRUCTURE.

10. (Optional) Enter a space.

11. Enter the search operator SSS. This portion of your query executes a reactant substructure search (SSS) that retrieves all reaction records with reactants that contain your target value (in this case, the substructure STEROID) embedded wholly within them.

12. (Optional) Enter a space.

13. Enter the target value that is the file name of the graphical substructure that you want to use. For example, enter the file name STEROID.MOL (Mac = STEROID). Alternatively, if you want to use the graphical query that you see on the form in ISIS/Base, you can enter the temporary file name QUERY. If you cannot remember the file name of the stored query that you want to use, you are prompted to browse specific directories and to read in the file name that you want.

14. Conduct a QB search in the remote reaction database of you choice, such as the ISISRX demo database.

51.11.3 Query

In the Query Builder text box, you see the following query:

51.11.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for QB, how to/examples.

51.11.5 Results

You retrieve records with molecules that have a melting point greater than 220 and that contain the steroid substructure in your query.


Local QB in a Reaction Database: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Local QB Search in a Reaction Database	52.1

*	Specifying a QB Query	52.2

*	Definition of Aromaticity	52.3

*	Specifying Query Features on Atoms and Bonds in Structures	52.4

*	Specifying Stereochemistry	52.5

*	Guidelines for Revising the Query	52.6

*	Searching Example 1: Combining Text/Numeric Queries	52.7

*	Searching Example 2: Combining Text/Numeric and Graphical Queries	52.8

We recommend that you print this 15-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a local QB search in a reaction database, click here.

52.1 Definition of a Local QB Search in a Reaction Database

You can use the local Query Builder (QB) search to create any of the other remote searches in ISIS. However, you must use an all-text search query. Thus, we recommend that you use another type of search where possible!

A QB search does have one unique feature: You can combine AND, OR and NOT boolean operators in a search query. For example:

To find all reactants that contain benzaldehyde AND all reactants with a melting point greater than 220 degrees, enter:

To find all reactants that contain both indole and a molecular weight greater than 200 but NOT those reactants with a melting point below 190, enter:

To find all reactants that do NOT contain benzaldehyde embedded wholly within them, enter:

A local search is a search over a database that typically exists on your hard disk. To do a local search on your hard disk, you do not need to input network information.

Note: To do a local search that is accessed from a shared network, you need to input network information.

52.2 Specifying a QB Query

Each QB query contains:

*	The database field that you want to search.

For example, to search the melting point field of a reactant, enter either the full path name, RXN>reactant_link>MELTING.POINT>MELTING.POINT, or the minimum tree name that uniquely identifies the field, namely MELTING.POINT. To search the reactant structure field, enter either the full path name RXN>reactant_link>MOL>MOLSTRUCTURE.

*	A search operator that specifies the type of search (such as a greater than sign, >, to specify a search that finds solely the target text in the query).

*	The text or numeric target value (specific data) that you want to find. (In addition, your target value can be a file name that corresponds to a structure that you want to retrieve.)

A text or numeric target value can contain wildcards. A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. For example, you can specify the query LIKE "%ALD%" (instead of the query LIKE "BENZALDEHYDE"). The wildcard _ is a placeholder for solely one unspecified character. For example, you can specify the query LIKE "_CHLOROBENZENE" (instead of the query LIKE "2-CHLOROBENZENE"). Target values that contain text or wildcards require double quotation marks.

Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

Note: You cannot use the query LIKE "_" if you search a REACCS database.

For example, to find records that contain reactant structures with a melting point that is greater than 220, enter:

RXN>reactant_link>MELTING.POINT>MELTING.POINT>MELTING.POINT > 220

Note: You can combine statements in a single text/numeric string with one of the logical operators AND, OR, and NOT. When you use the NOT operator, enclose the text/numeric string in parentheses. For example, enter:

NOT (RXN>reactant_link>MELTING.POINT>MELTING.POINT>MELTING.POINT > 220)

52.2.1 The Search Operators

<, <=, >, >=, and <>

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Search Operator	Definition	Examples

=	equal (numeric)	MOLECULAR.WEIGHT = 350

<	less than (numeric)	MOLECULAR.WEIGHT < 350

<=	less than or equal to (numeric)	MOLECULAR.WEIGHT <= 350

>	greater than (numeric)	MOLECULAR.WEIGHT > 350

>=	greater than or equal to (numeric)	MOLECULAR.WEIGHT >= 350

<>	not equal to (text or numeric)	MOLECULAR.WEIGHT <> 350

ACTIVITY <> "inhibitor"

For a MOLFORMULA field, an exact formula query retrieves records that contain solely the exact atoms that you specify. To create an exact formula query, specify the target value for the formula. The target value must include all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required. The equals operator (=) and quotes are optional. For example:

Exact Formula Query	Examples of Records Retrieved

c6 h6 O	Phenol

c6h6o

C20 H12 Na2 O4	Sodium salt of phenolphthalein

C20H12Na2O4

= C20 H12 Na2 O4

= C20H12Na2O4

= "C20 H12 Na2 O4"

= "C20H12Na2O4"

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Exact Formula Query	Examples of Records Retrieved

C17 H19 N 03	Piperine

C17H19N 03	Piperine

C17H19N103	Piperine

C17H19N03	No molecules retrieved. ISIS interprets "NO3" as 3 Nobelium atoms.

LIKE

Use LIKE with text enclosed in double quotation marks. Enter your query as follows:

Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. For example:

Query	Examples of Records Retrieved

COMPOUND.NAME LIKE "methane"	Methane

COMPOUND.NAME LIKE "benzoic acid"	Benzoic Acid

COMPOUND.NAME LIKE "%acid"	Benzoic Acid

Acetic Acid

COMPOUND.NAME LIKE "%acid%"	Benzoic Acid Sodium Salt

Acetic Acid Sodium Salt

COMPOUND.NAME LIKE "%but_ne"	Trans 2-Butene

2-Butene

N-Butane

Butane

Butene

COMPOUND.NAME LIKE "_ethyl"	Methyl

Ethyl

ACTIVITY LIKE "antibiotic"	Antibiotic

ACTIVITY LIKE "%antibiotic%"	Antibiotic activity

Resistance to antibiotics

Note: To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice. To retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: ACTIVITY LIKE "aa""a" or ACTIVITY LIKE"%aa""a%".

For a MOLFORMULA field, a subformula query retrieves records that contain the specific atoms that you specify, and any additional atoms. To create a subformula query, use the LIKE operator with a target value. The target value can include a range of atom counts, and typically excludes the hydrogens. To exclude specific atoms from the molecules that you retrieve, specify zero for that atom. You can use a single space to separate atoms. Capital letters are not required. Quotes are optional.

Subformula Query	Examples of Records Retrieved

LIKE Na	All sodium salts

LIKE c12 Br(1-2) S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE "C12Br(1-2)S2"	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE c6 h6	All molecules that contain six carbon atoms, six hydrogen atoms, and any number of other atoms

LIKE C5 H10 N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

LIKE C5H10N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Subformula Query	Examples of Records Retrieved

LIKE C12 Br S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12Br1S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12BrS2	No molecules retrieved. ISIS interprets "BrS" as an atom symbol, and gives an error message.

BETWEEN

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks. For example:

CORPORATE.ID BETWEEN "XR11" "XZ15"

CORPORATE.ID BETWEEN 95 100

EXISTS

Use EXISTS to retrieve all records in the database that contain data in a specific database field. For example:

RXN>reactant_link>MOL>MOLSTRUCTURE EXISTS

To retrieve all records in the database that contain no data in a specific database field, use NOT in your query:

NOT (RXN>reactant_link>MOL>MOLSTRUCTURE EXISTS)

Note: You can only use the EXISTS search operator for certain types of database fields. Using EXISTS with other types of fields produces an error message.

SSS

Use SSS to retrieve database structures that contain your graphical query as a reactant substructure (without a reaction arrow) or a product substructure (without a reaction arrow) embedded wholly within them. For example (query is the file name of your graphical query):

RXN>reactant_link>MOL>MOLSTRUCTURE SSS query

RSS

Use RSS to retrieve database structures that contain your graphical query as a reaction substructure, a reactant substructure (with a reaction arrow), or a product substructure (with a reaction arrow) embedded wholly within them. For example (query is the file name of your graphical query):

RXN>RXNSTRUCTURE RSS query

52.2.2 Specifying a Structure in a QB Query

To include a structure (a graphical component) in your QB query, such as a reactant, a product, or a reaction, you need to do the following in the Query Builder text box:

*	Enter the name of the database field that will hold your graphical search results. For a reactant record, enter RXN>reactant_link>MOL>MOLSTRUCTURE. For a product record, enter RXN>product_link>MOL>MOLSTRUCTURE. For a reaction record, enter RXN>RXNSTRUCTURE.

*	Enter the search operator, such as SSS, the equal sign (to specify that the structures retrieved contain your graphical query as a substructure embedded wholly within them).

Note: You can only use SSS as a search operator if your query is a structure without a reaction arrow. If your structure contains a reaction arrow, use RSS instead.

*	Enter the file name (not the structure) of the structure. For example, you might enter the file name BENZALD for the 2D structure (the two-dimensional representation of a molecule) of Benzaldehyde:

Or, you might enter the file name BENZFRAG for any of these 2D substructures (any portion of a 2D structure) of Benzaldehyde:

Entering the File Name of a Structure

You can enter the file name of the structure in several ways:

*	To enter a structure that is on the form in ISIS/Base, double-click query (or mquery) in the Structures box.

*	To enter a structure that was saved in the database, double-click the name of the structure in the Structures box.

*	To enter a structure that was saved as a molfile (without a reaction arrow), click Read Structure, enter the name of the structure in the Files text box, click OK, and then double-click the name of the structure in the Structures box. A molfile is a file in CTfile (chemical table files) format that contains either a single molecular structure or disjointed structural fragments.

*	To enter a reaction component (with a reaction arrow) or an entire reaction that was saved as a rxnfile, click Read Structure, enter the name of the reaction in the Files text box, click OK, and then double-click the name of the reaction in the Structures box. A rxnfile is a file in CTfile (chemical table files) format that contains the structural information for the reactants and products of a single reaction.

You see the structure in the box at the bottom-right corner of the Query Builder.

52.2.3 Searching Top-Level and Lower Level Records

When you combine two or more queries of any type into a single QB search, the search results that you obtain depend on both the specifications and accuracy of your query and the way that information is stored in your database.

How Information Can Be Stored

Information in a database is stored either in a single level (called a flat database) or in multiple levels (called a hierarchical database). Storage in a hierarchical database is more efficient, but it requires you to enter your queries in the correct location on the form to obtain the search results that you want.

A typical hierarchical database is as follows:

The top (or root) level in the hierarchy stores the reaction structure and ID number for each reaction record, and the lower level in the hierarchy stores the literature references and variations for each reaction structure. LITREF is the parent field for the database fields journal and author, and VARIATION is the parent field for the database fields variation number (varno), solvent, and yield. Each reaction record might have multiple literature references and multiple variation subrecords associated with it.

Obtaining the Correct Search Results From a Hierarchical Database

If you search a hierarchical database for lower level records with multiple text/numeric strings in a single QB search, how you enter your query into the Query Builder text box is significant.

For example, the following hierarchical database stores data for multiple decomposition tests that are conducted under different atmospheric conditions:

(In this database, structures are stored at the top (or root) level, and the percentage of oxygen and the number of peaks are stored at a lower level, under the parent field Decomposition. A parent field is a branch in the hierarchy that contains a set of child fields, such as percent O2 and number of peaks.)

You want specific decomposition data from different tests. Your multiple query in a single QB search specifies that you want all compounds within a single test that contain: Query 1, greater than 65% O2; Query 2, less than three peaks.

To obtain search results that match either one query or the other (Query 1 OR Query 2), enter:

ROOT>DECOMPOSITION>Percent_O2 > 65 OR ROOT>DECOMPOSITION > Peaks < 3

This search gives you all compounds within a single test that meet either requirement in your query (but not necessarily both requirements).

To obtain search results that match all queries (Query 1 AND Query 2), specify the hierarchy level that you want to search at the beginning of the search syntax. Then enclose the remainder of the query in double parentheses (If you do not specify a hierarchy level that you want to search, ISIS searches the top-level records in the database.):

ROOT>DECOMPOSITION ((ROOT>DECOMPOSITION>Percent_O2 > 65 AND ROOT>DECOMPOSITION > Peaks < 3))

This search does gives you all compounds within a single test that meet both requirements in your query.

When you filter your search results, you see solely those lower-level records that meet your search requirements.

52.3 Definition of Aromaticity

For local databases: A bond is aromatic if it is in a six-membered ring with alternating double and single bonds, such as benzene.

Note: Aromaticity is not perceived for fused rings in which the double bonds are arranged in a way that cannot be defined as aromatic.

52.4 Specifying Query Features on Atoms and Bonds in Structures

A query feature on an atom and/or a bond in a reaction component is a restriction that specifies the retrieval of certain types of reaction records from an ISIS/Base database.

If you do not use query features, the records retrieved contain solely your exact substructure query embedded wholly within them. For example:

52.4.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

52.4.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of hydrogens. For example:

52.4.3 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

52.4.4 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

52.4.5 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

52.4.6 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

52.5 Specifying Stereochemistry

For local databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve reactions with matching stereochemistry on the reaction components. For example:

An SSS search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve reactions with matching cis or trans stereochemistry on the reaction components. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An SSS search produces the following results:

52.6 Guidelines for Revising the Query

If your QB search retrieved no records or too few records, you might want to:

*	Conduct a QB search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the structural constraints in your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, remove substituent limits, or remove stereochemical requirements.

*	Make the text/numeric strings in your query more general, and then search the same set of records. For example, you can apply operators that partially restrict, such as > or between instead of =, or you can apply wildcards. (A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters.)

Note: For REXACT or MEXACT searches in REACCS databases (Version 8.3 or higher) only: If your database is set up to allow duplicate reaction components to be retrieved in different orientations and you use a reaction as your query, you will not retrieve duplicate reaction components that were registered in a different orientation to those in your query.

If your QB search retrieved too many records, you might want to:

*	Refine the structural constraints in your query, and then search the same set of records. For example, you can limit substitution at specific positions, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Mark the reacting centers in your query, and then search the same set of records.

*	Make the text/numeric string in your query more restrictive, and then search the same set of records. For example, you can use the operator = instead of >.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	Filter your search results so that you view solely the lower-level records. (This assumes that you are viewing both upper- and lower-level records.)

52.7 Searching Example 1: Combining Text/Numeric Queries

This searching example shows you how to conduct a single QB search with a query that contains two text/numeric strings.

52.7.1 Problem

You want to retrieve all reaction records that meet both of the following requirements:

*	Use the catalyst Na

*	Give product yields that are greater than 90%

52.7.2 Approach

To find results that match one or the other of the text/numeric query components, in the Query Builder text box in ISIS/Base:

1.	Enter the database field:

RXN>VARIATION>catalyst_link>MOL>*fmla_MOLSTRUCTURE

2.	(Optional) Enter a space.

3.	Enter the search operator LIKE.

4.	(Optional) Enter a space.

5.	Enter the target value "Na". Enter all target values with the search operator LIKE in double quotation marks.

6.	(Optional) Enter a space.

7.	Enter the boolean algebraic operator AND.

8.	(Optional) Enter a space.

9.	Enter the database field RXN>VARIATION>PRODUCT>YIELD.

10. (Optional) Enter a space.

11. Enter the search operator >.

12. (Optional) Enter a space.

13. Enter the target value 90. In the Query Builder text box, you see the following QB query:

RXN>VARIATION>catalyst_link>MOL>*fmla_MOLSTRUCTURE LIKE "Na" AND RXN>VARIATION>PRODUCT>YIELD > 90

This query does not specify which level in the database to search. By default, ISIS searches the top level of the database for reaction records.

14. Do one of the following:

*	To specify that both data requirements must be met within the same variation subrecord, enter your query in the following way in the Query Builder text box:

VARIATION(RXN>VARIATION>catalyst_link>MOL>*fmla_MOLSTRUCTURE LIKE "Na" AND RXN>VARIATION>PRODUCT>YIELD > 90)

ISIS must search the database for lower-level variation subrecords instead of top-level reaction records.

*	To find records that match one or the other text/numeric query components, in the Query Builder text box in ISIS/Base, enter:

VARIATION(RXN>VARIATION>catalyst_link>MOL>*fmla_MOLSTRUCTURE LIKE "Na" OR RXN>VARIATION>PRODUCT>YIELD > 90)

15. Conduct a QB search in the local reaction database of you choice, such as the LOCALRX demo database.

52.7.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for QB, how to/examples.

52.7.4 Results

If you joined the query components by AND, you retrieve records that match both text/numeric string query components.

Note: If you joined the query components by OR, you retrieve records that match one text/numeric string query component or the other (but not necessarily both).

If you filter your search results, you see solely those lower-level records that meet your search requirements.

52.8 Searching Example 2: Combining Text/Numeric and Graphical Queries

This searching example shows you how to conduct a single QB search with a query that contains a text/numeric string query component and a graphical (structure) query component.

52.8.1 Problem

You want to retrieve all reaction records that meet both of the following requirements:

*	Contain reactants that have a molecular weight greater than 250

*	Contain reactants that contain a steroid substructure embedded wholly within them

52.8.2 Approach

Note: This example assumes that you have previously created a graphical structure with the file name STEROID.MOL (Mac = STEROID) that you stored with the database.

To find results that match either the text/numeric string query component or the graphical query component, in the Query Builder text box in ISIS/Base:

1.	Enter the database field RXN>reactant_link>MOL>MOLECULAR.WEIGHT.

2.	(Optional) Enter a space.

3.	Enter the search operator >. This portion of your query executes a search that retrieves all reaction records with reactants that are greater than your target value.

4.	(Optional) Enter a space.

5.	Enter the target value 250.

6.	(Optional) Enter a space.

7.	Enter the boolean algebraic operator AND.

8.	(Optional) Enter a space.

9.	Enter the database field RXN>reactant_link>MOL>MOLSTRUCTURE.

10. (Optional) Enter a space.

11. Enter the search operator SSS. This portion of your query executes a reactant substructure search (SSS) that retrieves all reaction records with reactants that contain your target value (in this case, the substructure STEROID) embedded wholly within them.

12. (Optional) Enter a space.

13. Enter the target value that is the file name of the graphical substructure that you want to use. For example, enter the file name STEROID.MOL (Mac = STEROID). Alternatively, if you want to use the graphical query that you see on the form in ISIS/Base, you can enter the temporary file name QUERY. If you cannot remember the file name of the stored query that you want to use, you are prompted to browse specific directories and to read in the file name that you want.

14. Conduct a QB search in the local reaction database of you choice, such as the LOCALRX demo database.

52.8.3 Query

In the Query Builder text box, you see the following query:

52.8.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for QB, how to/examples.

52.8.5 Results

You retrieve records with molecules that have a melting point greater than 220 and that contain the steroid substructure in your query.


Remote QB for 3D Databases: Searching Concepts/Examples

Click [image] to print Part 1.    Click [image] to go to Part 2.    Click [image] to close this Request-A-Document.

This Request-A-Document contains:

Part 1:

*	Definition of QB Search	53.1

*	Specifying a QB Query	53.2

*	Searching Top-Level and Lower-Level Records	53.3

*	Specifying Searchable Keys as a Query	53.4

*	Specifying Stereochemistry in 2D Graphical Queries	53.5

*	Specifying Query Features on Atoms and Bonds	53.6

*	Specifying Rgroup Query Features	53.7

*	Specifying Chemical Environments	53.8

*	Specifying Submodel Components	53.9

*	Specifying 3D Objects and Constraints	53.10

---------------------------------------------------------------------------------------------------------------------

Part 2:

*	Specifying 3D Objects and Constraints (Continued)	53.10

*	Using Receptor Information in 3D Queries	53.11

*	Specifying Flexmatch Parameters	53.12

*	The CFS Search Process and Its Options	53.13

*	Sprouting Hydrogens and Lone Pairs on 3D Queries	53.14

*	Guidelines for Revising the Search	53.15

*	Guidelines for Improving Search Speed in 3D Substructure Searches	53.16

We recommend that you print this Request-A-Document, and then browse through it. For technical reasons, this 77-page Request-A-Document has been divided into two parts. To print Part 1, click the Printer icon at the top of the screen. To print Part 2, first click the Part 2 icon, and then click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a QB for 3D Databases search, click here.

53.1 Definition of a Remote QB Search in a 3D Database

You can use the remote Query Builder (QB) search to create any of the other remote searches in ISIS. However, you must use an all-text search query. Thus, we recommend that you use another type of search where possible!

A QB search does have one unique feature: You can combine AND, OR and NOT boolean operators in a search query. For example, to find all 3D structures (MODELSTRUCTURE field) that contain the 3D substructure spirapril embedded wholly within them AND have a molecular weight less than 500, enter:

MODEL>MODELSTRUCTURE SSS spirap
AND MODEL>MOL>MOLECULAR.WEIGHT < 500

where spirap is the name of the file that contains the 3D substructure spirapril.

To find all 3D structures that do NOT contain the 3D substructure spirapril embedded wholly within them, enter:

NOT (MODEL>MODELSTRUCTURE SSS spirap)

To find all 2D structures (MOLSTRUCTURE field) that contain both indole and a molecular weight greater than 200 but NOT those molecules with a melting point below 190, enter:

(MODEL>MOL>MOLSTRUCTURE SSS indole
AND MODEL>MOL>MOLECULAR.WEIGHT > 200)
AND NOT (MODEL>MOL>MELTING.POINT < 190)

where indole is the name of the file that contains the indole structure.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

53.2 Specifying a QB Query

Each QB query contains:

*	The database field that you want to search.

For example, to search the melting point field, enter either the full path name, MODEL>MOL>MELTING.POINT>MELTING.POINT, or the minimum tree name that uniquely identifies the field, namely MELTING.POINT. To search the 3D structure field, enter either the full path name MODEL>MODELSTRUCTURE, or the minimum tree name that uniquely identifies the field, namely MODELSTRUCTURE.

*	A search operator that specifies the type of search (such as a greater than sign, >, to specify a search that finds solely the target text in the query).

*	The text or numeric target value (specific data) that you want to find. (In addition, your target value can be a file name that corresponds to a 2D or 3D structure that you want to retrieve.)

A text or numeric target value can contain wildcards. A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. For example, you can specify the query LIKE "%ALD%" (instead of the query LIKE "BENZALDEHYDE"). The wildcard _ is a placeholder for solely one unspecified character. For example, you can specify the query LIKE "_CHLOROBENZENE" (instead of the query LIKE "2-CHLOROBENZENE"). Target values that contain text or wildcards require double quotation marks.

Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

For example, to find records that contain structures with a melting point that is greater than 220, enter:

MODEL>MOL>MELTING.POINT>MELTING.POINT > 220

Note: You can combine statements in a single text/numeric string with one of the logical operators AND, OR, and NOT. When you use the NOT operator, enclose the text/numeric string in parentheses. For example, enter:

NOT (MODEL>MOL>MELTING.POINT>MELTING.POINT > 220)

53.2.1 The Search Operators

=, <, <=, >, =>, <>

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Search Operator	Definition	Examples

=	equal (numeric)	MOLECULAR.WEIGHT = 350

<	less than (numeric)	MOLECULAR.WEIGHT < 350

<=	less than or equal to (numeric)	MOLECULAR.WEIGHT <= 350

>	greater than (numeric)	MOLECULAR.WEIGHT > 350

>=	greater than or equal to (numeric)	MOLECULAR.WEIGHT >= 350

<>	not equal to (text or numeric)	MOLECULAR.WEIGHT <> 350

ACTIVITY <> "inhibitor"

For a MOLFORMULA field, an exact formula query retrieves records that contain solely the exact atoms that you specify. To create an exact formula query, specify the target value for the formula. The target value must include all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required. The equals operator (=) and quotes are optional. For example:

Exact Formula Query	Examples of Records Retrieved

c6 h6 O	Phenol

c6h6o

C20 H12 Na2 O4	Sodium salt of phenolphthalein

C20H12Na2O4

= C20 H12 Na2 O4

= C20H12Na2O4

= "C20 H12 Na2 O4"

= "C20H12Na2O4"

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Exact Formula Query	Examples of Records Retrieved

C17 H19 N 03	Piperine

C17H19N 03	Piperine

C17H19N103	Piperine

C17H19N03	No molecules retrieved. ISIS interprets "NO3" as 3 Nobelium atoms.

LIKE

Use LIKE with text enclosed in double quotation marks. Enter your query as follows:

Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. For example:

Query	Examples of Records Retrieved

COMPOUND.NAME LIKE "methane"	Methane

COMPOUND.NAME LIKE "benzoic acid"	Benzoic Acid

COMPOUND.NAME LIKE "%acid"	Benzoic Acid

Acetic Acid

COMPOUND.NAME LIKE "%acid%"	Benzoic Acid Sodium Salt

Acetic Acid Sodium Salt

COMPOUND.NAME LIKE "%but_ne"	Trans 2-Butene

2-Butene

N-Butane

Butane

Butene

COMPOUND.NAME LIKE "_ethyl"	Methyl

Ethyl

ACTIVITY LIKE "antibiotic"	Antibiotic

ACTIVITY LIKE "%antibiotic%"	Antibiotic activity

Resistance to antibiotics

Note: To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice. To retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: ACTIVITY LIKE "aa""a" or ACTIVITY LIKE"%aa""a%".

For a MOLFORMULA field, a subformula query retrieves records that contain the specific atoms that you specify, and any additional atoms. To create a subformula query, use the LIKE operator with a target value. The target value can include a range of atom counts, and typically excludes the hydrogens. To exclude specific atoms from the molecules that you retrieve, specify zero for that atom. You can use a single space to separate atoms. Capital letters are not required. Quotes are optional.

Subformula Query	Examples of Records Retrieved

LIKE Na	All sodium salts

LIKE c12 Br(1-2) S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE "C12Br(1-2)S2"	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE c6 h6	All molecules that contain six carbon atoms, six hydrogen atoms, and any number of other atoms

LIKE C5 H10 N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

LIKE C5H10N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Subformula Query	Examples of Records Retrieved

LIKE C12 Br S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12Br1S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12BrS2	No molecules retrieved. ISIS interprets "BrS" as an atom symbol, and gives an error message.

BETWEEN

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks. For example:

CORPORATE.ID BETWEEN "XR11" "XZ15"

CORPORATE.ID BETWEEN 95 100

EXISTS

Use EXISTS to retrieve all records in the database that contain data in a specific database field. For example:

MODEL>MOL>MOLSTRUCTURE EXISTS

To retrieve all records in the database that contain no data in a specific database field, use NOT in your query:

NOT (MODEL>MOL>MOLSTRUCTURE EXISTS)

Note: You can only use the EXISTS search operator for certain types of database fields. Using EXISTS with other types of fields produces an error message.

ISOMER

Use ISOMER to retrieve 2D structures that contain your graphical query as a geometric isomer or a stereoisomer. For example (query is the file name of your graphical query):

MODEL>MOL>MOLSTRUCTURE ISOMER query

TAUTOMER

Use TAUTOMER to retrieve 2D structures that contain your graphical query as a tautomer. For example:

MODEL>MOL>MOLSTRUCTURE TAUTOMER query

PARENT

Use PARENT to retrieve 2D structures that are the parent molecules of your salt query. For example (query is the file name of your graphical query):

MODEL>MOL>MOLSTRUCTURE PARENT query

FLEXMATCH

Use FLEXMATCH to find 2D structures that are an exact match of your query, except in the ways that you specify with any of the flexmatch parameters. You specify features of retrieved structures that must match your query. This allows you to find structures that:

*	Have different counterions than the salt in your query.

*	Match your query, but have different isotopic labels.

*	Match your query, but might be represented differently in the database. For example, the pi-metal bonds in ferrocene can be represented in different ways:

For example, to specify the loosest possible definition of exact match, you specify the FLEXMATCH operator without flexmatch parameters:

MODEL>MOL>MOLSTRUCTURE FLEXMATCH steroid ""

To specify that all bond types must match (BON, in single or double quotes) for a graphical query that you named steroid, enter:

MODEL>MOL>MOLSTRUCTURE FLEXMATCH steroid "BON"

To specify that all bond types must match (BON) and that all metal bonds must match (MET), enter:

MODEL>MOL>MOLSTRUCTURE FLEXMATCH steroid "BON/MET"

When you specify multiple flexmatch parameters, separate them with a forward slash, /. In addition, enclose all flexmatch parameters within the same set in single or double quotes. For more information and examples of flexmatch parameters, see Section 53.12.

MSIMILAR

Use MSIMILAR to retrieve 2D structures that are structurally similar to your graphical query. With this search operator, you can define the degree of similarity in your query to be an arbitrary value between 0 and 100 (these are not actual units). The higher the value, the more similarity. For example, to specify a structural similarity value of 10 (in single or double quotes) for a 2D graphical query that you named steroid, enter:

MODEL>MOL>MOLSTRUCTURE MSIMILAR steroid '10'

You can also specify that the retrieved records contain the same structural complexity as your query (enter NORMAL), more structural complexity than your query (enter SUB), or less structural complexity than your query (enter SUPER). For example, to specify that the retrieved records contain more structural complexity than your query, enter:

MODEL>MOL>MOLSTRUCTURE MSIMILAR steroid 'SUB 10'

SSS

Use SSS to retrieve structures that contain your graphical query as a substructure embedded wholly within them. For example (query is the file name of your graphical query):

MODEL>MOL>MOLSTRUCTURE SSS query

Your graphical query can contain 2D query features that restrict the retrieval of specific structural features. 2D query features include atom and bond query features, Rgroups, and chemical environments. For more information on atom and bond query features, see Section 53.6. For more information on Rgroup query features, see Section 53.7. For more information on chemical environments, see Section 53.8.

You can also use the SSS operator with a 3D graphical query. Use SSS to retrieve 3D structures that contain your graphical query as a substructure embedded wholly within them. For example (query3d is the file name of your 3D graphical query):

MODEL>MODELSTRUCTURE SSS query3D

Your 3D graphical query can contain 2D query features, and any of the following 3D query features:

*	3D geometric constraints. You construct geometric constraints from atoms or from 3D objects such as points, lines, planes, and centroids. For example, you can specify that the centers (centroids) of two rings must be separated by a distance of 2 to 10 Angstroms:

For more information on 3D geometric constraints, see Section 53.10.

*	3D data constraints that you apply to individual atoms or to pairs of atoms. The following example shows calculated values (in Hz) for the ring proton spin-spin couplings of methyl 2-furoate:

For more information on 3D data constraints, see Section 53.10.

The SSS operator has the following limitations for 3D graphical queries:

*	Your graphical query can not contain submodel components. A submodel is a three-dimensional (3D) representation of a portion of a molecule. A submodel contains two or more atoms in a fixed spatial arrangement (F). You construct a submodel from an existing 3D structure. For example:

For more information on submodels, see Section 53.9.

*	You can not specify a Conformationally Flexible Substructure (CFS) search. A CFS search retrieves 3D structures that can be made to fit the query by rotating single bonds. The SSS operator conducts a rigid 3D substructure search. Consequently, a rigid 3D substructure search retrieves solely 3D structures that are actually stored in the database.

To use a submodel query, or to specify a CFS search, you must use the SSS3D operator. For more information the SSS3D operator, see SSS3D later in this section.

SAMEAS3D

Use SAMEAS3D to retrieve 3D structure records that are duplicates of your 3D search query. The atoms in a duplicate 3D structure have the same 3D coordinates within allowed deviations. The allowed deviations are the two fixed-atom tolerances:

*	Maximum atomic displacement specifies the allowed deviation (in Angstroms) of individual atoms in a 3D structure from the corresponding atoms in the query. For example, if the maximum atomic displacement is 0.1, then the displacement between any atom in the retrieved structure and the corresponding atom in the query cannot exceed 0.1 Angstroms.

*	Maximum RMS deviation specifies allowed root-mean-square (RMS) deviation of all the atoms in a 3D structure from the atoms in the query. For example, if the maximum RMS deviation is 0.5, then the root mean square deviation of atoms in the structure from atoms in the query cannot exceed 0.5 Angstroms.

For example, to allow individual atoms in retrieved 3D structures to deviate 0.1 Angstroms and overall atoms to deviate 0.5 Angstroms from a 3D graphical query named SPIRAP, enter:

MODEL>MODELSTRUCTURE SAMEAS3D spirap "0.1 0.5"

SSS3D

Use SSS3D to retrieve 3D structures that contain your 3D graphical query as a substructure embedded wholly within them. Your 3D graphical query can contain any of the 2D and 3D query features that the SSS operator allows. In addition, SSS3D allows you to use submodel components in your 3D graphical query.

A submodel is a three-dimensional (3D) representation of a portion of a molecule. A submodel contains two or more atoms in a fixed spatial arrangement (F). You construct a submodel from an existing 3D structure. For example:

If your 3D graphical query contains submodel components, use fixed-atom tolerances to specify the deviations of individual and overall atoms in the structures that you retrieve from the fixed atoms in the submodel. For example, to allow individual atoms in retrieved 3D structures to deviate 0.1 Angstroms and overall atoms to deviate 0.5 Angstroms from the fixed atoms in the 3D query FIXATOM, enter:

MODEL>MODELSTRUCTURE SSS3D fixatom "0.1 0.5"

Note: To specify SSS3D when your query does not contain submodel components, use:

MODEL>MODELSTRUCTURE SSS3D query ""

Note: If you specify "" as the fixed-atom tolerances for a query that contains submodel components, ISIS uses the default tolerances "0.0 0.1" in the search.

For more information on submodels, see Section 53.9.

Use the SSS3D operator to specify either of the following 3D substructure searches:

*	A rigid 3D substructure search. This search retrieves structures that contain the query embedded within them, but does not attempt to fit structures to the query by rotating single bonds. Consequently, a rigid 3D substructure search retrieves solely 3D structures that are actually stored in the database.

*	A Conformationally Flexible Substructure (CFS) search. A CFS search retrieves structures that contain the query embedded within them, and that can be made to fit the query by rotating single bonds. Consequently, the 3D structures that you obtain from a CFS search do not necessarily have the same conformations as the 3D structures in the database. For example:

To specify a rigid 3D substructure search, specify fixed-atom tolerances after the query name:

MODEL>MODELSTRUCTURE SSS3D fixatom "0.1 0.5"

If your query does not contain fixed atoms, use SSS3D with empty quotes, or use the SSS operator with out quotes:

MODEL>MODELSTRUCTURE SSS3D query ""

MODEL>MODELSTRUCTURE SSS query

CFS searching provides many options that control how ISIS fits 3D structures to the constraints of your query. To specify a search with default CFS options, insert the text "/CFS" after the fixed-atom tolerances in the query. For example, the following query specifies a CFS search with fixed-atom tolerances of 0.1 and 0.5 Angstroms, and with default values for the other CFS options:

MODEL>MODELSTRUCTURE SSS3D fixatom "0.1 0.5/CFS"

Or, if your query does not contain fixed atoms, use:

MODEL>MODELSTRUCTURE SSS3D query "/CFS"

To specify a CFS search with nondefault CFS options, insert the text "/CFS=<options-list>" after the fixed-atom tolerances in the query, where <options-list> is the list of nondefault CFS options. For example, the following query specifies a CFS search with fixed-atom tolerances of 0.5 and 0.1 Angstroms, with RFLEX on, and with a value of 25 for MAXFIT, and with default values for the other CFS options:

MODEL>MODELSTRUCTURE SSS3D fixatom "0.5 0.1/CFS=RFLEX:ON;MAXFIT:25"

Or, if your query does not contain fixed atoms, use:

MODEL>MODELSTRUCTURE SSS3D query "/CFS=RFLEX:ON;MAXFIT:25"

Caution: The CFS options subtly interact with each other and can produce undesirable results if improperly used. Therefore, we strongly recommend that you use the default CFS options. After you have more experience with CFS searching, you might want to experiment with changing additional CFS options. For information on specifying meaningful combinations of CFS options, see Section 53.13.

53.2.2 Specifying a Structure in a QB Query

To include a graphical (structural) component in your QB query, you must enter the following in the Query Builder text box in the order shown:

*	The name of the database field that will hold your graphical search results. For a 3D structure record, enter MODEL>MODELSTRUCTURE. For a 2D structure subrecord within a 3D structure record, enter MODEL>MOL>MOLSTRUCTURE.

*	The search operator. For example, enter SSS to specify that the structures retrieved contain your graphical query embedded wholly within them. OR, enter the equal sign (=) to specify that the structures retrieved contain your graphical query exactly as drawn.

*	The file name (not the structure) of the structure. For example, enter the file name BENZALD for the 2D structure (the two-dimensional representation of a molecule) of Benzaldehyde:

Or, enter the file name BENZFRAG for any of these 2D substructures (any portion of a 2D structure) of Benzaldehyde:

Entering the File Name of a Structure

You can enter the file name of the structure in several ways:

*	To enter a structure that is on the form in ISIS/Base, double-click query (or mquery, if present) in the Structures box.

*	To enter a structure that was saved as an object in the database, double-click the name of the structure in the Structures box.

*	To enter a structure that was saved as a molfile, click Read Structure, enter the name of the structure in the Files text box, click OK, and then double-click the name of the structure in the Structures box. (A molfile is a file in CTfile (chemical table files) format that contains either a single molecular structure or disjointed structural fragments.)

You see the structure in the box at the bottom-right corner of the Query Builder.

53.3 Searching Top-Level and Lower-Level Records

When you combine two or more queries of any type into a single QB search, the search results that you obtain depend on both the specifications and accuracy of your query and the way that information is stored in your database.

Information in a database is stored either in a single level (called a flat database) or in multiple levels (called a hierarchical database). Storage in a hierarchical database is more efficient, but it requires you to enter your queries in the correct location on the form to obtain the search results that you want. For example, the following hierarchical database stores data for multiple decomposition tests that are conducted under different atmospheric conditions:

In this database, structures are stored at the top (or root) level, and the percentage of oxygen and the number of peaks are stored at a lower level, under the parent field Decomposition. A parent field is a branch in the hierarchy that contains a set of child fields, such as percent O2 and number of peaks.

You want specific decomposition data from different tests. Your multiple query in a single QB search specifies that you want all compounds within a single test that contain: Query 1, greater than 65% O2; Query 2, less than three peaks. To obtain search results that match either one query or the other (Query 1 OR Query 2), enter:

ROOT>DECOMPOSITION>Percent_O2 > 65 OR ROOT>DECOMPOSITION > Peaks < 3

This search gives you all compounds within a single test that meet either requirement in your query (but not necessarily both requirements). To obtain search results that match all queries (Query 1 AND Query 2), specify the hierarchy level that you want to search at the beginning of the search syntax. Then enclose the remainder of the query in double parentheses (If you do not specify a hierarchy level that you want to search, ISIS searches the top-level records in the database.):

ROOT>DECOMPOSITION ((ROOT>DECOMPOSITION>Percent_O2 > 65 AND ROOT>DECOMPOSITION > Peaks < 3))

This search does gives you all compounds within a single test that meet both requirements in your query.

Note: When you filter your search results, you see solely those lower-level records that meet your search requirements.

53.4 Specifying Searchable Keys as a Query

If your database contains the database field MOLSKEYS, you can use numbered keys to retrieve specific substructures or chemical representations. You must separate multiple keys with a comma (do not include spaces):

*	Use parentheses to specify the retrieval of all the keys in your query. Example: To specify the retrieval of molecules that contain 6-membered rings and bromine, enter the following into the Query Builder text box:

MODEL>MOL>MOLSKEYS = "(163,46)"

*	Use square brackets to specify the retrieval of one ore more keys in your query. Example: To specify the retrieval of molecules that contain 6-membered rings or bromine, enter the following into the Query Builder text box:

MODEL>MOL>MOLSKEYS = "[163,46]"

*	Use angle brackets to specify the retrieval of none of the keys in your query. Example: To specify the retrieval of molecules that do not contain 6-membered rings or bromine, enter the following into the Query Builder text box:

MODEL>MOL>MOLSKEYS = "<163,46>"

*	Use braces to specify the retrieval of solely one of the keys in your query but not any others in your query. Example: To specify the retrieval of molecules that contain either 6-membered rings or bromine but not both 6-membered rings and bromine, enter the following into the Query Builder text box:

MODEL>MOL>MOLSKEYS = "{163,46}"

*	Use no restrictors to specify the retrieval of one and/or any other keys in your query. Example: To specify the retrieval of molecules that contain 6-membered rings and/or bromine, enter the following into the Query Builder text box:

MODEL>MOL>MOLSKEYS = "163,46"

Additional Examples

The query MODEL>MOL>MOLSKEYS = "161,[11,96]" specifies the retrieval of N and a 4- or 5-membered ring.

The query MODEL>MOL>MOLSKEYS = "[(161,96),(164,163)]" specifies the retrieval of N and a 5-membered ring or O and a 6-membered ring. Both sets of molecules can be retrieved.

The query MODEL>MOL>MOLSKEYS = "[42,46,103],<27>" specifies the retrieval of at least one halogen, which cannot be iodine.

The List of Searchable Keys

If you search a MACCS-II database, there are 166 numbered keys that you can use. If you do not recognize the words for a specific key, the words might be in a special type of language called query language. (For more information on query language, see your ISIS Administrator.) The list of searchable keys is as follows:

Key	Description	Key	Description

1	ISOTOPE	84	NH2

2	103 < ATOMIC NO. < 256	85	CN(C)C

3	GROUP IVA,VA,VIA PERIODS 4-6 (GE..)	86	CH2QCH2

4	ACTINIDE	87	X!A$A

5	GROUP IIIB,IVB (SC..)	88	S

6	LANTHANIDE	89	OAAAO

7	GROUP VB,VIB,VIIB (V..)	90	QHAACH2A

8	QAAA@1	91	QHAAACH2A

9	GROUP VIII (FE..)	92	OC(N)C

10	GROUP IIA (ALKALINE EARTH)	93	QCH3

11	4M RING	94	QN

12	GROUP IB,IIB (CU..)	95	NAAO

13	ON(C)C	96	5M RING

14	S-S	97	NAAAO

15	OC(O)O	98	QAAAAA@1

16	QAA@1	99	C=C

17	CTC	100	ACH2N

18	GROUP IIIA (B..)	101	8M RING OR LARGER

19	7M RING	102	QO

20	Si	103	CL

21	C=C(Q)Q	104	QHACH2A

22	3M RING	105	A$A($A)$A

23	NC(O)O	106	QA(Q)Q

24	N-O	107	XA(A)A

25	NC(N)N	108	CH3AAACH2A

26	C$=C($A)$A	109	ACH2O

27	I	110	NCO

28	QCH2Q	111	NACH2A

29	P	112	AA(A)(A)A

30	CQ(C)(C)A	113	Onot%A%A

31	QX	114	CH3CH2A

32	CSN	115	CH3ACH2A

33	NS	116	CH3AACH2A

34	CH2=A	117	NAO

35	GROUP IA (ALKALI METAL)	118	ACH2CH2A>1

36	S HETEROCYCLE	119	N=A

37	NC(O)N	120	HETEROCYCLICATOM>1 (&..)

38	NC(C)N	121	N HETEROCYCLE

39	OS(O)O	122	AN(A)A

40	S-O	123	OCO

41	CTN	124	QQ

42	F	125	AROM RING>1

43	QHAQH	126	A!O!A

44	OTHER	127	A$A!O>1 (&..)

45	C=CN	128	ACH2AAACH2A

46	BR	129	ACH2AACH2A

47	SAN	130	QQ>1 (&..)

48	OQ(O)O	131	QH>1

49	CHARGE	132	OACH2A

50	C=C(C)C	133	A$A!N

51	CSO	134	X (HALOGEN)

52	NN	135	Nnot%A%A

53	QHAAAQH	136	O=A.1

54	QHAAQH	137	HETEROCYCLE

55	OSO	138	QCH2A>1 (&..)

56	ON(O)C	139	OH

57	O HETEROCYCLE	140	O>3 (&..)

58	QSQ	141	CH3>2 (&..)

59	Snot%A%A	142	N>1

60	S=O	143	A$A!O

61	AS(A)A	144	Anot%A%Anot%A

62	A$A!A$A	145	6M RING>1

63	N=O	146	O>2

64	A$A!S	147	ACH2CH2A

65	C%N	148	AQ(A)A

66	CC(C)(C)A	149	CH3>1

67	QS	150	A!A$A!A

68	QHQH (&..)	151	NH

69	QQH	152	OC(C)C

70	QNQ	153	QCH2A

71	NO	154	C=O

72	OAAO	155	A!CH2!A

73	S=A	156	NA(A)A

74	CH3ACH3	157	C-O

75	A!N$A	158	C-N

76	C=C(A)A	159	O>1

77	NAN	160	CH3

78	C=N	161	N

79	NAAN	162	AROM

80	NAAAN	163	6M RING

81	SA(A)A	164	O

82	ACH2QH	165	RING

83	QAAAA@1	166	FRAGMENTS

Where (&..) is equivalent to "and other rare features;" and Key 166 corresponds to molecules that consist of more than one fragment. (A molecule has more than one fragment if its structure cannot be drawn in one connected set of bonds.) Structural keys specify 2D structural features only. You cannot use searchable keys to specify the 3D spatial arrangement of atoms in the structures that you retrieve.

Some of the keys that you see are encoded in a substructure-search query language, such as QAAAA@1 for Key 83. This language allows atoms to be expressed as follows:

*	Unbracketed for C, N, O, P, and S; but bracketed for all other single element symbols, such as [CL] for chlorine, or multiple element symbols in lists, such as [N,O] for nitrogen and oxygen, or [F,CL,BR,I] for halogens.

*	A for any atom except hydrogen, and Q for any atom except carbon or hydrogen.

*	Substituted with a specific number of hydrogens: H0 on an atom prohibits hydrogens at that position, such as CH0; and Hn allows at least that number (n) of hydrogens, such as CH2 (methyl or methylene).

*	Charged: A plus sign (+) on an atom is a positive charge, such as +, +2, or +3; a single quote (') is a monoradical; a double quote (") is a negative charge; and an asterisk (*) is a neutral atom.

*	Variable in mass: The isotopic label M+n indicates a difference of n from the standard mass, such as CM+1 to indicate the isotope carbon 13, or OM-1 to indicate the isotope oxygen 15.

*	Variable in atom number: The notation @n at the end of the atom to which it refers indicates that atom number (n) is attached here. Atoms (except hydrogen) are numbered from left to right, such as C-C-C-@1 (but not @3-C-C-C) to indicate a three-membered ring, or CH3-C-C-C-@2 to indicate (methyl or methylene).

*	Branched: The parentheses around an atom or group indicates that the atom or group branches from the atom at its left (but not its right) in the string. For example, C-C-C-C is butane, while C-C(C)-C-C is 2-methyl butane. N+(-C)(-C)(-C)(-C) is a quaternary ammonium salt.

This language allows bonds to be expressed as follows:

*	Variable bond type: A hyphen (-) is a single bond; an equal sign (=) is a double bond; a (T) is a triple bond; a percent sign (%) is an aromatic bond; a tilde (~) is either a single or a double bond; and an unspecified bond type is the omission a bond marker. For example, the two carbon chain CC contains any type of bond.

*	Variable numbers of fragments: A space between strings indicates that there is no connection between the groups. For example, C=O C-OH retrieves a carbonyl and a hydroxyl, but the groups cannot be centered on the same carbon (the fragments cannot overlap).

*	Part of a ring: A dollar sign ($) that precedes a bond indicates that the bond is part of a ring.

*	Part of a chain: An exclamation sign (!) that precedes a bond indicates that the bond is part of a chain.

53.5 Specifying Stereochemistry in 2D Graphical Queries

For 2D graphical queries, you can specify stereochemistry with Up and Down bonds, stereo boxes on cis or trans configurations, and chiral flags on molecules.

Note: You can not use the query features in this section in a 3D graphical query.

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

An SSS search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve molecules with matching cis or trans stereochemistry. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An SSS search produces the following results:

Chiral Flags on Molecules

In a remote database, you can create a query with a chiral flag on a molecule with at least one asymmetric center or on a molecule that is asymmetric to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

53.6 Specifying Query Features on Atoms and Bonds

A query feature on an atom and/or a bond in a molecule is a restriction that specifies the retrieval of certain types of molecule records from an ISIS/Base database. If you do not use query features, the molecules retrieved contain solely your exact substructure query embedded wholly within them. For example:

You can also define Rgroups that specify a root structure with defined Rgroup substituents attached to it at specific positions. For more information on Rgroups, see Section 53.7.

Note: You can use query features on atoms and bonds solely for the following search operators:

SSS
SSS3D

Caution: Atom and bond query features are 2D query features. 2D query features specify solely the number, type, and connectivity of atoms in a molecule. A 3D graphical query should contain at least one component that specifies the spatial distribution of atoms in a 3D structure. To specify the spatial distribution of atoms, you can use a submodel with two or more fixed atoms, and/or use 3D geometric constraints such as distances and angles. For more information on submodels, see Section 53.9. For more information on 3D geometric constraints, see Section 53.10.

53.6.1 Definition of Aromaticity

For remote databases: ISIS interprets the following ring systems as aromatic:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:

Note: The bonds of six-membered aromatic ring systems and the perimeter bonds of azulenes are stored as aromatic bonds in the database. The bonds of five-membered aromatic rings, however, are stored as single and double bonds and interpreted as aromatic during a search. The differences between five-membered rings and other types of aromatic rings can cause different search results for five- and six-membered rings/azulenes when you use the following bonds in queries: Single, Double, and Single/Double query bonds. For more information on the Single/Double query bond, see Section 53.6.8.

53.6.2 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except implicit or explicit hydrogens:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve neither carbons nor hydrogens.

53.6.3 Prohibiting Hydrogens on an Atom

Use an atom query feature to prohibit the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature: H0

Prohibits the attachment of hydrogens. For example:

53.6.4 Allowing an Unsaturated Atom

Use an atom query feature to specify that an atom is attached to at least one multiple bond (double, triple, or aromatic).

Atom Query Feature: Unsaturated Atom (u)

Specifies that the atom of your choice is attached to at least one multiple bond (double, triple, or aromatic). For example, the following query specifies both an unsaturated atom (u) and single or double bonds (the double dashed lines).

53.6.5 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

Atom Query Feature: Substitution Count of Zero, s0

Specifies that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of a single atom with attached hydrogens (if any).

Atom Query Feature: Substitution Count of One, s1

Specifies that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Two, s2

Specifies that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Three, s3

Specifies that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Four, s4

Specifies that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Five, s5

Specifies that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of at Least Six, s6

Specifies that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count as Drawn, s*

Specifies that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:

53.6.6 Allowing a Specific Number of Ring Bond Attachments

Use atom query features to specify the number of ring bond attachments.

Atom Query Feature: Ring Bond Count of Zero, r0

Specifies that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:

Atom Query Feature: Ring Bond Count of Two, r2

Specifies that the records retrieved have solely two ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of Three, r3

Specifies that the records retrieved have solely three ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of at Least Four, r4

Specifies that the records retrieved have at least four ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count as Drawn, r*

Specifies that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:

53.6.7 Allowing Additional Atoms and/or Bonds in a Chain or a Ring

Use a query feature to specify the addition of atoms and/or bonds in a chain or a ring.

Atom or Bond Query Feature: Link Node

Use a link node to specify the addition of variable numbers repeating units (atoms and/or bonds) to a ring or chain. A repeating unit must be attached to two adjacent bonds. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the link node [L1-3]:

Or, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the link node [L1-3]:

53.6.8 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Note: An aromatic query bond hits any bond in all types of aromatic rings: 6-membered ring bonds, 5-membered ring bonds, and azulene perimeter bonds. For more information on the structures that ISIS interprets as aromatic, see Section 53.6.1.

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

Note: A Single/Double query bond does not hit bonds in 6-membered aromatic rings, or perimeter bonds of azulenes, because bonds in these structures are stored in the database as aromatic bonds. However, a Single/Double query bond does hit bonds in 5-membered rings that ISIS interprets as aromatic. For more information on the structures that ISIS interprets as aromatic, see Section 53.6.1.

Bond Query Feature: Single/Aromatic Bond

Specifies either a single or an aromatic bond at that position:

Bond Query Feature: Double/Aromatic Bond

Specifies either a double or an aromatic bond at that position:

53.6.9 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

53.6.10 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

53.7 Specifying Rgroup Query Features

An Rgroup query finds structures that contain your query as a root structure with defined Rgroup substituents attached to it at specific positions. Your query can contain restrictions on the Rgroup substituents, called Rgroup conditions: You can specify the number of Rgroup sites that must be occupied in the records retrieved, specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site, or specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

Your Rgroup query can also contain restrictions on atoms and bonds of the root structure and Rgroup substituents. For example, you can use the atom query feature H(0) to prohibit the attachment of implicit hydrogens on a specific atom in the structures retrieved.

An example of an Rgroup query is as follows:

You can use Rgroups and atom and bond query features to specify chemical environments such as basic nitrogens and acidic centers. For more information on chemical environments, see Section 53.8.

Note: You can use query features on atoms and bonds solely for the following search operators:

SSS
SSS3D

Caution: Like atom and bond query features, Rgroup queries contain no information about the spatial distribution of atoms in a 3D structure. A 3D graphical query should contain at least one component that specifies the spatial distribution of atoms in a 3D structure. To specify the spatial distribution of atoms, you can use a submodel with two or more fixed atoms, and/or use 3D constraints such as distances and angles. For more information on submodels, see Section 53.9. For more information on 3D constraints, see Section 53.10.

53.7.1 The Root Structure

The root structure contains the portion of the structure that does not vary among the structures retrieved. For example, if you want to find 2, 5-Dihydroxypyridine in which the substituent at position 2 can be COOH, CN, or Ph, and the substituent at position 5 can be OH or CH3, the root structure is 2, 5-Dihydroxypyridine with Rgroups (such as R1 and R2):

Rgroups

On the root structure, Rgroups (R1 through R32) are placeholders that designate where the lists of functional groups and atoms that can attach to the root structure. In the example above, the Rgroup R1 designates that the members of the list R1 (the Rgroup substituents) are allowed at position 5 on the root structure. The Rgroup R2 designates that the members of the list R2 (the Rgroup substituents) are allowed at position 2 on the root structure.

Multiple Rgroups at One Position

You can specify multiple Rgroups at a single site on the root structure. For example:

One Rgroup at Multiple Positions

You can specify a single Rgroup (such as R1) at multiple positions on the root structure. For example:

Note: See Section 53.7.3 to restrict the number of Rgroups that must be occupied in the records retrieved. A molecule might not have to satisfy all the Rgroup sites on the root structure to be retrieved. For example, the Rgroup condition R1 > 0 specifies that any molecule in which at least one of the R1 sites is filled by an R1 member will be retrieved. In addition, the Rgroup condition RestH determines whether the unsatisfied sites must be filled with hydrogen atoms or if other molecule fragments are allowed to be attached if they are not on the list.

Multiple Root Structures in a Single Rgroup Query

If you choose to specify multiple root structures in a single Rgroup query, you must group the root structures before you do a search. To group multiple root structures, select them, and then choose Object > Group.

53.7.2 Rgroup Substituents

Rgroup substituents are the members of the list of Rgroups. You define the Rgroup substituents that you will allow to be found at specified positions in the molecules retrieved. Rgroup substituents can be any structural fragment, including functional groups and single atoms.

In the example below, the Rgroup substituents COOH, CN, or Ph are allowed at position 5 (R1) on the root structure and the Rgroup substituents OH or CH3 are allowed at position 2 (R2) on the root structure:

Attachment Points

An attachment point (marked with an arrow and an asterisk) designates the atom on the Rgroup substituent that is attached to the root structure:

You must designate an attachment point on an Rgroup substituent for each bond that is attached to the substituent.

If an Rgroup is attached to two bonds on the root structure, you must designate two attachment points:

In this example, one bond on the root structure is marked with a single quote that corresponds to the attachment point with a single quote on the Rgroup substituent. The other bond on the root structure is marked with a double quote that corresponds to the attachment point with a double quote on the Rgroup substituent.

Rule: To obtain the correct search results, be certain to assign the attachment point with a single quote on the Rgroup substituent to the corresponding atom on the root structure that contains the lower atom number of the two attachment sites. In the above example, you cannot see the atom numbers on the root structure, which are assigned automatically to the root structure during the drawing process.

Nested Rgroups

A nested Rgroup is an Rgroup that is a placeholder within another Rgroup rather than within the root structure. (You cannot nest an Rgroup any lower than this level.) In the following example, Rgroup R2 is nested within the Rgroup R1:

Nested Rgroups are equivalent to the following structures:

Note: You cannot specify more than one nested occurrence of a single Rgroup substituent (such as R2) within another (unnested) Rgroup substituent (such as R1). For example, you cannot specify that the nested Rgroup R2 be retrieved at both positions 1 and 2 within the R1 Rgroup substituent benzene. Instead, create a query in which a set of nested Rgroups (such as R2 and R3) contains identical substituents. Then specify the occurrence of each nested Rgroup only one time. For example, specify that the nested Rgroup R2 be retrieved at position 1 and that the nested Rgroup R3 be retrieved at position 2 within the R1 Rgroup substituent benzene.

53.7.3 Rgroup Conditions

You can apply restrictions to each Rgroup in your query after you assemble all the Rgroups. The set of restrictions is called the Rgroup conditions.

If you do not apply Rgroup conditions, ISIS assigns the default conditions: Occurrence > 0 and RestH off for each Rgroup.

Occurrence

With the Rgroup condition Occurrence, you can specify the number of Rgroup sites that must be occupied in the records retrieved. For example, the occurrence designation R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved. Type one of the following values in the Occurrence range text box:

Value	Explanation

0	All members of the Rgroup are excluded from the Rgroup site (such as R1). To allow any other Rgroup substituent at the Rgroup site, set RestH to off.

> 0	At least one Rgroup must be satisfied. If RestH is off, any other substituent can attach to unsatisfied sites. If RestH is on, unsatisfied sites must be filled solely by hydrogens.

n	Exactly n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

< n	Less than n number of sites (including zero) must be satisfied. RestH controls substitution at unsatisfied sites.

m - n	Any number of sites falling within the range of m to n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

m,n,...	Any combination of the above expressions, separated by commas. For example: 1, 3-5, 9, >12.

For example, the Rgroup condition R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved.

In another example, the Rgroup condition R1 > 0 and R2 > 0 specifies that an Rgroup substituent from the R1 list AND an Rgroup substituent from the R2 list must occupy at least one site on the root structure in the records retrieved.

Finally, the Rgroup conditions R1 = 1, 3-5, 9, >12 specify that either 1, 3, 4, 5, 9, or more than 12 sites must be satisfied:

RestH

With the Rgroup condition RestH, you can specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site.

An unsatisfied Rgroup site is an Rgroup site on the root structure that does not have an Rgroup member attached: If RestH is off, any functional group or atom may be attached at unsatisfied Rgroup sites on the root structure. If RestH is on, solely hydrogens are allowed to be attached at unsatisfied Rgroup sites on the root structure.

If/Then

With the Rgroup condition If/then, you can specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

For example, If R1 then R2 specifies that if the conditions for R1 are satisfied, then the conditions for R2 must also be satisfied. (If the conditions for R1 are not satisfied, then the conditions for R2 are ignored.) The If/then condition implies that a molecule may be retrieved even though R1 is not satisfied.

In the following query, R1 contains a nitro group and a sulfonic acid group. R2 contains a chlorine atom. The condition If R1 then R2 specifies that if a nitro group or a sulfonic acid group is attached at R1 on the root structure, then a chlorine must also be attached at R2. However, if the R1 site on the root structure does not have either the nitro or the sulfonic acid group (R1 is unsatisfied), then R2 can have any substituent (R2 is ignored):

53.8 Specifying Chemical Environments

You can incorporate specific chemical environments into your graphical query. This section contains examples of several chemical environments that you can create with 2D query features and Rgroups. MDL supplies ISIS/Draw sketch files that contain specific types of chemical environments. You can incorporate these structures into your own queries and modify them if desired.

Note: The chemical environments in this section use 2D query features only. 2D query features specify solely the number, type, and connectivity of atoms in a molecule. You can use 2D query features in both 2D and 3D graphical queries. However, a 3D graphical query should contain at least one component that specifies the spatial distribution of atoms in a 3D structure. To specify the spatial distribution of atoms, you can use a submodel with two or more fixed atoms, and/or use 3D geometric constraints such as distances and angles. For more information on submodels, see Section 53.9. For more information on 3D geometric constraints, see Section 53.10.

53.8.1 Acidic Center

The file ACID_CTR.SKC contains the following definition of an acidic center:

This query defines an acidic center as either an oxygen of a carboxylic acid or any nitrogen of an unsubstituted tetrazole.

53.8.2 Basic Nitrogen

BSC_N_1.SKC File

The file BSC_N_1.SKC contains a definition of a basic nitrogen that includes alkyl amines (nsp3), amidines (nsp2), and guanidines (nsp2). This definition excludes other nitrogens such as aromatic nitrogens, aniline-type nitrogens, N=O, NHC=O, and NHC=C:

You can change this definition to fit your needs. For example, if you want to include aromatic nitrogens, delete R2 from the definition.

BSC_N_2.SKC File

The definition of basic nitrogen in the file BSC_N_2.SKC excludes all amides or anilines, and other conjugated systems that reduce the accessibility of the electron pair on the nitrogen atom:

Simple Definition

The following is a simple definition of a basic nitrogen:

53.8.3 Hydrogen-Bond Acceptor

The definition of a hydrogen bond acceptor in the file H_ACCEPT.SKC extends the definition of a basic nitrogen to include oxygen and sulfur:

Note: There are two different conventions for defining hydrogen-bond donors and acceptors. This help file uses the definition of a hydrogen-bond donor that is generally used by medicinal chemists. By this convention, the donor of a hydrogen bond is the group to which the hydrogen atom is attached:

An alternative definition of hydrogen-bond donors and acceptors defines a hydrogen-bond donor as the group that provides the lone-pair electrons (LP) to the hydrogen bond.

53.8.4 Hydrogen-Bond Donor

The following is an example of a hydrogen bond donor:

53.9 Specifying Submodel Components

Note: You can use submodel components solely in 3D graphical queries, and solely for the SSS3D search operator.

A submodel is a three-dimensional (3D) representation of a portion of a molecule. A submodel search retrieves all models that contain the same spatial arrangement of atoms as those specified in your submodel query, within specified deviations of the individual and overall atoms.

You specify the spatial arrangement of atoms in a submodel query by fixing the 3D coordinates of two or more atoms in the structure. To create a submodel, you eliminate parts of an existing 3D structure until you have the submodel that you want to find in other 3D structures. Then, you fix the positions of the atoms of your choice. The figure below shows how you create a submodel query from the 3D structure of Trandolapril. Circles mark the atoms in Trandolapril that are fixed (F) in the query:

When you conduct a search with a submodel query, you must specify how closely the 3D structures that you retrieve must match the spatial arrangement of the fixed atoms in the submodel query. Two fixed-atom tolerances specify how closely the structures must match the query:

*	Maximum atomic displacement specifies the maximum allowed deviation of individual fixed atoms in the query from those in the structures that you retrieve.

*	Maximum RMS deviation specifies the maximum allowed deviation of all fixed atoms in the query from fixed atoms in the structures that you retrieve. During the search, ISIS superimposes the fixed atoms in the 3D structure on those of the query and performs a least-squares calculation.

When your query contains fixed atoms, you must specify at least one fixed-atom tolerance for the SSS3D search. You can specify:

*	Maximum atomic displacement only (structures with 2 or 3 fixed atoms)

*	Maximum RMS deviation only (structures with at least 4 fixed atoms)

*	Both fixed-atom tolerances (structures with at least 4 fixed atoms)

Your ISIS Administrator sets default fixed-atom tolerances that your site uses to register 3D structures to the database. These tolerances are specified in the Session Settings file that your ISIS Administrator supplies you. To change fixed-atom tolerances for searching, follow the step-by-step instructions. Alternatively, choose Help > Index, and search for fixed-atom tolerances, changing.

Caution: If you change the default fixed-atom tolerances for searching, you must restore the default fixed-atom tolerances before you register 3D structures.

The following are examples of the 3D structures that you retrieve from a search with the query that you derive from Trandolapril, with both fixed-atom tolerances set to 0.5:

Note: Queries that contain fixed atoms produce slower search speeds than queries that do not contain fixed atoms. As an alternative to the fixed-atom query shown previously, you can use a query with distance constraints that incorporate the fixed-atom tolerances:

You can also use other 3D query features to specify the spatial distribution of atoms within a 3D structure. For more information on distance constraints and other 3D constraints, see Section 53.10.

53.10 3D Objects and Constraints

To specify the spatial relationships between atoms, you can construct 3D objects and create 3D constraints that use atoms and/or constructed 3D objects.

53.10.1 Specifying 3D Objects

You can set geometric constraints on various molecular or constructed geometric 3D objects. These objects can be points, lines, planes, centroids, and normal vectors. Lines, planes, and normal vectors actually extend infinitely, but are represented in ISIS as shown below:

Centroid

Use a centroid to define the geometric center of a set of reference points or atoms of your choice. For example, the centroids in the structures below (depicted by the triangles) are the geometric centers of selected atoms. The centroid on the left is created when all six ring atoms are selected. The centroid on the right is created when the atoms in the box are selected (the box is used here to indicate atoms selected, and does not appear in the query):

Line

Use a line to define a path through two or more reference positions, such as points, atoms, or centroids:

ISIS derives a best-fit line if you use at least three reference positions to define the line. You can specify a linearity constraint for a best-fit line. For more information, see Section 53.10.2.

Normal

Use a normal to specify a line (with an arrowhead) that is perpendicular to a plane and that passes through a reference position (a point, atom, or centroid):

In ISIS, the direction of the normal arrow is defined by the sequence in which you selected the first three components of the plane. To reverse the direction of the arrow, simply reverse the order in which you define the components of a plane.

Plane

Use a plane to define a surface that consists of three or more reference positions (points, atoms, or centroids). A plane actually extends infinitely in all directions, but is depicted in ISIS as a small rectangular surface. In the following figure, the entire molecule specifies the plane:

ISIS derives a best-fit plane if you use at least four reference positions to define the line. You can specify a planarity constraint for a best-fit plane. For more information, see Section 53.10.2.

Point

A point is a reference position. You specify a point at a defined distance and direction from a distance reference position (another point, atom or centroid). To specify the direction, you can use either another reference position (called the direction reference position) or a normal.

You can specify the distance from the distance reference position to the direction reference position in Angstroms or as a percentage. Angstrom distances must lie between -100 and +100 Angstroms. Percentage distances must lie between -1,000% and +1,000%, and must include the % sign.

The following example defines a point at a distance of 1.4 Angstroms from a ring nitrogen (the distance reference position) to a ring oxygen (the direction reference position):

The point that you specify need not lie between the two reference positions. The following example shows a point projected 2.8 Angstroms along a line between the nitrogen atom (the distance reference position) and the hydrogen (the direction reference position):

When you use a normal to specify the direction of the point from the distance reference position, you must specify the distance from the distance reference position in Angstroms.

The following example uses a normal to create points that lie 2.8 Angstroms above and below the center of a phenyl ring. The normal is perpendicular to the plane of the ring and passes through the ring centroid. The direction of the normal is undefined, because the point that defines it lies in the plane. To define points on both sides of the plane, use plus (+) and minus (-) signs with Angstrom values to specify the distances:

To create a point on only one side of the plane, specify a distance of 2.8 Angstroms without the plus (+) or minus (-) sign:

Note: You can use points to represent features on a receptor. For examples, see Section 53.11.

53.10.2 Specifying 3D Constraints

You can apply 3D geometric constraints to 3D objects. 3D geometric constraints include distances, angles, dihedral angles, exclusion spheres, linearity constraints, and planarity constraints:

You can also apply 3D data constraints to atoms and atom pairs. Data constraints are listed under “Atom" and “Atom Pair" later in this section.

Distance

You can define a distance constraint between two reference positions (atoms, centroids, or points), from a reference position to a line or normal, or from a reference position to a plane:

The distance constraint is a range of values. Both values in the range must be greater than zero and equal or less than 1,000. The following query has a distance constraint of 2 to 10 Angstroms between the center of a phenol ring and the center of a phenyl ring:

The following are examples of the 3D structures that you retrieve:

(Continued in Part 2)


Remote QB for 3D Databases: Searching Concepts/Examples Part 2

Click [image] to print Part 2.    Click [image] to return to Part 1.    Click [image] to close this Request-A-Document.

To print Part 2 of this Request-A-Document, click the Printer icon at the top of the screen.

To return to Part 1, click the Part 1 icon at the top of the screen.

---------------------------------------------------------------------------------------------------------------------

53.10 3D Objects and Constraints (Continued)

53.10.2 Specifying 3D Constraints (Continued)

Angle

You can define an angle constraint with three points, centroids, or atoms; or with two planes, lines, or normals:

The vertex of the angle for two lines or normals that do not intersect is an imaginary point. An angle drawn with two lines that do not intersect is equivalent to a dihedral angle through an imaginary line that connects the two lines with the shortest distance.

The angular range that you specify depends on the way that you defined the angle:

*	If you used lines or planes to define the angle, the range must lie between 0 and 90 degrees.

*	If you used three points to define the angle, the range must lie between 0 and 180 degrees.

The following query has a constraint of 30- 65 degrees on the angle between the line between two phenyl centers and a phenol oxygen:

The following are examples of the 3D structures that you retrieve:

Exclusion sphere

Use an exclusion sphere to exclude atoms within a sphere surrounding a reference position. You define the radius of the exclusion sphere. You can ignore unconnected atoms within the radius of the sphere or specify exactly which atoms that you want to be included. The radius of the sphere must be between 0.1 and 20 Angstroms.

Note: In a CFS search, you cannot use a graphical query that consists solely of exclusion spheres. A CFS query must contain at least one of the following 3D query components: distance, angle, dihedral angle, linearity constraint, planarity constraint, or two or more fixed atoms.

For example, the exclusion spheres in the following query ensure that you select compounds that have no atoms within the circled areas of 1.0-Angstrom radius:

The following is an example of the 3D structures that you retrieve (For clarity, the measured values of the four distance constraints are not displayed):

You can specify that atoms that are part of the query can lie within the exclusion sphere. In the following query, for example, you might want to allow atoms from the carboxyl group within the exclusion spheres, but exclude all other atoms:

To allow other atoms in the query within the exclusion sphere, you must include these atoms in the basis of the exclusion sphere. (The basis of a 3D object or constraint is the set of atoms or 3D objects that comprise the object.) For an exclusion sphere, the basis always includes the reference position at the center of the sphere. To include additional atoms, you edit the basis to include these atoms. For example, you can edit the basis of the exclusion spheres in the previous query to include the carboxyl group. The following are examples of the 3D structures that you retrieve (For clarity, the measured value of one distance constraint is not displayed):

You can also specify that unconnected atoms that are not part of the query can lie within the volume of the exclusion spheres. For example, you might want to allow salt ions or water molecules within the volume of the exclusion sphere. To allow these atoms, you specify the following setting when you create the exclusion sphere: Allow nonquery atoms within exclusion sphere.

Note: You can use exclusion spheres to represent regions on a receptor. For examples, see Section 53.11.

Dihedral

When two planes intersect, a dihedral angle is created from the common vertex of reference positions 1 and 2 and reference positions 3 and 4:

Atoms 1 and 2 are adjacent reference points for the phenol structure, and atoms 3 and 4 are adjacent reference points for the phenyl structure. Reference points 1, 2, and 3 lie along the first plane, and reference points 2, 3, and 4 lie along the second plane. Reference points 2 and 3 share both planes and form the vertex of the dihedral angle.

The angular range that you specify must be between -180 and +180 degrees.

The following query specifies a dihedral angle between two atoms on a phenyl ring and two atoms on a phenol ring:

The following are examples of the 3D structures that you retrieve:

Linearity

You can specify that three or more reference positions (atoms, points, or ring centroids) must lie along the same line. To do this, you specify the maximum average distance (RMS deviation) of the reference positions from the best-fit line derived from the reference positions. The following shows a linearity constraint for all atoms in a trialkene:

The value that you specify must lie between 0 and 1,000.

Planarity

You can specify that four or more reference positions (atoms, points, or ring centroids) must lie along the same plane. To do this, you specify the maximum average distance (RMS deviation) of the reference positions from the best-fit plane derived from the reference positions. The following shows a planarity constraint for all atoms in a benzaldehyde:

The value that you specify must lie between 0 and 1,000.

Atom

Use atom data to specify a data constraint for selected atoms in your query, such as spectroscopic and quantum mechanical data or partial charges. For example:

The atom data constraint specifies the partial charge on the oxygen. Rn specifies that the oxygen must appear in a ring. For more information on Rn and other atom and bond query features, see Section 53.6.

Atom-Pair

Use atom-pair data to specify a data constraint between two atoms in your query. For example, you can specify bond order, lower/upper distance constraints, and spectroscopic and quantum mechanical data. The following query specifies values for the ring proton spin-spin couplings of methyl 2-furoate:

53.11 Using Receptor Information

The previous sections showed how to use information about active compounds (that is, information about the pharmacophore) to specify query constraints. This section shows how you can use information about the receptor to specify geometric constraints in your query. Use these examples as a starting point for creating your own queries.

Note: For simplicity, the queries in this section use a simple definition of a basic nitrogen. For more refined definitions of basic nitrogen, see Section 53.8.2.

53.11.1 Hydrogen-Bond Interactions

You can use projected points and exclusion spheres to represent hydrogen bond donors and acceptors on the receptor.

Note: There are two different conventions for defining hydrogen-bond donors and acceptors. This help file uses the definition of a hydrogen-bond donor that is generally used by medicinal chemists. By this convention, the donor of a hydrogen bond is the group to which the hydrogen atom is attached:

An alternative definition of hydrogen-bond donors and acceptors defines a hydrogen-bond donor as the group that provides the lone-pair electrons (LP) to the hydrogen bond.

Hydrogen-Bond Donor on Receptor

The following example shows how to construct an exclusion sphere that represents a hydrogen-bond donor on the receptor. The hydrogen-bond donor on the receptor forms a hydrogen bond with a complementary hydrogen-bond acceptor on the ligand. You construct the exclusion sphere around a point that you construct from two atoms of the hydrogen-bond acceptor on the ligand.

Hydrogen-Bond Acceptor on Receptor

The following example shows how to construct an exclusion sphere that represents a hydrogen-bond acceptor on the receptor. The hydrogen-bond acceptor on the receptor forms a hydrogen bond with a complementary hydrogen-bond donor on the ligand. You construct the exclusion sphere around a point that you construct from two atoms of the hydrogen-bond donor on the ligand.

Distance Constraint Between Features on the Receptor

Specifying distance constraints between points on the receptor rather than the ligand can produce highly specific queries. For example, suppose you know that the receptor contains a hydrogen bond donor that is 10 - 11.5 Angstroms from a basic nitrogen. The following figure schematically shows how two topologically different drugs that can bind to the same receptor site.

If you use a query that uses information about the pharmacophore (ligand-based query), you must specify a large distance range (4 - 10 Angstroms) to retrieve both classes of compounds. The ligand-based query retrieves the compounds that you want, but also retrieves many false hits. If you use a query that uses information about the receptor (receptor-based query), you can specify a much narrower distance range. For example:

The greater specificity in the receptor-based query allows you to retrieve the compounds that you want while eliminating many of the false hits that the ligand-based query might produce.

53.11.2 Pi-Pi Interactions

You can use projected points and exclusion spheres to represent pi-pi interactions with aromatic groups on the receptor.

Pi-Pi Interactions Alone

Use exclusion spheres above and below aromatic rings that interact with aromatic groups on the receptor. The exclusion spheres eliminate 3D structures with atoms that intrude into the excluded area. Consequently, all 3D structures that you retrieve can contain phenyl rings that can interact freely with the receptor.

To create the exclusion spheres, you create a normal to the plane of the phenyl ring. On that normal, you place a point that is 3.0 Angstroms above (+ 3.0 Angstroms) the plane of the ring, and another point that is 3.0 Angstroms below (- 3.0 Angstroms) the plane of the ring. Around each point, you create exclusion spheres that are 1.5 Angstroms in diameter.

The following query uses exclusion spheres and a distance constraint:

Pi-Pi Interactions With a Distance Constraint

To specify a distance constraint between a lipophilic site and another site on the receptor, use a projected point on one side of an aromatic ring. Use exclusion spheres to eliminate 3D structures that do not permit the aromatic ring to interact freely with the receptor.

To construct the exclusion spheres and projected points, create a normal to the plane of the phenyl ring. On that normal, you place a point that is 2.0 Angstroms above (+ 2.0 Angstroms) the plane of the ring, and another point that is 2.0 Angstroms below (- 2.0 Angstroms) the plane of the ring. On the normal, you place another point that is 3.5 Angstroms from the plane of the ring. Around the two points at 2.0 Angstroms from the aromatic ring, you create exclusion spheres that are 1.5 Angstroms in diameter.

The following query specifies a distance constraint of 6 - 10 Angstroms between a lipophilic site on the receptor and a hydrogen-bond donor on the receptor (for clarity, the query uses a simple definition of a basic nitrogen):

53.12 Specifying Flexmatch Parameters

This section contains information on the parameters that you specify with the FLEXMATCH search operator.

53.12.1 Flexmatch Parameters

A Flexmatch (FLEX) search finds records that are an exact match of your query, except in the ways that you specify with any of the flexmatch parameters. You specify features of retrieved structures that must match your query. If you specify flexmatch parameters, you tighten the definition of an exact match. This allows you to find structures that:

*	Have different counterions than the salt in your query.

*	Match your query, but have different isotopic labels.

*	Match your query, but might be represented differently in the database. For example, the pi-metal bonds in ferrocene can be represented in different ways.

Flexmatch parameters define the features of retrieved 2D structures that must match your query molecule. When you specify flexmatch parameters, you tighten the definition of an exact match. (If you do not specify flexmatch parameters, you retrieve the loosest possible match that is possible for an exact match.) The flexmatch parameters are as follows:

Bond Type (BON)

BON specifies that all bond types must match.

Tautomer (TAU)

TAU specifies that tautomer groups must contain the same number of hydrogens in the tautomeric region, within a tolerance limit. The tolerance limit is the sum of the absolute values of charges plus the sum of the number of radicals plus the number of metal bonds. Diradicals count as two radicals. (If you specify TAU and also specify HYD, the tolerance limit is zero.)

A tautomer is a group of atoms with any of the following patterns:

Where	Q = O, N, S, Se, or Te

X = C, O, N, S, Se, or Te

Y = C, I, P, As, Sb, Cl, or Br

You can have multiple tautomeric groups in a single molecule. For example:

In addition, any bonds in the tautomeric region can be aromatic. For example:

Atom charges (CHA)

CHA specifies that the charge on each atom must match those in your query. This automatically ensures that the sum of the charges on each fragment must match.

Ion charges (ION)

ION specifies that the total charge for each fragment in the query must match.

Fragments (FRA)

FRA specifies that all fragments must match your query, and that no additional fragments are allowed.

For example, a single query that contains solely fragments A and B retrieves molecules that contain solely fragments A and B. However, the same query does not retrieve molecules that contain solely fragment A, solely fragment B, or fragments A, B, and C (where C is any fragment that is not in the query).

Note: Salt queries that contain fragment B as the counterion retrieve solely Fragment A, where A is the parent of the salt.

Hydrogen (HYD)

HYD specifies that hydrogen count must match for each fragment in your query.

If you do not specify HYD, the hydrogen count within a tolerance limit for each of the fragments must match. The tolerance limit is the sum of the absolute values of charges plus the sum of the number of radicals plus the number of metal bonds. Diradicals count as two radicals.

If you specify TAU and HYD, the hydrogen count must match exactly in both the tautomeric regions and in the individual atoms of non-tautomeric regions.

If you specify TAU, but do not specify HYD, the hydrogen count must match within the tolerance limit in both the tautomeric regions and in the individual atoms of non-tautomeric regions.

Isotopes (MAS)

MAS specifies that the isotopic labels on each atom must match those in your query. (Isotopic labels include H, D, and T.)

If you do not specify MAS, you retrieve molecules in the database that have different isotopic labels, and H, D, and T are equivalent to each other.

Metal (MET)

MET specifies that the connectivity of all metals must match your query. A metal is any atom other than H, D, T, He, B through Ne, Si through Ar, As through Kr, Te, I, Xe, At, and Rn.

If you do not specify MET, you can retrieve all the different representations of your query. For example, to retrieve all representations of ferrocene even though the pi-metal bonds are represented in different ways in your database, do not specify MET.

If you do not specify MET, and also do not specify SAL, any counterions that are attached to the metal are removed.

Radicals (RAD)

RAD specifies that the radical value on each atom must match those in your query.

Salts (SAL)

SAL specifies that the counterions in the structures retrieved must match the counterion in your query. A counterion is any fragment or single atom in the SALTS.DAT file (or equivalent). This file is customizable. For more information, see your ISIS Administrator.

If you do not specify SAL, you retrieve molecules with different counterions than those in your salt query.

If you do not specify SAL, and also specify FRA, you retrieve solely the parent structures of salts.

Stereoconfiguration (STE)

You can specify that the configuration of stereo centers (in geometric and optical stereoisomers) must match. You can only use this feature if you also specify BON.

If your query contains unspecified stereo centers, you retrieve solely those structures with unspecified stereo centers. An unspecified stereo center is the asymmetric center of atoms C, N, O, P, S, or Si, that is connected to one of the following:

*	No stereo bonds

*	An EITHER query bond (specifies either the Up or Down stereoconfiguration)

*	A DOUBLE EITHER bond that (specifies either the cis or trans stereoconfiguration)

Valence (VAL)

VAL specifies that the valence on each atom must match those in your query.

Notes: (1) If no valence is specified, an implicit valence is calculated from the structure. A query with an unspecified valence (with a calculated implicit valence) might retrieve a structure that contains the matching explicit valence. Or, a query with an explicit valence might retrieve a structure that does not contain an explicit valence (that contains a calculated implicit valence). (2) Some valences are illegal. For transition metals, a valence is illegal if it is smaller than the number of bonds to the atom. For other real atom types, an illegal valence is ignored in a FLEX search and the query retrieves any valence.

53.12.2 Combinations of Flexmatch Parameters

The Most Restricted Flexmatch Parameters

To retrieve the most restricted exact match of your FLEX query from the database, specify all flexmatch parameters. For example:

MODEL>MOL>MOLSTRUCTURE FLEXMATCH query "FRA/HYD/MAS/MET/RAD/SAL/STE/VAL/BON/TAU/ION/CHA"

The Least Restricted Flexmatch Parameters

To retrieve the least restricted exact match of your FLEX query from the database, specify no flexmatch parameters. For example:

MODEL>MOL>MOLSTRUCTURE FLEXMATCH query ""

53.12.3 Examples of the Interactivity of Flexmatch Parameters

The flexmatch parameters are typically interactive. To obtain the correct results, you need to know which flexmatch parameters require other flexmatch parameters to function correctly. With the correct interactive settings, you can retrieve closely related structures that are represented in a variety of ways in your database. For example:

*	MDL depicts sulfones with undisplayed charges in which two of the four bonds on the sulfur atom are double bonds. In your database, these compounds might be displayed with charges instead:

You need to consider both charges and bond types. To retrieve all representations of a specific sulfone, use the following query:

MODEL>MOL>MOLSTRUCTURE FLEXMATCH query ""

Note: You can specify other flexmatch parameters to tighten the definition of exact match. However, you must not specify TAU or ION.

*	MDL depicts sulfoxides with undisplayed charges in which there is a double bond on the sulfur atom. In your database, these compounds might be displayed with charges instead:

You need to consider both charges and bond types. To retrieve all representations of a specific sulfoxide, use the following query:

MODEL>MOL>MOLSTRUCTURE FLEXMATCH query "TAU/ION"

Note: You can specify other flexmatch parameters to tighten the definition of exact match. However, you must not specify CHA or BON.

*	MDL depicts thiocarboxylic acid salts with undisplayed charges in which there is a bond from the ion to the counterion. In your database, these compounds might be displayed with charges instead:

You need to consider charges, bond types, and metal bonds. To retrieve all representations of a specific salt, use the following query:

MODEL>MOL>MOLSTRUCTURE FLEXMATCH query "BON/TAU"

Note: You can specify other flexmatch parameters to tighten the definition of exact match. However, you must not specify MET, CHA, SAL, FRA, or ION.

*	MDL depicts π ligands in organometallic complexes with radicals or with covalent bonds. You need to consider charges, bond types, metal bonds, and radicals. To retrieve all representations of a specific organometallic complex, use the following query:

MODEL>MOL>MOLSTRUCTURE FLEXMATCH query "TAU"

Note 1: You can specify other flexmatch parameters to tighten the definition of exact match. However, you must not specify BON, CHA, ION, MET, or RAD.

Note 2: You can also retrieve specific organometallic complexes with an exact formula query in an FMLA search.

53.13 The CFS Search Process and Its Options

This section contains information on the parameters that you specify when you use the SSS3D search operator with the option that specifies Conformationally Flexible Substructure (CFS) searching, (SSSS3D/CFS).

53.13.1 Understanding the CFS Search Process

During a CFS search, ISIS subjects each 3D structure in the search domain to the following three-step process:

The following sections describe each step of this process in detail.

Step 1: 2D Key Screening

Every structure in a database is associated with a set of binary representations of its structural entities, called keys. The 2D key screening step retrieves all the static 3D models in the database that contain the structural fragments of your query embedded in them. The presence of structural fragments and their combinations can be represented by one or more of 960 key codes.

Step 2: Upper/Lower Distance Screening

The upper/lower distance screening step tests the fit of certain geometric constraints for those conformations from the 2D key screening step. ISIS tests the fit solely of distance and angle constraints that are defined by atoms and ring centroids. The process rotates single bonds between two atoms to find the maximum and minimum separation possible. At this stage of the process, ISIS tests the fit of each distance and angle constraint independently of the other constraints.

Step 3: Conformational Fitting

If your 3D query contains more than one distance constraint, ISIS uses a torsional fitter to retrieve those conformations from the upper or lower distance screening that can be suitably rotated about their rotatable single bonds. The torsional fitter attempts to minimize the deviations between measured values of 3D constraints and the values that are specified in your search query.

ISIS omits conformational fitting if the query contains only one distance or angle constraint.

The conformational fitting step is optional. If you do not perform conformational fitting during the search, ISIS performs conformational fitting on each 3D structure as you view it (view-time fitting).

53.13.2 Using the Default CFS Options

CFS searching provides many options that allow you to control how ISIS fits 3D structures to your query. The default CFS options generally provide the best balance between accuracy and speed for most CFS searches. This section explains how the default options affect the CFS search results.

Caution: The CFS options subtly interact with each other and can produce undesirable results if improperly used. If you are not sure how to use the CFS options, we strongly recommend that you use the default CFS options.

When you perform a CFS search, you want to balance the following factors:

*	Quality of fitted 3D structures. You want to retrieve 3D structures that are realistic. That is, you want the fitted 3D structures to be as close as possible to minimum-energy conformations.

*	Quantity of fitted 3D structures. You want to retrieve as many 3D structures as possible that can be fitted to the constraints in your query.

*	Speed of searching.

To achieve the best balance among these three factors, you generally perform a CFS search in two distinct passes:

1.	An initial CFS search. This CFS search ignores non-bonded (van der Waals) interactions between parts of the molecule that are rotated to fit the query, because calculating nonbonded interactions can slow search speeds. You generally use the default CFS options for this search.

2.	An optional bump-checking CFS search over the set of records that you retrieved in the initial CFS search. Bump checking eliminates fitted conformations that have unfavorable nonbonded interactions (that is, conformations in which atoms bump into one another) by calculating nonbonded interactions between parts of the molecule that are rotated to fit the query. The slow search speeds caused by calculating nonbonded interactions are less important, because you perform the search over a smaller set of records.

If you want, you can eliminate the bump-checking CFS search and perform bump checking as you view your search results (view-time bump checking). If any structures on your list have unfavorable nonbonded interactions, ISIS displays these structures without overlaying the query.

When you specify the default CFS options, ISIS does the following during the CFS search:

*	Automatically chooses the more appropriate torsional fitting algorithm (simplex or derivative) for your query.

*	Rotates solely acyclic single bonds that contain at least one atom that is sp3-hybridized. An exception is made for amide bonds, which are not rotated. This definition of a rotatable bond produces a high proportion of fitted structures with low-energy conformations.

*	Ignores nonbonded (van der Waals) interactions between atoms during the search and calculates nonbonded interactions for each fitted structure as you view it (that is, performs bump checking at view time only). This produces faster search speeds, yet allows you to find structures that contain unfavorable nonbonded interactions.

*	Avoids calculating derived data on van der Waals energy difference, torsional degrees of freedom (TDF), and RMS deviation for sorting, viewing, or search cutoffs. These calculations can slow search speeds. For more information on derived data, see Section 53.13.4.

*	Makes at least five attempts to fit (map) the query to each 3D structure in the search domain. This generally produces the maximum number of hits without sacrificing search speed.

If you want to experiment with the CFS options, we strongly recommend that you study Section 53.13.3 so that you can make meaningful choices.

53.13.3 Options for CFS Searching

This section describes each option for the conformational fitting step of CFS searches and explains how that option affects the search.

Fitter Selection (METHOD)

Use METHOD to specify either the simplex or derivative torsional fitter:

*	The simplex torsional fitter was originally developed in collaboration with Molecular Simulations, Inc. and uses the Nelder-Mead sequential simplex minimizer. The fitter uses variable rotation increments to approach a minimum in the objective function. You can use the simplex fitter with any 3D query components, including fixed atoms.

*	The derivative torsional fitter was developed at Zeneca Pharmaceuticals Group and attempts to minimize a differentiable objective function with a combination of first- and second-order optimization techniques. 3D query components are restricted to the following: atoms, ring centroids, angles that are defined by three atoms or ring centroids, and distances that are defined by two atoms or ring centroids.

*	If you do not specify either of these fitters, you can specify Automatic to allow ISIS to choose the fitter automatically. If the query contains solely distances and angles, the automatic setting chooses the derivative fitter. If the query contains additional types of 3D constraints, the automatic setting chooses the simplex fitter.

By default, ISIS uses Automatic.

The following table shows the components of the 3D query that you can use with the simplex and derivative fitters:

Note: Both the simplex and derivative fitters attempt to optimize the conformation over the range of the distance or angle constraint. For the derivative fitter alone, you can also optimize the fit to the midpoint of the distance or angle constraint. That is, the derivative fitter can not only find a conformation that fits the query, but can also find the conformation that fits the query as closely as possible. If you want ISIS to optimize to the midpoint, however, you must either specify a search cutoff for RMS deviation, or specify that ISIS calculate RMS deviation for sorting and viewing. For more information on derived data and RMS deviation, see Section 53.13.4.

The following query specifies a CFS search that uses the derivative fitter:

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS=METHOD:DERIVATIVE"

Fitting at Search Time (SFIT)

Use SFIT to specify whether ISIS performs conformational fitting during the search (search-time fitting) or during viewing (view-time fitting). If your query contains solely atoms, ring centroids, distances that are defined by two atoms or ring centroids, and angles defined by three atoms or ring centroids, you can specify conformational fitting at view time (SFIT:OFF). If you specify SFIT:OFF, ISIS performs only 2D key screening and upper/lower bounds checking during the CFS search. Consequently, your search speed increases, but your search results might contain some false hits.

You must perform conformational fitting at search time (SFIT:ON) if you want ISIS to calculate certain types of derived data such as RMS deviation and van der Waals energy difference. For more information on derived data, see Section 53.13.4

Note: You can specify SFIT:OFF only if your query consists solely of the following 3D query components: atoms, ring centroids, distances that are defined by two atoms or ring centroids, and angles that are defined by three atoms or ring centroids. If your query contains any other 3D query features, you must specify SFIT:ON.

By default, conformational fitting occurs at search time (SFIT:ON).

The following example specifies a CFS search without fitting at search time:

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS=SFIT:OFF"

Maximum Number of Attempted Fittings (MAXFIT)

The torsional fitter can attempt up to 1000 unique mappings that match the conformation to your query specifications. Use MAXFIT to specify the number of mappings.

In general, the higher the number of attempted fittings, the longer the search, and the more 3D structures you potentially retrieve. If your database has many large, complex 3D structures, you might want to use a low value to maximize your search speed. For typical queries that use interatomic distances, the time that the search requires increases linearly with the value of the distance constraint. However, ISIS generally retrieves very few extra hits when you specify a number greater than 5. Also, a value of 1000 might not assure that ISIS attempts all possible mappings for each 3D model.

You can specify any value from 1 to 1000. The default value is 5. However, if you activate ring flexing, we recommend that you increase this number to at least 25.

The following example specifies a CFS search with up to 99 attempted fittings:

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS=MAXFIT:99"

Ring Flexing (RFLEX, RMIN:<value>, RMAX:<value>)

Use RFLEX to specify that single bonds in rings be considered rotatable. ISIS rotates only rings that are nonaromatic and that contain some rotatable single bonds.

Use RMIN and RMAX to specify the minimum and maximum sizes, respectively, of rings that you want to be flexible during conformational fitting. For example, a setting of 4 atoms for the minimum ring size and 8 atoms for the maximum ring size allows rotations about all single bonds in 4- to 8-membered rings. The suggested range is between 6 and 24 ring atoms.

If you activate ring flexing, we recommend that you increase the maximum number of attempted fittings (MAXFIT) to at least 25. When you activate ring flexing with a suitable number of attempted fittings (25 or more), you generally obtain more hits. However, ring flexing also decreases search speed.

By default, RFLEX is OFF. The default value of RMIN is 6, and the default value of RMAX is 24.

The following example specifies a CFS search with ring flexing for rings of 6 to 24 atoms:

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS=MAXFIT:25,RFLEX:ON"

The following example specifies a CFS search with ring flexing for rings of 6 to 12 atoms:

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS=MAXFIT:25,RFLEX:ON,RMAX:12"

The following example specifies a CFS search with ring flexing for rings of 4 to 12 atoms:

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS=MAXFIT:25,RFLEX:ON,RMIN:4,RMAX:12"

Rotating Single Bonds Between Unsaturated Atoms (ROTSP2)

Use ROTSP2 to specify that single bonds between unsaturated centers (for example, biphenyl) be considered flexible. When this option is inactive (the default), ISIS rotates only acyclic single bonds with the following hybridizations:

sp3 - sp3
sp3 - sp2 (except amides and similar bonds)
sp3 - sp

The definition of amides includes the following:

When you activate bond rotation between unsaturated centers, ISIS extends the definition of an acyclic single bond so that bonds with the following hybridzations can rotate:

sp3 - sp3
sp3 - sp2 (except amides and similar bonds)
sp3 - sp
sp2 - sp2
sp2 - sp
sp - sp

If you activate bond rotation between unsaturated centers, you retrieve more hits. However, some of the fitted structures might have higher-energy conformations. Single bond rotation also requires additional calculations that produce slower search speeds.

By default, ROTSP2 is OFF.

The following example specifies a CFS search that allows bond rotation between unsaturated centers:

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS=ROTSP2:ON"

Bump Checking (SBUMP, VBUMP)

You can specify that nonbonded atoms within a conformation are not in close contact (that is, do not bump into one another). Bump checking calculations use the van der Waals radii of atoms. If you activate bump checking, ISIS takes nonbonded interactions into account during the conformational fitting step.

Note: The additional calculations for bump checking during conformational fitting produce slower search speeds than conformational fitting without bump checking. Consequently, we strongly recommend that you not activate bump checking when you search medium or large databases. Instead, we recommend that you perform the CFS search in two phases. First, perform an initial CFS search without bump checking. Then, set the search domain to the results of the initial CFS search and perform a bump-checking CFS search to remove the invalid hits.

SBUMP specifies whether to perform bump checking during the search (search-time bump checking). VBUMP specifies whether to perform bump checking when you are viewing your search results (view-time bump checking). You must perform bump checking during the search (SBUMP:ON) when you want to:

*	Specify a search cutoff for van der Waals energy difference.

*	Sort your search results by van der Waals energy difference.

*	Specify global relaxation (GRELAX:ON) during a search.

Also, we strongly recommend that you perform bump checking during the search when you want to export fitted 3D structures to a CFS SDfile for use in a modeling software program.

Note: For more information on calculations for van der Waals energy difference, see Section 53.13.4. Information on global relaxation appears later in this section.

You can specify bump checking at search time alone (SBUMP:ON,VBUMP:OFF), at view time alone (SBUMP:OFF,VBUMP:ON), at both search and view time (SBUMP:ON,VBUMP:ON), or no bump checking (SBUMP:OFF,VBUMP:OFF). The following table shows the four bump checking scenarios that you can specify. The default setting is bump checking at view time alone (Scenario 1).

We recommend that you use the following guidelines for bump checking:

Scenario 1 (SBUMP:OFF,VBUMP:ON): This is the default scenario, and is especially useful in improving the speed of your searches over medium or large databases. We recommend that you use this scenario for the initial phase of CFS searching. You retrieve approximately 10 to 15 percent additional false hits in your search results. The bump-checking CFS search removes these false hits.

Scenario 2 (SBUMP:OFF,VBUMP:OFF): You can use this scenario if you want to view the false hits and unacceptable conformations in your search results. You might want to use this information as a way of gathering ideas for creating better search queries, or as a way of determining the contents of your database.

Scenarios 3 (SBUMP:ON,VBUMP:OFF) and 4 (SBUMP:ON,VBUMP:ON): Use either scenario during the bump-checking CFS search, after you have set your search domain to the results of the initial CFS search. We strongly recommend that you do not use this scenario when you search over the entire database.

Note: To sort your search results by van der Waals energy difference (vdW), or to specify a vdW search cutoff, you must perform bump checking at search time (SBUMP:ON). If you want to specify a vdW search cutoff or sort by vdW, you must do so during the bump-checking CFS search.

The following examples specify an initial CFS search (view-time bump checking alone):

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS"

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS=SBUMP:OFF,VBUMP:ON"

The following examples specify a bump-checking CFS search (both search-time and view-time bump checking):

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS=SBUMP=ON"

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS=SBUMP:ON,VBUMP:ON"

Global Relaxation (GRELAX)

By default, ISIS rotates single bonds solely in the region of the structure that matches the query (the mapped region of the structure). Therefore, atoms that are outside this region might interfere during the bond rotations and result in the exclusion of a valid hit. Use GRELAX to specify that ISIS rotate single bonds in other parts of the structure to reduce nonbonded interactions throughout the molecule. Global relaxation increases the size of your hit list and produces more realistic 3D structures. However, global relaxation also requires additional calculations that can slow search speeds.

To activate global relaxation, bump checking must also be active.

By default, GRELAX is OFF.

The following examples specify a bump-checking CFS search (search-time bump checking) with global relaxation:

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS=SBUMP:ON,GRELAX:ON"

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS=SBUMP:ON,VBUMP:ON,GRELAX:ON"

53.13.4 Derived Data for Search Cutoffs, Display, and Sorting

ISIS can derive specific kinds of data from the 3D structures that it retrieves during a CFS search. This derived data is stored in fields that you see in the database definition. You can display this data in a form and use it for sorting, just like data in an actual database field. You can also specify search cutoffs that use the derived data. When you specify a search cutoff, ISIS eliminates any fitted 3D structure for which the calculated value is greater than the value that you specify.

If you want to sort your search results by derived data, we strongly recommend that you define sorting instructions before the search, and sort search results automatically after the search. If you sort search results manually after the search ISIS must repeat the search to calculate derived data. For more information on sorting, see the 3D Sorting Examples Request-A-Document.

ISIS can calculate three types of derived data during the search: torsional degrees of freedom (CFS_TDF field), root mean square deviation (CFS_RMS field), and van der Waals energy difference (CFS_VDW field). A fourth derived data field, CFS_FITTER, stores the name of the fitter (Simplex or Derivative) that ISIS used in the search.

Torsional Degrees of Freedom or TDF (CALC:TDF, TDF:<value>)

The number of rotatable bonds on the paths that connect the mapped atoms (Mapped atoms are the atoms in the hit that correspond to atoms in the query). The higher the TDF value, the more flexible is the portion of the 3D structure that maps to your query.

Use TDF:<value> to specify a search cutoff value (where <value> is the number of rotatable bonds), ISIS excludes fitted structures that have more than the value that you specify. We suggest a search cutoff value of 10 rotatable bonds.

Use CALC:TDF to calculate the TDF of each structure that you retrieve. You can use TDF values to sort your search results and/or view the TDF values on your form. To view TDF values on your form, connect a form box or table column to MODEL>CFS_TDF.

By default, ISIS does not calculate TDF or use a search cutoff.

The following example specifies a CFS search that eliminates 3D structures with more than 10 rotatable bonds in the mapped region:

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS=TDF:10"

The following example specifies a CFS search that calculates the TDF for each fitted 3D structure:

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS=CALC:TDF"

The following example specifies a CFS search that calculates the TDF value for each fitted 3D structure and eliminates 3D structures with more than 10 rotatable bonds in the mapped region:

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS=CALC:TDF,TDF:10"

RMS Deviation (CALC:RMS, RMS:<value>)

The root mean square value for the goodness-of-fit of the fitted 3D structure to the 3D features that you specified in your query. This is a composite measure of the goodness-of-fit to the query. RMS deviation appears in Angstrom deviations for distances, lines, planes, and fixed atoms and in cosine deviations for angles and dihedrals.

Use RMS:<value> to specify a search cutoff value (where <value> is RMS deviation search cutoff in RMS units), ISIS excludes fitted structures that have more than the value that you specify. The RMS values that ISIS calculates during the search can range from 0.0 to 1e20 RMS units. We suggest a search cutoff value of 0.7 RMS units.

Use CALC:RMS to calculate the RMS deviation of each structure that you retrieve. You can use RMS deviations to sort your search results and/or view the RMS deviations on your form. To view RMS deviations on your form, connect a form box or table column to MODEL>CFS_RMS.

By default, ISIS does not calculate RMS deviation or use a search cutoff.

You can calculate RMS deviation for either the simplex or derivative fitters. However, we recommend that you not use RMS deviation data to sort your search results unless you also specify the derivative fitter for the CFS search. The RMS deviation values that the simplex fitter calculates are not suitable for sorting because they are not optimized to the midpoint of the distance or angle constraint. Both the simplex and derivative fitters attempt to optimize the conformation over the range of the distance or angle constraint. However, only the derivative fitter optimizes the fit to the midpoint of the distance or angle constraint. That is, the derivative fitter can not only find a conformation that fits the query, but can optimize that conformation to fit the query as closely as possible. For more information on the simplex and derivative fitters, see Section 53.13.3.

Note: If you want the derivative fitter to optimize to the midpoints of the distance and angle constraints, you must specify a search cutoff for RMS deviation and/or specify that ISIS calculate derived data on RMS deviation. If you do not calculate RMS deviation, the derivative fitter optimizes the fitted structure only to the ranges of the distance or angle constraints.

The RMS deviation is expressed as follows:

That is, the RMS deviation is the sum of the RMS deviations of the individual 3D query features. The RMS deviations from each of the individual 3D query features are computed in the following way:

where RMS(p) is the p-th constraint, n is the number of type p constraints in the query, vi is the measured value of constraint i, vu is the upper bound of constraint i, and vl is the lower bound of constraint i.

Note: To calculate RMS deviation, you must specify fitting at search time (SFIT:ON, and specify a maximum number of attempted fittings (MAXFIT) that is greater than zero. (If you do not set these CFS options, ISIS sets them for you.)

The following example specifies a CFS search that eliminates 3D structures with an RMS deviation that is greater than 0.7 RMS units:

MODEL>MODELSTRUCTURE SSS3D query3D "/CFS=METHOD:DERIVATIVE,RMS:0.7"

The following example specifies a CFS search that calculates the RMS deviation for each fitted 3D structure:

MODEL>MODELSTRUCTURE SSS3D query3D "/CFS=CALC:RMS"

The following example specifies a CFS search that calculates the RMS deviation for each fitted 3D structure and eliminates 3D structures with an RMS deviation greater than 0.7 RMS units:

MODEL>MODELSTRUCTURE SSS3D query3D "/CFS=CALC:RMS,RMS:0.7"

Van der Waals Energy Difference (CALC:VDW, VDW:<value>)

The difference in van der Waals (vdW) nonbonded interaction energy between the fitted conformation and the conformation that is stored in the database. The values of vdW can fall within the range of -10,000 to 1e20 Kcals.

Use VDW:<value> to specify a search cutoff value (where <value> is the vdW search cutoff in Kcals), ISIS excludes fitted structures that have more than the value that you specify. The vdW energies that ISIS calculates during the search can range from -10,000 to 1e20 Kcals. We suggest a search cutoff value of 5 Kcals.

Use CALC:VDW to calculate the van der Waals (VDW) energy difference of each structure that you retrieve. You can use VDW to sort your search results and/or view the VDW values on your form. To view VDW values on your form, connect a form box or table column to MODEL>CFS_VDW.

The vdW energy is expressed as the following Lennard-Jones 6-12 potential:

Where Ri and Rj are the van der Waals radii of atoms i and j, respectively, and rij is the measured distance between atoms i and j. Atoms i and j must be at least four bonds apart.

The calculated vdW energy difference can be compared to nonbonded interaction energy in molecular mechanics solely if the fitted 3D structures contain hydrogens. If the stored 3D models in your database do not contain explicit hydrogens, then you must sprout hydrogens at all sites on the fitted 3D structures. For more information on hydrogen sprouting, see Section 53.14.

Note: To calculate data on van der Waals energy difference, you need to specify fitting at search time, bump checking at search time (SBUMP:ON), and a maximum number of attempted fittings (MAXFIT) that is greater than zero (If you do not set these CFS options, ISIS sets them for you.).

By default, ISIS does not calculate van der Waals energy, nor use a search cutoff for van der Waals energy.

The following example specifies a bump-checking CFS search that eliminates 3D structures with a van der Waals energy difference that is greater than 7 Kcals:

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS=SBUMP:ON,VDW:7"

The following example specifies a CFS search that calculates the van der Waals energy difference for each fitted 3D structure::

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS=SBUMP:ON,CALC:VDW"

The following example specifies a CFS search that calculates the van der Waals energy difference for each fitted 3D structure and eliminates 3D structures with a van der Waals energy difference that is greater than 7 Kcals:

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS=SBUMP:ON,CALC:VDW,VDW:7"

Fitter

The type of fitter (Simplex or Derivative) that ISIS used in the CFS search. This data is the same for all records from a CFS search, so it is not suitable for sorting. To view the fitter information on a form, connect a form box or table column to MODEL>CFS_FITTER. For more information on fitters, see Section 53.13.3.

53.13.5 Requirements of CFS search options

Some CFS options require specific settings for other CFS search options. If you do not specify the correct values, ISIS changes them automatically. These requirements are listed as follows:

For Bump Checking at Search Time (SBUMP:ON)

To specify bump checking at search time, MAXFIT must be greater than zero. We suggest a value of 5 (the default). If you also specify ring flexing (RFLEX:ON), specify MAXFIT:25.

You must specify bump checking during the CFS search if you want to:

*	Use van der Waals energy difference to sort your search results or as a search cutoff.

*	Specify global relaxation during the CFS search.

Derived Data For Search Cutoffs, Viewing, and Sorting

To sort your search results by RMS deviation, you must use the derivative fitter (METHOD:DERIVATIVE). Also, MAXFIT must be greater than zero.

To calculate van der Waals energy difference for viewing, for sorting, or as a search cutoff, MAXFIT must be greater than zero. You must also specify bump checking at search time (SBUMP:ON).

53.13.6 Limitations of CFS Searches

In a CFS search, 3D models are filtered out of the results through the three-step searching process. However, the CFS search might overlook 3D structures in the following ways:

Conformational Fitting Limitations

The number of iterations of attempted unique mappings required to retrieve all of the important 3D models (MAXFIT) might not be enough. Iterations depend on such factors as the number and type of query constraints, the number and mapping locale of atoms in the stored 3D models (especially for 3D models with highly symmetric or many aromatic rings), and the sizes of the 3D models. In addition, the fitter might converge to a false minimum (or local minimum) and reject a valid hit.

You can mitigate this limitation by increasing the maximum number of attempted fittings, allowing ring flexing (RFLEX:ON), and by turning off bump checking (SBUMP:OFF). This increases the number of hits but can also produce false hits.

Bump Checking Limitations

During conformational fitting, ISIS rotates solely bonds in the region that matches the query. Therefore, atoms that are outside this region might interfere during the bond rotations and result in the exclusion of a valid hit. You can, however, remove this limitation by activating global relaxation (GRELAX:ON).

53.14 Sprouting Hydrogens and Lone Pairs on 3D Structures

Note: This section contains information on search options that you use with the SSS3D search operator with the /CFS option.

3D structures in a molecule database generally do not contain explicit representations of hydrogen atoms. You can, however, create explicit hydrogen atoms on the structures that you retrieve by sprouting hydrogen atoms on 3D structures. You must sprout hydrogen atoms in the following situations:

*	To use bump checking during a CFS search (/CFS=SBUMP:ON). This produces more realistic 3D structures and allows ISIS to correctly calculate data on van der Waals energy difference.

*	To export 3D structures to modeling software programs that cannot sprout hydrogens.

Note: If your query contains lone pairs, sprouting hydrogen atoms also sprouts lone pairs at sites that correspond to lone pairs on the query.

Note: You can also specify hydrogen sprouting with the Sprout hydrogens and lone pairs option in the Search tab of Session Settings. For information on changing the Sprout hydrogens and lone pairs option in Session Settings, see the step-by-step instructions. Alternatively, choose Help > Index, and search for hydrogens, changing setting for sprouting on 3D structures. The settings in the Query Builder override the value in Session Settings.

You have three options for displaying hydrogen atoms and lone pairs on the structures that you retrieve.

Off (SPROUT:OFF)

Prevents sprouting of hydrogens and lone pairs on retrieved 3D structures. Use this setting when the 3D structures in your database already contain explicit hydrogens and lone pairs, or when your 3D graphical query does not contain explicit hydrogens and lone pairs.

The following example shows a CFS search with hydrogen sprouting off:

MODEL>MODELSTRUCTURE SSS3D spirap "0.5 0.5/CFS=SBUMP:ON,SPROUT:OFF"

If your 3D graphical query does not contain fixed atoms, the query is:

MODEL>MODELSTRUCTURE SSS3D query3D "/CFS=SBUMP:ON,SPROUT:OFF"

The following example shows a rigid 3D substructure search with hydrogen and lone-pair sprouting off:

MODEL>MODELSTRUCTURE SSS3D spirap "0.5 0.5 SPROUT:OFF"

If your 3D graphical query does not contain fixed atoms, the query is:

MODEL>MODELSTRUCTURE SSS3D query3D "SPROUT:OFF"

Query Atoms Only (SPROUT:QUERY)

Sprouts hydrogens and lone pairs on retrieved 3D structures, but solely at sites where hydrogens and lone pairs appear on the query. Use this setting during the initial CFS search, for faster searching. This setting is the default.

The following examples show a rigid 3D substructure search with hydrogen and lone-pair sprouting on query atoms only:

MODEL>MODELSTRUCTURE SSS3D spirap "SPROUT:QUERY"

MODEL>MODELSTRUCTURE SSS3D spirap ""

All (SPROUT:ALL)

Sprouts hydrogens at all sites on retrieved 3D structures, and sprouts lone pairs on retrieved structures at sites where lone pairs appear on the query. In a bump-checking CFS search, use this setting to produce fitted structures that are more realistic. You must use this setting if you want to export 3D structures to a modeling software program that does not sprout hydrogens.

The following example shows a CFS search with hydrogens sprouted at all atoms, and lone-pairs sprouted at atoms where lone pairs appear on the query:

MODEL>MODELSTRUCTURE SSS3D spirap "/CFS=SPROUT:ALL"

53.15 Guidelines for Revising the Search

If your QB search retrieved no records or too few records, you might want to:

*	Conduct a QB search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the structural constraints in your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, remove substituent limits, or remove stereochemical requirements.

*	Make the text/numeric strings in your query more general, and then search the same set of records. For example, you can apply operators that partially restrict, such as > or between instead of =, or you can apply wildcards. (A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters.)

*	For the "=" (exact match) operator and a 2D graphical query: Conduct a different search on the same set of records with the same query. For example, you might use one of the following operators: Molecule Similarity (MSIMILAR), Tautomer (TAUTOMER), Isomer (ISOMER), or Flexmatch (FLEXMATCH).

*	For the "=" (exact match) operator and a 3D graphical query: Increase the fixed-atom tolerances.

*	For the ISOMER, TAUTOMER, or PARENT operators: Conduct a different search on the same set of records with the same query. For example, you might use one of the following operators: Molecule Similarity (MSIMILAR), Tautomer (TAUTOMER), Isomer (ISOMER), or Flexmatch (FLEXMATCH).

*	For the FLEXMATCH operator: Specify looser flexmatch parameters. If your query contains stereochemistry, add or delete the stereochemistry in your query. If you omit the stereochemistry in your query, the records retrieved will contain no stereochemistry. The records match your search query exactly, except where you specify a looser fit with flexmatch parameters.

*	For the SSS operator and a 2D graphical query: Make your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, remove substituent limits, or remove stereochemical requirements. If your query contains Rgroups, make the Rgroup conditions in your query more general, and then search the same set of records. For example, you can decrease the number of Rgroup sites that must be satisfied or allow unsatisfied Rgroup sites to be filled with non-Rgroup substituents (instead of with hydrogens solely)

*	For the SSS operator and a 3D graphical query: Use the same guidelines as for the SSS3D operator (Section 53.2).

*	For the MSIMILAR operator: Specify a lower similarity value. Or, specify SUPER as the similarity type.

*	For the SSS3D operator: Make your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, or increase the range of distance, angle, and other 3D constraints. If your query contains a submodel, you can increase the fixed-atom tolerances.

If your QB search retrieved too many records, you might want to:

*	Make the text/numeric string in your query more restrictive, and then search the same set of records. For example, you can use the operator = instead of >.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	First, conduct a formula search (or a data search on molecular weight) to screen out large and complex molecules that are stored in your database, and then conduct a search on the less complex molecules. If your query is not able to map a stored molecule within a specific length of time, the molecule is added to the search results.

*	Filter your search results so that you view solely the lower-level records. (This assumes that you are viewing both upper- and lower-level records.)

*	For the SSS operator and a 2D graphical query: Refine the structural constraints in your query, and then search the same set of records. For example, you can limit substitution at specific positions, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query. If your query contains Rgroups, make the Rgroup conditions in your query more specific, and then search the same set of records. For example, you can increase the number of Rgroup sites that must be satisfied or restrict unsatisfied Rgroup sites to be filled solely with hydrogens.

*	For the MSIMILAR operator: Specify a lower similarity value. Or, specify SUB as the similarity type.

*	For the FLEXMATCH operator: Specify stricter flexmatch parameters.

*	For the SSS operator and a 3D graphical query: Refine your query, and then search the same set of records. For example, you can restrict atom or bond variation with explicit atoms or bonds, add additional substructures to the query, narrow the ranges of distance, angle, and other 3D constraints.

*	For the SSS3D operator: Refine your query, and then search the same set of records. For example, you can restrict atom or bond variation with explicit atoms or bonds, add additional substructures to the query, narrow the ranges of distance, angle, and other 3D constraints. If your query contains a submodel, you can decrease fixed-atom tolerances.

53.16 Guidelines for Improving Search Speed in 3D Substructure Searches

You use the SSS3D or SSS operator with a 3D graphical query to find the query that best describes the geometry of active compounds. You generally conduct several 3D substructure searches with increasingly refined queries. However, 3D substructure searches can require a long time. The methods that you use to optimize search speed while retrieving as many structures as possible depend on the type of search:

*	To optimize search speed in a rigid 3D substructure search (SSS; or SSS3D without /CFS), study the Request-A-Document SSS3D Searching Concepts/Examples.

*	To optimize search speed in a CFS search (SSS3D with the /CFS option), study the Request-A-Document CFS Searching Concepts/Examples.


Local QB for 3D Databases: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a QB Search in a Local 3D Database	54.1

*	Specifying a QB Query	54.2

*	Definition of Aromaticity	54.3

*	Specifying Query Features on Atoms and Bonds in Structures	54.4

*	Specifying Stereochemistry	54.5

*	Guidelines for Revising the Query	54.6

We recommend that you print this 11-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a QB search in a local 3D database, click here.

54.1 Definition of a Local QB Search in a Molecule Database

You can use the local Query Builder (QB) search to create any of the other remote searches in ISIS. However, you must use an all-text search query. Thus, we recommend that you use another type of search where possible!

A QB search does have one unique feature: You can combine AND, OR and NOT boolean operators in a search query. For example, to find all 3D structures (MODELSTRUCTURE field) that contain the 3D substructure spirapril embedded wholly within them AND have a molecular weight less than 500, enter:

MODEL>MODELSTRUCTURE SSS spirap
AND MODEL>MOL>MOLECULAR.WEIGHT < 500

where spirap is the name of the file that contains the 3D substructure spirapril.

To find all 3D structures that do NOT contain the 3D substructure spirapril embedded wholly within them, enter:

NOT (MODEL>MODELSTRUCTURE SSS spirap)

To find all 2D structures (MOLSTRUCTURE field) that contain both indole and a molecular weight greater than 200 but NOT those molecules with a melting point below 190, enter:

(MODEL>MOL>MOLSTRUCTURE SSS indole
AND MODEL>MOL>MOLECULAR.WEIGHT > 200)
AND NOT (MODEL>MOL>MELTING.POINT < 190)

where indole is the name of the file that contains the indole structure.

A local search is a search over a database that typically exists on your hard disk. To do a local search on your hard disk, you do not need to input network information.

Note: To do a local search that is accessed from a shared network, you need to input network information.

54.2 Specifying a QB Query

Each QB query contains:

*	The database field that you want to search.

For example, to search the melting point field, enter either the full path name, MOL>MELTING.POINT>MELTING.POINT, or the minimum tree name that uniquely identifies the field, namely MELTING.POINT. To search the structure field, enter either the full path name MODEL>MOL>MOLSTRUCTURE, or the minimum tree name that uniquely identifies the field, namely MOLSTRUCTURE.

*	A search operator that specifies the type of search (such as a greater than sign, >, to specify a search that finds solely the target text in the query).

*	The text or numeric target value (specific data) that you want to find. (In addition, your target value can be a file name that corresponds to a structure that you want to retrieve.)

A text or numeric target value can contain wildcards. A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. For example, you can specify the query LIKE "%ALD%" (instead of the query LIKE "BENZALDEHYDE"). The wildcard _ is a placeholder for solely one unspecified character. For example, you can specify the query LIKE "_CHLOROBENZENE" (instead of the query LIKE "2-CHLOROBENZENE"). Target values that contain text or wildcards require double quotation marks.

Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

For example, to find records that contain structures with a melting point that is greater than 220, enter:

MOL>MELTING.POINT>MELTING.POINT > 220

Note: You can combine statements in a single text/numeric string with one of the logical operators AND, OR, and NOT. When you use the NOT operator, enclose the text/numeric string in parentheses. For example, enter:

NOT (MOL>MELTING.POINT>MELTING.POINT > 220)

54.2.1 The Search Operators

Use one of the following search operators with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005): <, <=, >, >=, and <>. With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

<, <=, >, >=, and <>

Search Operator	Definition	Examples

=	equal (numeric)	MOLECULAR.WEIGHT = 350

<	less than (numeric)	MOLECULAR.WEIGHT < 350

<=	less than or equal to (numeric)	MOLECULAR.WEIGHT <= 350

>	greater than (numeric)	MOLECULAR.WEIGHT > 350

>=	greater than or equal to (numeric)	MOLECULAR.WEIGHT >= 350

<>	not equal to (text or numeric)	MOLECULAR.WEIGHT <> 350

ACTIVITY <> "inhibitor"

For a MOLFORMULA field, an exact formula query retrieves records that contain solely the exact atoms that you specify. To create an exact formula query, specify the target value for the formula. The target value must include all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required. The equals operator (=) and quotes are optional. For example:

Exact Formula Query	Examples of Records Retrieved

c6 h6 O	Phenol

c6h6o

C20 H12 Na2 O4	Sodium salt of phenolphthalein

C20H12Na2O4

= C20 H12 Na2 O4

= C20H12Na2O4

= "C20 H12 Na2 O4"

= "C20H12Na2O4"

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Exact Formula Query	Examples of Records Retrieved

C17 H19 N 03	Piperine

C17H19N 03	Piperine

C17H19N103	Piperine

C17H19N03	No molecules retrieved. ISIS interprets "NO3" as 3 Nobelium atoms.

LIKE

Use LIKE with text enclosed in double quotation marks. Enter your query as follows:

Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. For example:

Query	Examples of Records Retrieved

COMPOUND.NAME LIKE "methane"	Methane

COMPOUND.NAME LIKE "benzoic acid"	Benzoic Acid

COMPOUND.NAME LIKE "%acid"	Benzoic Acid

Acetic Acid

COMPOUND.NAME LIKE "%acid%"	Benzoic Acid Sodium Salt

Acetic Acid Sodium Salt

COMPOUND.NAME LIKE "%but_ne"	Trans 2-Butene

2-Butene

N-Butane

Butane

Butene

COMPOUND.NAME LIKE "_ethyl"	Methyl

Ethyl

ACTIVITY LIKE "antibiotic"	Antibiotic

ACTIVITY LIKE "%antibiotic%"	Antibiotic activity

Resistance to antibiotics

Note: To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice. To retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: ACTIVITY LIKE "aa""a" or ACTIVITY LIKE"%aa""a%".

For a MOLFORMULA field, a subformula query retrieves records that contain the specific atoms that you specify, and any additional atoms. To create a subformula query, use the LIKE operator with a target value. The target value can include a range of atom counts, and typically excludes the hydrogens. To exclude specific atoms from the molecules that you retrieve, specify zero for that atom. You can use a single space to separate atoms. Capital letters are not required. Quotes are optional.

Subformula Query	Examples of Records Retrieved

LIKE Na	All sodium salts

LIKE c12 Br(1-2) S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE "C12Br(1-2)S2"	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE c6 h6	All molecules that contain six carbon atoms, six hydrogen atoms, and any number of other atoms

LIKE C5 H10 N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

LIKE C5H10N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Subformula Query	Examples of Records Retrieved

LIKE C12 Br S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12Br1S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12BrS2	No molecules retrieved. ISIS interprets "BrS" as an atom symbol, and gives an error message.

BETWEEN

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks. For example:

CORPORATE.ID BETWEEN "XR11" "XZ15"

CORPORATE.ID BETWEEN 95 100

EXISTS

Use EXISTS to retrieve all records in the database that contain data in a specific database field. For example:

MODEL>MOL>MOLSTRUCTURE EXISTS

To retrieve all records in the database that contain no data in a specific database field, use NOT in your query:

NOT (MODEL>MOL>MOLSTRUCTURE EXISTS)

Note: You can only use the EXISTS search operator for certain types of database fields. Using EXISTS with other types of fields produces an error message.

SSS

Use SSS to retrieve database structures that contain your graphical query as a substructure embedded wholly within them. For example (query is the file name of your graphical query):

MODEL>MOL>MOLSTRUCTURE SSS query

54.2.2 Specifying a Structure in a QB Query

To include a graphical (structural) component in your QB query, you must enter the following in the Query Builder text box in the order shown:

*	The name of the database field that will hold your graphical search results. For a molecule record, enter MODEL>MOL>MOLSTRUCTURE.

*	The search operator. For example, enter SSS to specify that the structures retrieved contain your graphical query embedded wholly within them. OR, enter the equal sign (=) to specify that the structures retrieved contain your graphical query exactly as drawn.

*	The file name (not the structure) of the structure. For example, enter the file name BENZALD for the 2D structure (the two-dimensional representation of a molecule) of Benzaldehyde:

Or, enter the file name BENZFRAG for any of these 2D substructures (any portion of a 2D structure) of Benzaldehyde:

Entering the File Name of a Structure

You can enter the file name of the structure in several ways:

*	To enter a structure that is on the form in ISIS/Base, double-click query (or mquery) in the Structures box.

*	To enter a structure that was saved in the database, double-click the name of the structure in the Structures box.

*	To enter a structure that was saved as a molfile, click Read Structure, enter the name of the structure in the Files text box, click OK, and then double-click the name of the structure in the Structures box. (A molfile is a file in CTfile (chemical table files) format that contains either a single molecular structure or disjointed structural fragments.)

You see the structure in the box at the bottom-right corner of the Query Builder.

54.2.3 Searching Top-Level and Lower Level Records

When you combine two or more queries of any type into a single QB search, the search results that you obtain depend on both the specifications and accuracy of your query and the way that information is stored in your database.

Information in a database is stored either in a single level (called a flat database) or in multiple levels (called a hierarchical database). Storage in a hierarchical database is more efficient, but it requires you to enter your queries in the correct location on the form to obtain the search results that you want. For example, the following hierarchical database stores data for multiple decomposition tests that are conducted under different atmospheric conditions:

In this database, structures are stored at the top (or root) level, and the percentage of oxygen and the number of peaks are stored at a lower level, under the parent field Decomposition. A parent field is a branch in the hierarchy that contains a set of child fields, such as percent O2 and number of peaks.

You want specific decomposition data from different tests. Your multiple query in a single QB search specifies that you want all compounds within a single test that contain: Query 1, greater than 65% O2; Query 2, less than three peaks. To obtain search results that match either one query or the other (Query 1 OR Query 2), enter:

ROOT>DECOMPOSITION>Percent_O2 > 65 OR ROOT>DECOMPOSITION > Peaks < 3

This search gives you all compounds within a single test that meet either requirement in your query (but not necessarily both requirements). To obtain search results that match all queries (Query 1 AND Query 2), specify the hierarchy level that you want to search at the beginning of the search syntax. Then enclose the remainder of the query in double parentheses (If you do not specify a hierarchy level that you want to search, ISIS searches the top-level records in the database.):

ROOT>DECOMPOSITION ((ROOT>DECOMPOSITION>Percent_O2 > 65 AND ROOT>DECOMPOSITION > Peaks < 3))

This search does gives you all compounds within a single test that meet both requirements in your query.

Note: When you filter your search results, you see solely those lower-level records that meet your search requirements.

54.3 Definition of Aromaticity

For local databases: A bond is aromatic if it is in a six-membered ring with alternating double and single bonds, such as benzene.

Note: Aromaticity is not perceived for fused rings in which the double bonds are arranged in a way that cannot be defined as aromatic.

54.4 Specifying Query Features on Atoms and Bonds in Structures

A query feature on an atom and/or a bond in a molecule is a restriction that specifies the retrieval of certain types of molecule records from an ISIS/Base database.

If you do not use query features, the molecules retrieved contain solely your exact substructure query embedded wholly within them. For example:

54.4.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

54.4.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature: H0

Prohibits the attachment of hydrogens. For example:

54.4.3 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

54.4.4 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

54.4.5 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

54.4.6 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

54.5 Specifying Stereochemistry

For local databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

An SSS search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve molecules with matching cis or trans stereochemistry. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An SSS search produces the following results:

54.6 Guidelines for Revising the Query

If your QB search retrieved no records or too few records, you might want to:

*	Conduct a QB search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the structural constraints in your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, or remove stereochemical requirements.

*	Make the text/numeric strings in your query more general, and then search the same set of records. For example, you can apply operators that partially restrict, such as > or between instead of =, or you can apply wildcards. (A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters.)

If your QB search retrieved too many records, you might want to:

*	Refine the structural constraints in your query, and then search the same set of records. For example, you can limit substitution at specific positions with explicit hydrogens, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Make the text/numeric string in your query more restrictive, and then search the same set of records. For example, you can use the operator = instead of >.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	First, conduct a formula search (or a data search on molecular weight) to screen out large and complex molecules that are stored in your database, and then conduct a search on the less complex molecules. If your query is not able to map a stored molecule within a specific length of time, the molecule is added to the search results.

*	Filter your search results so that you view solely the lower-level records. (This assumes that you are viewing both upper- and lower-level records.)


Remote MEXACT: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote MEXACT Search	21.1

*	Specifying Stereochemistry	21.2

*	Specifying Mixtures and Attached Data	21.3

*	Guidelines for Revising the Query	21.4

*	Searching Example 1: Duplicates in the Database	21.5

We recommend that you print this 5-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote MEXACT search, click here.

21.1 Definition of a Remote MEXACT Search

A remote Molecule Exact Match (MEXACT) search finds molecule records in your remote database that match your structure query exactly. Your structure query is a two-dimensional representation of a molecule (a 2D structure). For example:

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

Note: If your search query does not contain the exact stereochemistry of the molecules that you want to retrieve from the database, you will not retrieve those molecules.

21.2 Specifying Stereochemistry

For remote databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

An MEXACT search produces the following results:

Cis or Trans Configurations

Your structure query must contain the exact configuration that you want to retrieve. For example, an MEXACT search produces the following results:

Chiral Flags on Molecules

In a remote database, you can create a query with a chiral flag on a molecule with at least one asymmetric center to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

21.3 Specifying Mixtures and Attached Data

You can use mixture brackets, component brackets, and attached data in MEXACT search queries. For example, the following structure represents a mixture of two components: aspirin (80% by weight) and a binder of unknown structure called Binder 46 (20% by weight):

In an MEXACT search, the mixture brackets, component brackets, and attached data must match exactly. For example:

For more information and examples of structures that use mixtures, see Drawing Mixtures: MDL Requirements for Database Searching and Registration.

21.4 Guidelines for Revising the Query

If your MEXACT search retrieved no records, you might want to:

*	Conduct an MEXACT search on a different set of records with the same query.

*	Conduct a different search on the same set of records with the same query. For example, you might conduct one of the following searches: Molecule Similarity (MSim), Tautomer (TAUT), Isomer (ISOMER), and Flexmatch (FLEX). For more information on these searches, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click the search of your choice. You will see the full definition of the search and how to do it.

*	Check that search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Add or delete the stereochemistry in your query. If you omit the stereochemistry in your query, the records retrieved will contain no stereochemistry. The records match your search query exactly.

21.5 Searching Example 1: Duplicates in the Database

The following searching example shows you how to retrieve all molecules that match the molecule search query exactly.

21.5.1 Problem

You want to retrieve molecules with the following structure:

21.5.2 Approach

Draw the structure and add all stereochemistry that you want to see in the molecules retrieved. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE.

Conduct an MEXACT search in the remote molecule database of your choice, such as the ISISMX demo database.

21.5.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for MEXACT, how to/examples.

21.5.4 Results

You retrieve all records that contain solely this exact structure. (You do not retrieve closely related structures.)


Local MEXACT: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Local MEXACT Search	22.1

*	Specifying Stereochemistry	22.2

*	Guidelines for Revising the Query	22.3

*	Searching Example 1: Duplicates in the Database	22.4

We recommend that you print this 3-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a local MEXACT search, click here.

22.1 Definition of a Local MEXACT Search

A local Molecule Exact Match (MEXACT) search finds molecule records in your local database that match your structure query exactly. Your structure query is a two-dimensional representation of a molecule (a 2D structure). For example:

A local search is a search over a database that typically exists on your hard disk. To do a local search on your hard disk, you do not need to input network information.

Note 1: To do a local search that is accessed from a shared network, you need to input network information.

Note 2: If your search query does not contain the exact stereochemistry of the molecules that you want to retrieve from the database, you will not retrieve those molecules.

22.2 Specifying Stereochemistry

For local databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

An MEXACT search produces the following results:

Cis or Trans Configurations

Your query retrieves both cis and trans configuration. For example, an MEXACT search produces the following results:

22.3 Guidelines for Revising the Query

If your MEXACT search retrieved no records, you might want to:

*	Conduct an MEXACT search on a different set of records with the same query.

*	Check that search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Add or delete the stereochemistry in your query. If you omit the stereochemistry in your query, the records retrieved will contain no stereochemistry. The records match your search query exactly.

22.4 Searching Example 1: Duplicates in the Database

The following searching example shows you how to retrieve all molecules that match the molecule search query exactly.

22.4.1 Problem

You want to retrieve molecules with the following structure:

22.4.2 Approach

Draw the structure and add all stereochemistry that you want to see in the molecules retrieved. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE.

Conduct an MEXACT search in the local molecule database of your choice, such as the LOCALMX demo database.

22.4.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for MEXACT, how to/examples.

22.4.4 Results

You retrieve all records that contain solely this exact structure. (You do not retrieve closely related structures.)


Remote REXACT/Comp: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote REXACT/Comp Search	23.1

*	Specifying Stereochemistry	23.2

*	Guidelines for Revising the Query	23.3

*	Searching Example 1: Exact Reactant in the Database	23.4

*	Searching Example 2: Exact Product in the Database	23.5

We recommend that you print this 5-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote REXACT/Comp search, click here.

23.1 Definition of a Remote REXACT/Comp Search

A remote Reaction Exact Match for Reaction Components (REXACT/Comp) search finds reaction records in your remote database that match your reaction component query exactly. Your reaction component query is a two-dimensional representation of a reaction component (a 2D structure with a reaction arrow). For example, a reactant query is as follows:

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

Note 1: If your search query does not contain the exact stereochemistry of the reaction components that you want to retrieve from the database, you will not retrieve those records.

Note 2: If your query retrieves data that you perceive to be in the wrong place on the form, see your ISIS Administrator. (This might be the result of specifying the same name for multiple database fields on your form or in the Hview.)

23.2 Specifying Stereochemistry

For remote databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve reactions with matching stereochemistry on the reaction components. For example:

An REXACT/Comp search produces the following results:

Cis or Trans Configurations

Your structure query must contain the exact configuration that you want to retrieve. For example, an REXACT/Comp search produces the following results:

Chiral Flags on Reaction Components

In a remote database, you can create a query with a chiral flag on a reaction component with at least one asymmetric center or on a reaction component that is asymmetric to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

23.3 Guidelines for Revising the Query

If your REXACT/Comp search retrieved no records, you might want to:

*	Conduct an REXACT/Comp search on a different set of records with the same query.

*	Conduct a different search on the same set of records with the same query. For example, you might conduct a Reaction Similarity (RSim) search. For more information on this search, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click the RSim search. You will see the full definition of the search and how to do it.

*	Check that search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Add or delete the stereochemistry in your query. If you omit the stereochemistry in your query, the records retrieved will contain no stereochemistry. The records match your search query exactly.

23.4 Searching Example 1: Exact Reactant in the Database

The following searching example shows you how to retrieve all records that match the reactant query exactly.

23.4.1 Problem

You want to retrieve reaction records that use the reactant pyridine:

23.4.2 Approach

Draw a partial reaction that designates the exact reactant. Enter the query into the Reaction Structure box or table cell on the form in ISIS/Base that connects to the database field RXN>RXNSTRUCTURE.

Conduct an REXACT/Comp search in the remote reaction database of your choice, such as the ISISRX demo database.

23.4.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for REXACT/Comp, how to/examples.

23.4.4 Results

Because the query does not specify any product structures, reactions that transform pyridine into any products are received. For example, the query might retrieve the following reaction from the ISISRX demo database:

23.5 Searching Example 2: Exact Product in the Database

The following searching example shows you how to retrieve all records that match the product query exactly.

23.5.1 Problem

You want to retrieve reaction records with an easy and stereoselective synthesis of the following product:

23.5.2 Approach

Draw a partial reaction that designates the exact product. Enter the query into the Reaction Structure box or table cell on the form in ISIS/Base that connects to the database field RXN>RXNSTRUCTURE.

Conduct an REXACT/Comp search in the remote reaction database of your choice, such as the ISISRX demo database.

23.5.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for REXACT/Comp, how to/examples.

23.5.4 Results

Because the query does not specify any reactant structures, reactions that convert any reactants into the specific product are received. For example, the query might retrieve the following reaction from the ISISRX demo database:


Remote MEXACT: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote MEXACT Search	59.1

*	Specifying Stereochemistry	59.2

*	Guidelines for Revising the Query	59.3

*	Searching Example 1: Duplicates in the Database	59.4

We recommend that you print this 4-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote MEXACT search, click here.

59.1 Definition of a Remote MEXACT Search

A remote Molecule Exact Match (MEXACT) search finds reaction records in your remote database that match your reaction component query exactly. Your reaction component query is a two-dimensional representation of a reaction component (a 2D structure without a reaction arrow). For example, a reactant query is as follows:

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

Note 1: If your search query does not contain the exact stereochemistry of the reaction components that you want to retrieve from the database, you will not retrieve those reaction components.

Note 2: If your query retrieves data that you perceive to be in the wrong place on the form, see your ISIS Administrator. (This might be the result of specifying the same name for multiple database fields on your form or in the Hview.)

59.2 Specifying Stereochemistry

For remote databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve reactions with matching stereochemistry on the reaction components. For example:

An MEXACT search produces the following results:

Cis or Trans Configurations

Your structure query must contain the exact configuration that you want to retrieve. For example, an MEXACT search produces the following results:

Chiral Flags on Reaction Components

In a remote database, you can create a query with a chiral flag on a reaction component with at least one asymmetric center or on a reaction component that is asymmetric to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

59.3 Guidelines for Revising the Query

If your MEXACT search retrieved no records, you might want to:

*	Conduct an MEXACT search on a different set of records with the same query.

*	Conduct a different search on the same set of records with the same query. For example, you might conduct one of the following searches: Molecule Similarity (MSim), Tautomer (TAUT), Isomer (ISOMER), and Flexmatch (FLEX). For more information on these searches, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click the search of your choice. You will see the full definition of the search and how to do it.

*	Check that search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Add or delete the stereochemistry in your query. If you omit the stereochemistry in your query, the records retrieved will contain no stereochemistry. The records match your search query exactly.

59.4 Searching Example 1: Duplicates in the Database

The following searching example shows you how to retrieve all records that match your reactant query exactly.

59.4.1 Problem

You want to retrieve reaction records in which at least one of the reactants contains the following structure:

59.4.2 Approach

Draw the structure and add all stereochemistry that you want to see in the reaction components retrieved. (Do not add a reaction arrow.) Enter the query into the box or table cell on the form in ISIS/Base that will hold reactant structures (without a reaction arrow), such as the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE.

Conduct an MEXACT search in the remote reaction database of your choice, such as the ISISRX demo database.

59.4.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for MEXACT, how to/examples.

59.4.4 Results

You retrieve all records that contain solely this exact structure. (You do not retrieve closely related structures.)


Local MEXACT: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Local MEXACT Search	60.1

*	Specifying Stereochemistry	60.2

*	Guidelines for Revising the Query	60.3

*	Searching Example 1: Duplicates in the Database	60.4

We recommend that you print this 4-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a local MEXACT search, click here.

60.1 Definition of a Local MEXACT Search

A local Molecule Exact Match (MEXACT) search finds reaction records in your local database that match your reaction component query exactly. Your reaction component query is a two-dimensional representation of a reaction component (a 2D structure without a reaction arrow). For example, a reactant query is as follows:

A local search is a search over a database that typically exists on your hard disk. To do a local search on your hard disk, you do not need to input network information.

Note 1: To do a local search that is accessed from a shared network, you need to input network information.

Note 2: If your search query does not contain the exact stereochemistry of the reaction components that you want to retrieve from the database, you will not retrieve those reaction components.

60.2 Specifying Stereochemistry

For local databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve reactions with matching stereochemistry on the reaction components. For example:

An MEXACT search produces the following results:

Cis or Trans Configurations

Your structure query must contain the exact configuration that you want to retrieve. For example, an MEXACT search produces the following results:

60.3 Guidelines for Revising the Query

If your MEXACT search retrieved no records, you might want to:

*	Conduct an MEXACT search on a different set of records with the same query.

*	Check that search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Add or delete the stereochemistry in your query. If you omit the stereochemistry in your query, the records retrieved will contain no stereochemistry. The records match your search query exactly.

60.4 Searching Example 1: Duplicates in the Database

The following searching example shows you how to retrieve all records that match your reactant query exactly.

60.4.1 Problem

You want to retrieve reaction records in which at least one of the reactants contains the following structure:

60.4.2 Approach

Draw the structure and add all stereochemistry that you want to see in the reaction components retrieved. (Do not add a reaction arrow.) Enter the query into the box or table cell on the form in ISIS/Base that will hold reactant structures (without a reaction arrow), such as the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE.

Conduct an MEXACT search in the local reaction database of your choice, such as the LOCALRX demo database.

60.4.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for MEXACT, how to/examples.

60.4.4 Results

You retrieve all records that contain solely this exact structure. (You do not retrieve closely related structures.)


Remote REXACT/Rxn: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote REXACT/Rxn Search	77.1

*	Specifying Stereochemistry	77.2

*	Guidelines for Revising the Query	77.3

*	Searching Example 1: Exact Reaction in the Database	77.4

We recommend that you print this 3-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote REXACT/Rxn search, click here.

77.1 Definition of a Remote REXACT/Rxn Search

A remote Reaction Exact Match for Reactions (REXACT/Rxn) search finds reaction records in your remote database that match your reaction query exactly. Your reaction query is a reaction with two-dimensional representations of reactants and products (a 2D reaction structure). For example:

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

Note 1: If your search query does not contain the exact stereochemistry of the reaction components that you want to retrieve from the database, you will not retrieve those records.

Note 2: If your query retrieves data that you perceive to be in the wrong place on the form, see your ISIS Administrator. (This might be the result of specifying the same name for multiple database fields on your form or in the Hview.)

77.2 Specifying Stereochemistry

For remote databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve reactions with matching stereochemistry on the reaction components. For example:

Cis or Trans Configurations

Your structure query must contain the exact configuration that you want to retrieve.

Chiral Flags on Reaction Components

In a remote database, you can create a query with a chiral flag on a reaction component with at least one asymmetric center or on a reaction component that is asymmetric to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

77.3 Guidelines for Revising the Query

If your REXACT/Rxn search retrieved no records, you might want to:

*	Conduct an REXACT/Rxn search on a different set of records with the same query.

*	Conduct a different search on the same set of records with the same query. For example, you might conduct a Reaction Similarity (RSim) search. For more information on this search, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click the RSim search. You will see the full definition of the search and how to do it.

*	Check that search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Add or delete the stereochemistry in your query. If you omit the stereochemistry in your query, the records retrieved will contain no stereochemistry. The records match your search query exactly.

77.4 Searching Example 1: Exact Reaction in the Database

The following searching example shows you how to retrieve all records that match the reaction query exactly.

77.4.1 Problem

You want to retrieve exact duplicates of the following reaction:

77.4.2 Approach

Draw the reaction and add all stereochemistry that you want to see in the structures retrieved. Enter the query into the Reaction Structure box or table cell on the form in ISIS/Base that connects to the database field RXN>RXNSTRUCTURE.

Then conduct an REXACT/Rxn search in the remote reaction database of your choice, such as the ISISRX demo database.

77.4.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for REXACT/Rxn, how to/examples.

77.4.4 Results

You retrieve all records that contain solely this exact reaction. (You do not retrieve closely related reactions.)


Local REXACT/Rxn: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Local REXACT/Rxn Search	78.1

*	Specifying Stereochemistry	78.2

*	Guidelines for Revising the Query	78.3

*	Searching Example 1: Exact Reaction in the Database	78.4

We recommend that you print this 3-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a local REXACT/Rxn search, click here.

78.1 Definition of a Local REXACT/Rxn Search

A local Reaction Exact Match for Reactions (REXACT/Rxn) search finds reaction records in your local database that match your reaction query exactly. Your reaction query is a reaction with two-dimensional representations of reactants and products (a 2D reaction structure). For example:

A local search is a search over a database that typically exists on your hard disk. To do a local search on your hard disk, you do not need to input network information.

Note 1: To do a local search that is accessed from a shared network, you need to input network information.

Note 2: If your search query does not contain the exact stereochemistry of the reaction components that you want to retrieve from the database, you will not retrieve those records.

78.2 Specifying Stereochemistry

For local databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve reactions with matching stereochemistry on the reaction components. For example:

Cis or Trans Configurations

Your structure query must contain the exact configuration that you want to retrieve.

78.3 Guidelines for Revising the Query

If your REXACT/Rxn search retrieved no records, you might want to:

*	Conduct an REXACT/Rxn search on a different set of records with the same query.

*	Check that search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Add or delete the stereochemistry in your query. If you omit the stereochemistry in your query, the records retrieved will contain no stereochemistry. The records match your search query exactly.

78.4 Searching Example 1: Exact Reaction in the Database

The following searching example shows you how to retrieve all records that match the reaction query exactly.

78.4.1 Problem

You want to retrieve exact duplicates of the following reaction:

78.4.2 Approach

Draw the reaction and add all stereochemistry that you want to see in the structures retrieved. Enter the query into the Reaction Structure box or table cell on the form in ISIS/Base that connects to the database field RXN>RXNSTRUCTURE.

Then conduct an REXACT/Rxn search in the local reaction database of your choice, such as the LOCALRX demo database.

78.4.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for REXACT/Rxn, how to/examples.

78.4.4 Results

You retrieve all records that contain solely this exact reaction. (You do not retrieve closely related reactions.)


Remote SSS: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote SSS Search	27.1

*	Definition of Aromaticity	27.2

*	Specifying Query Features on Atoms and Bonds in Structures	27.3

*	Specifying Stereochemistry	27.4

*	Mixtures and Attached Data	27.5

*	Guidelines for Revising the Query	27.6

*	Searching Example 1: General Classes of Compounds	27.7

*	Searching Example 2: Variable Ring Systems	27.8

*	Searching Example 3: Multiple Fragments in a Single Query	27.9

*	Searching Example 4: Unsubstituted Rings	27.10

*	Searching Example 5: Excluding Functional Groups	27.11

*	Searching Example 6: Order of Components in a Mixture	27.12

We recommend that you print this 32-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote SSS search, click here.

27.1 Definition of a Remote SSS Search

A remote Molecule Substructure (SSS) search finds molecule records in your remote database that contain your query as a substructure wholly within a larger structure. Your substructure query is a two-dimensional representation of a portion of a molecule (a 2D substructure). For example:

You can also increase the power of an SSS search by the addition of specific restrictions (called query features) on atoms and/or bonds. There are a number of query features available for use.

In the following example, the ISIS atom-query feature (H0) prohibits the attachment of hydrogens on a specific atom in the records retrieved:

In addition, the hydrogens block substitutions at the specified positions.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

27.2 Definition of Aromaticity

For remote databases: ISIS interprets the following ring systems as aromatic:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:

Note: The bonds of six-membered aromatic ring systems and the perimeter bonds of azulenes are stored as aromatic bonds in the database. The bonds of five-membered aromatic rings, however, are stored as single and double bonds and interpreted as aromatic during a search. The differences between five-membered rings and other types of aromatic rings can cause different search results for five- and six-membered rings/azulenes when you use the following bonds in queries: Single, Double, and Single/Double query bonds. For more information on the Single/Double query bond, see Section 27.3.7.

27.3 Specifying Query Features on Atoms and Bonds in Structures

A query feature on an atom and/or a bond in a molecule is a restriction that specifies the retrieval of certain types of molecule records from an ISIS/Base database.

If you do not use query features, the molecules retrieved contain solely your exact substructure query embedded wholly within them. For example:

27.3.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

27.3.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of hydrogens. For example:

27.3.3 Allowing an Unsaturated Atom

Use an atom query feature to specify that an atom is attached to at least one multiple bond (double, triple, or aromatic).

Atom Query Feature: Unsaturated Atom (u)

Specifies that the atom of your choice is attached to at least one multiple bond (double, triple, or aromatic). For example, the following query specifies both an unsaturated atom (u) and single or double bonds (the double dashed lines).

27.3.4 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

Atom Query Feature: Substitution Count of Zero, s0

Specifies that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of a single atom with attached hydrogens (if any).

Atom Query Feature: Substitution Count of One, s1

Specifies that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Two, s2

Specifies that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Three, s3

Specifies that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Four, s4

Specifies that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Five, s5

Specifies that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of at Least Six, s6

Specifies that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count as Drawn, s*

Specifies that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:

27.3.5 Allowing a Specific Number of Ring Bond Attachments

Use atom query features to specify the number of ring bond attachments.

Atom Query Feature: Ring Bond Count of Zero, r0

Specifies that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:

Atom Query Feature: Ring Bond Count of Two, r2

Specifies that the records retrieved have solely two ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of Three, r3

Specifies that the records retrieved have solely three ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of at Least Four, r4

Specifies that the records retrieved have at least four ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count as Drawn, r*

Specifies that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:

27.3.6 Allowing Additional Atoms and/or Bonds in a Chain or a Ring

Use a query feature to specify the addition of atoms and/or bonds in a chain or a ring.

Atom or Bond Query Feature: Link Node

Use a link node to specify the addition of variable numbers repeating units (atoms and/or bonds) to a ring or chain. A repeating unit must be attached to two adjacent bonds. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the link node [L1-3]:

Or, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the link node [L1-3]:

27.3.7 Allowing a Specific Bond Type

Use bond query features to retrieve structures with a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Note: An aromatic query bond hits any bond in all types of aromatic rings: 6-membered ring bonds, 5-membered ring bonds, and azulene perimeter bonds. For more information on the structures that ISIS interprets as aromatic, see Section 27.2.

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

Note: A Single/Double query bond does not hit bonds in 6-membered aromatic rings, or perimeter bonds of azulenes, because bonds in these structures are stored in the database as aromatic bonds. However, a Single/Double query bond does hit bonds in 5-membered rings that ISIS interprets as aromatic. For more information on the structures that ISIS interprets as aromatic, see Section 27.2.

Bond Query Feature: Single/Aromatic Bond

Specifies either a single or an aromatic bond at that position:

Bond Query Feature: Double/Aromatic Bond

Specifies either a double or an aromatic bond at that position:

27.3.8 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

27.3.9 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

27.4 Specifying Stereochemistry

For remote databases: You can specify stereochemistry in the following ways:

Up and Down and Either Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

An SSS search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve molecules with matching cis or trans stereochemistry. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An SSS search produces the following results:

Chiral Flags on Molecules

In a remote database, you can create a query with a chiral flag on a molecule with at least one asymmetric center or on a molecule that is asymmetric to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

27.5 Specifying Mixtures and Attached Data in Queries

You can use mixture brackets, component brackets, and attached data in substructure search queries. For example, the following structure represents a mixture of two components: aspirin (80% by weight) and a binder of unknown structure called Binder 46 (20% by weight):

If your database contains structures with mixture brackets, component brackets, and/or attached data, study the following sections to learn how to create search queries for these structures.

27.5.1 Ordered and Unordered Mixtures

You can define both ordered and unordered mixtures as search queries:

*	If the order of addition of the components of a mixture is not important, specify an unordered mixture (mix). Unordered mixtures contain components (c) that are not numbered. For example, the following is a mixture of stereoisomers from a reaction product:

*	If the order of addition of components of the formulation is important, specify an ordered mixture (f). Ordered mixtures contain components that are numbered (c1, c2, c3, and so forth). In the following example, the acetaminophen (c1) must be added before the binder (c2) and other components (c3 and c4):

A query that contains ordered components finds structures that contain ordered components with the same relative (but not necessarily sequential) order. For example:

To find both unordered and ordered mixtures that contain specified components, use an unordered component without brackets. For example:

For more information and examples of structures that use mixtures, see Drawing Mixtures: MDL Requirements for Database Searching and Registration.

27.5.2 Attached Data

Attached data is chemically-significant text that you can associate with an atom, a bond, a set of atoms and bonds, or a set of brackets. Attached data differs from chemically-insignificant text (plain text), because attached data can be used in a graphical search query. In the following example, the data that is attached to the deuterium atoms in the retrieved structure matches the attached data in the query:

Each piece of attached data is associated with a special kind of database field, called a Substance Group (Sgroup) field. The Sgroup field defines what the data means. In the previous example, the attached data is associated with the Sgroup field PERCENT_DEUTERATION.

Caution: When you draw your search query, you must specify the correct Sgroup fields for the data that you attach to the structure. If you do not specify the correct Sgroup fields, you might not be able to retrieve the structures that you want. Your ISIS Administrator defines the Sgroup fields that you can use to specify attached data. For more information on the Sgroup fields that are available at your site, see your ISIS Administrator.

To retrieve structures with attached data, you can create the following queries:

*	To retrieve structures that contain any values of attached data, specify a query that contains no attached data. For example:

*	To retrieve structures that contain specific data (a target value) of attached data, specify the target value on the query. The query retrieves solely structures in which the attached data matches exactly:

*	To retrieve structures in which the attached data meets specific conditions (for example, the data must lie within a specified range), specify a text/numeric query for attached data. A text/numeric query contains a search operator (such as < or between) and a text or numeric target value (such as 25% mole fraction) that you want to find. In the following example, data attached to the double bond specifies the percentage of isomer in the trans configuration. The query retrieves only structures with attached data in the range that is specified in the text/numeric query (between 70 90 % trans):

Note: For more information on search operators for text/numeric queries, see Section 27.5.3.

27.5.3 Search Operators for Text/Numeric Queries in Attached Data

The following search operators are available in text/numeric queries for attached data.

<, <=, >, >=, and <>

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Search Operator	Definition	Examples

<	less than (numeric)	< 50

<=	less than or equal to (numeric)	<= 50

>	greater than (numeric)	> 50

>=	greater than or equal to (numeric)	>= 50

<>	not equal to (text or numeric)	<> 50

<> "active"

<> "ACTIVE"

BETWEEN

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks. For example:

BETWEEN "XR11" "XZ15"

BETWEEN "xR11" "xZ15"

BETWEEN 95 100

CONTAINS

Use CONTAINS with text. You retrieve all values that contain the text string that you specify embedded within them. For example:

Query	Examples of Records Retrieved
CONTAINS bind	Binder

Bind_46

Bind_23

CONTAINS BIND	Binder

Bind_46

Bind_23

LIKE

Use LIKE with text that is enclosed in double quotation marks. The text can include wildcards. A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. The wildcard _ is a placeholder for solely one unspecified character. Without a wildcard, you retrieve solely those records that contain exactly the target value that you specified. For example:

Query Without a Wildcard	Example of a Record Retrieved
LIKE "antibiotic"	Antibiotic

Query With the Wildcard %	Examples of Records Retrieved
LIKE "antibiotic%"	Antibiotic
Antibiotic activity

LIKE "%act%"	Inactive
Active
ACTIVE
Activity

Note1: To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice. To retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

Note2: The CONTAINS operator is a special case of the LIKE operator. For example, the query like "%act%" is equivalent to the query contains act.

27.6 Guidelines for Revising the Query

If your SSS search retrieved no records or too few records, you might want to:

*	Conduct an SSS search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, remove substituent limits, or remove stereochemical requirements.

*	Remove the attached data from your query, and then search the same set of records. For example, if your query contains the attached data values 0.7 and 0.3 attached to component brackets, you can delete the attached data.

If your SSS search retrieved too many records, you might want to:

*	Refine your query by specifying atom and bond query features that limit the types of structures that you retrieve, and then search the same set of records. For example, you can limit substitution at specific positions, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Refine your query by adding restrictions to the attached data in the structures that you retrieve. For example, if the component brackets on your query contain no attached data, you can attach a target value or a text/numeric query (such as < 90) to one or more components.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	Conduct a different search on the same set of records with the same query. For example, you might conduct one of the following searches: Molecule Similarity (MSim) and Rgroup (RGROUP). For more information on these searches, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click the search of your choice. You will see the full definition of the search and how to do it.

*	First conduct a formula search to screen out large and complex molecules that are stored in your database, and then conduct a search on the less complex molecules. If your query is not able to map a stored molecule within a specific length of time, the molecule is added to the search results.

27.7 Searching Example 1: General Classes of Compounds

To retrieve a general class of compounds, draw a substructure query that contains the minimum structural features needed to define the compound class. If you draw too many specific features, you might unintentionally eliminate some molecules.

27.7.1 Problem

You want to retrieve all compounds that are nucleic acids.

27.7.2 Approach

Draw a substructure that generally defines nucleic acids (purines and pyrimidines). The minimum structural features include a hetero-substituted six-membered ring with two nitrogen atoms and variable bond types. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE.

Conduct an SSS search in the remote molecule database of your choice, such as the ISISMX demo database.

27.7.3 Query

The atom query feature Q specifies the two heteroatoms.

There are two bond query features: ANY (dashed lines) allows any bond type and Ch allows solely an acyclic attachment.

27.7.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

27.7.5 Results

Some of the molecules that might be retrieved from the remote molecule database of your choice are as follows:

27.8 Searching Example 2: Variable Ring Systems

To retrieve a class of compounds that contains variable ring sizes, draw a substructure query that contains the minimum structural features needed to define both compound class and the ring size. If you draw too many specific features, you might unintentionally eliminate some molecules.

27.8.1 Problem

You want to retrieve isolated pairs of fused 5- or 6-membered rings, with heteroatoms in only one of the rings.

27.8.2 Approach

Draw the minimum structure and ring size for a class of compounds. Allow the rings to expand. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE.

Conduct an SSS search in the remote molecule database of your choice, such as the ISISMX demo database.

27.8.3 Query

There are two atom query features: A specifies a carbon or heteroatom. The r* on each atom specifies that solely those ring bonds drawn participate in a ring. (The r* allows the ring pair to be isolated from any other ring systems in the molecule.)

The bond query feature ANY (dashed lines) allows any bond type.

The atom and/or bond query feature link node [L1-2] allows each 5-membered ring to expand to a 6-membered ring.

27.8.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

27.8.5 Results

Some of the molecules that might be retrieved from the remote molecule database of your choice are as follows:

27.9 Searching Example 3: Multiple Fragments in a Single Query

To retrieve molecules that contain all the fragments that you specify in your query, draw each fragment separately, and then group them. In the molecules retrieved, you see:

*	All the fragments in your query. You do not retrieve molecules that contain solely some of the fragments and not all of them.

*	No overlapping fragments. You do not retrieve molecules that contain fragments that share atoms or bonds.

27.9.1 Problem

Find structures containing a halogen-substituted aromatic ring and a carboxylic acid group.

27.9.2 Approach

Draw a halogen-substituted aromatic ring fragment and a carboxylic acid fragment.

Select both fragments and enter them into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE.

Conduct an SSS search in the remote molecule database of your choice, such as the ISISMX demo database.

27.9.3 Query

The atom query feature LIST specifies that solely those halogens in the bracketed listed be attached at the specified position.

The bond query feature AROMATIC (adjacent solid and dashed lines) allows solely an aromatic bond at the specified position. In ISIS/Base, aromatic bonds occur only in aromatic ring systems. Therefore, you can draw one aromatic bond to represent the entire aromatic ring.

27.9.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

27.9.5 Results

Some of the molecules that might be retrieved from the remote molecule database of your choice are as follows:

Molecules that are not retrieved are as follows:

27.10 Searching Example 4: Unsubstituted Rings

To retrieve a class of compounds that contains unsubstituted rings, draw a substructure query that contains the minimum structural features needed to define both compound class and the unsubstituted rings. If you draw too many specific features, you might unintentionally eliminate some molecules.

27.10.1 Problem

You want to retrieve unsubstituted 5- to 8-membered rings with at least one multiple bond (double, triple, or aromatic).

27.10.2 Approach

Draw the minimum structure and ring size for a class of compounds. Allow the rings to expand and specify at least one multiple bond. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE.

Conduct an SSS search in the remote molecule database of your choice, such as the ISISMX demo database.

27.10.3 Query

There are two atom query features: A specifies any atom except hydrogen at the specified positions. The s* on each atom specifies that solely those non-hydrogen attachments that you see are allowed at the specified positions. (Because no other non-hydrogen attachments are allowed, the ring is unsubstituted.)

The bond query feature ANY (dashed lines) allows any bond type.

The atom and/or bond query feature link node [L1-4] allows the 5-membered ring to expand to an 8-membered ring.

27.10.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

27.10.5 Results

Some of the molecules that might be retrieved from the remote molecule database of your choice are as follows:

27.11 Searching Example 5: Excluding Functional Groups

To exclude molecules with unwanted functional groups, you need to conduct two searches: Search 1 retrieves a general category of compounds. Search 2 searches the results of Search 1 to retrieve unwanted functional groups. You then subtract the results of Search 2 from the results of Search 1.

27.11.1 Problem

You want to find benzoic acid derivatives that are not acid anhydrides.

27.11.2 Approach

Search 1: Draw the benzoic acid query. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE. Then conduct an SSS search in the ISISMX demo database. Save the list of search results and name it List1.

Search 2: Draw the anhydride query. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE. Then conduct an SSS search in the ISISMX demo database. Save the list of search results and name it List2.

Subtract List2 from List1. You want the search results that remain.

27.11.3 Query 1

This query retrieves all molecules that contain benzoic acid embedded wholly within them, including some unwanted anhydrides.

27.11.4 Search 1

To execute Search 1 and save the results as List1, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

27.11. 5 Query 2

This query retrieves all molecules that contain anhydride embedded wholly within them.

27.11.6 Search 2

A search domain is the database or list of results that you search. To set the search domain to List1, execute Search 2, and save the results as List2, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

27.11.7 Results

To subtract List2 from List1 (to manipulate the search results), follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

The set of search results that remains contains benzoic acid structures but no anhydrides. For example, some of the molecules that might be retrieved from the remote molecule database of your choice are as follows:

27.12 Searching Example 6: Order of Components in a Mixture

To retrieve structures that contain mixtures with components in the same relative order, you need to draw a query that contains an ordered mixture of the two components.

27.12.1 Problem

The database contains several formulations that contain a mixture of acetaminophen, aspirin, caffeine, and a binder of undefined structure. You want to find formulations in which the acetaminophen was added before the binder.

27.12.2 Approach

Draw a query that contains an ordered mixture of acetaminophen and the binder, with the acetaminophen as the first component. Use a *atom (star atom) with attached data to represent the binder. The attached data is the text "Binder", and is associated with the Sgroup field STRUCTURE_DATA.

27.12.3 Query

27.12.4 Search

To execute the search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

27.12.5 Results

The search results contain structures in which the acetaminophen was added before the binder. In the following example, the acetaminophen (c1) was added immediately before the binder (c2):

The following structure is retrieved because the acetaminophen (c1) and binder (c4) have the same relative (but not sequential) order:

The following structure is not retrieved, because the binder (c1) is added before the acetaminophen (c3):


Local SSS: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Local SSS Search	28.1

*	Definition of Aromaticity	28.2

*	Specifying Query Features on Atoms and Bonds in Structures	28.3

*	Specifying Stereochemistry	28.4

*	Guidelines for Revising the Query	28.5

*	Searching Example 1: General Classes of Compounds	28.6

*	Searching Example 2: Multiple Fragments in a Single Query	28.7

*	Searching Example 3: Excluding Functional Groups	28.8

We recommend that you print this 13-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a local SSS search, click here.

28.1 Definition of a Local SSS Search

A local Molecule Substructure (SSS) search finds molecule records in your local database that contain your query as a substructure wholly within a larger structure. Your substructure query is a two-dimensional representation of a portion of a molecule (a 2D substructure). For example:

You can also increase the power of an SSS search by the addition of specific restrictions (called query features) on atoms and/or bonds. There are a number of query features available for use.

In the following example, the ISIS atom-query feature (H0) prohibits the attachment of hydrogens on a specific atom in the records retrieved:

In addition, the hydrogens block substitutions at the specified positions.

A local search is a search over a database that typically exists on your hard disk. To do a local search on your hard disk, you do not need to input network information.

Note: To do a local search that is accessed from a shared network, you need to input network information.

28.2 Definition of Aromaticity

For local databases: A bond is aromatic if it is in a six-membered ring with alternating double and single bonds, such as benzene.

Note: Aromaticity is not perceived for fused rings in which the double bonds are arranged in a way that cannot be defined as aromatic.

28.3 Specifying Query Features on Atoms and Bonds in Structures

A query feature on an atom and/or a bond in a molecule is a restriction that specifies the retrieval of certain types of molecule records from an ISIS/Base database.

If you do not use query features, the molecules retrieved contain solely your exact substructure query embedded wholly within them. For example:

28.3.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

28.3.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of hydrogens. For example:

28.3.3 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

28.3.4 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

28.3.5 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

28.3.6 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

28.4 Specifying Stereochemistry

For local databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

An SSS search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve molecules with matching cis or trans stereochemistry. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An SSS search produces the following results:

28.5 Guidelines for Revising the Query

If your SSS search retrieved no records or too few records, you might want to:

*	Conduct an SSS search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, or remove stereochemical requirements.

If your SSS search retrieved too many records, you might want to:

*	Refine your query, and then search the same set of records. For example, you can limit substitution at specific positions with explicit hydrogens, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	First conduct a formula search to screen out large and complex molecules that are stored in your database, and then conduct a search on the less complex molecules. If your query is not able to map a stored molecule within a specific length of time, the molecule is added to the search results.

28.6 Searching Example 1: General Classes of Compounds

To retrieve a general class of compounds, draw a substructure query that contains the minimum structural features needed to define the compound class. If you draw too many specific features, you might unintentionally eliminate some molecules.

28.6.1 Problem

You want to retrieve all compounds that are nucleic acids.

28.6.2 Approach

Draw a substructure that generally defines nucleic acids (purines and pyrimidines). The minimum structural features include a hetero-substituted six-membered ring with two nitrogen atoms and variable bond types. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE.

Conduct an SSS search in the local molecule database of your choice, such as the LOCALMX demo database.

28.6.3 Query

The atom query feature Q specifies the two heteroatoms.

There are two bond query features: ANY (dashed lines) allows any bond type and Ch allows solely an acyclic attachment.

28.6.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

28.6.5 Results

Some of the molecules that might be retrieved from the local molecule database of your choice are as follows:

28.7 Searching Example 2: Multiple Fragments in a Single Query

To retrieve molecules that contain all the fragments that you specify in your query, draw each fragment separately, and then group them. In the molecules retrieved, you see:

*	All the fragments in your query. You do not retrieve molecules that contain solely some of the fragments and not all of them.

*	No overlapping fragments. You do not retrieve molecules that contain fragments that share atoms or bonds.

28.7.1 Problem

Find structures containing a halogen-substituted aromatic ring and a carboxylic acid group.

28.7.2 Approach

Draw a halogen-substituted aromatic ring fragment and a carboxylic acid fragment.

Select both fragments and enter them into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE.

Conduct an SSS search in the local molecule database of your choice, such as the LOCALMX demo database.

28.7.3 Query

The atom query feature LIST specifies that solely those halogens in the bracketed listed be attached at the specified position.

The bond query feature AROMATIC (adjacent solid and dashed lines) allows solely an aromatic bond at the specified position. In ISIS/Base, aromatic bonds occur only in aromatic ring systems. Therefore, you can draw one aromatic bond to represent the entire aromatic ring.

28.7.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

28.7.5 Results

Some of the molecules that might be retrieved from the local molecule database of your choice are as follows:

Three molecules that are not retrieved are as follows:

28.8 Searching Example 3: Excluding Functional Groups

To exclude molecules with unwanted functional groups, you need to conduct two searches: Search 1 retrieves a general category of compounds. Search 2 searches the results of Search 1 to retrieve unwanted functional groups. You then subtract the results of Search 2 from the results of Search 1.

28.8.1 Problem

You want to find benzoic acid derivatives that are not acid anhydrides.

28.8.2 Approach

Search 1: Draw the benzoic acid query. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE. Then conduct an SSS search in the LOCALMX demo database. Save the list of search results and name it List1.

Search 2: Draw the anhydride query. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE. Then conduct an SSS search in the LOCALMX demo database. Save the list of search results and name it List2.

Subtract List2 from List1. You want the search results that remain.

28.8.3 Query 1

This query retrieves all molecules that contain benzoic acid embedded wholly within them, including some unwanted anhydrides.

28.8.4 Search 1

To execute Search 1 and save the results as List1, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

28.8. 5 Query 2

This query retrieves all molecules that contain anhydride embedded wholly within them.

28.8.6 Search 2

A search domain is the database or list of results that you search. To set the search domain to List1, execute Search 2, and save the results as List2, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

28.8.7 Results

To subtract List2 from List1 (to manipulate the search results), follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

The set of search results that remains contains benzoic acid structures but no anhydrides. For example, some of the molecules that might be retrieved from the local molecule database of your choice are as follows:


Remote RGROUP: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a remote RGROUP Search	29.1

*	Definition of Aromaticity	29.2

*	Specifying Query Features on Atoms and Bonds in Structures	29.3

*	Specifying Stereochemistry	29.4

*	Guidelines for Revising the Query	29.5

*	Searching Example 1: Basic Rgroup Search	29.6

*	Searching Example 2: Nesting Rgroups	29.7

*	Searching Example 3: Specifying Zero Occurrence for an Rgroup	29.8

*	Searching Example 4: Applying Conditional Logic	29.9

We recommend that you print this 25-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote RGROUP search, click here.

29.1 Definition of a Remote RGROUP Search

An remote Rgroup (RGROUP) search finds molecule records that contain your query as a substructure wholly within a larger structure with additional restrictions. For example, you can:

*	Specify the structural fragments (such as functional groups or atoms) of your choice at specific sites within a molecule.

*	Exclude structural fragments of your choice at specific sites within a molecule.

*	Specify that the presence of one structural fragment requires the presence of another (Rgroup conditions).

You can also increase the power of an RGROUP search by the addition of specific restrictions (called query features) on atoms and/or bonds. There are a number of query features available for use.

An example of an Rgroup query is as follows:

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

29.1.1 The Root Structure

The root structure contains the portion of the structure that does not vary among the structures retrieved. For example, if you want to find 2, 5-Dihydroxypyridine in which the substituent at position 2 can be COOH, CN, or Ph, and the substituent at position 5 can be OH or CH3, the root structure is 2, 5-Dihydroxypyridine with Rgroups (such as R1 and R2):

Rgroups

On the root structure, Rgroups (R1 through R32) are placeholders that designate where the lists of functional groups and atoms that can attach to the root structure. In the example above, the Rgroup R1 designates that the members of the list R1 (the Rgroup substituents) are allowed at position 5 on the root structure. The Rgroup R2 designates that the members of the list R2 (the Rgroup substituents) are allowed at position 2 on the root structure.

Multiple Rgroups at One Position

You can specify multiple Rgroups at a single site on the root structure. For example:

One Rgroup at Multiple Positions

You can specify a single Rgroup (such as R1) at multiple positions on the root structure. For example:

Note: See Section 29.1.3 to restrict the number of Rgroups that must be occupied in the records retrieved. A molecule might not have to satisfy all the Rgroup sites on the root structure to be retrieved. For example, the Rgroup condition R1 > 0 specifies that any molecule in which at least one of the R1 sites is filled by an R1 member will be retrieved. In addition, the Rgroup condition RestH determines whether the unsatisfied sites must be filled with hydrogen atoms or if other molecule fragments are allowed to be attached if they are not on the list.

Multiple Root Structures in a Single Rgroup Query

If you choose to specify multiple root structures in a single Rgroup query, you must group the root structures before you do a search. To group multiple root structures, select them, and then choose Object > Group.

29.1.2 Rgroup Substituents

Rgroup substituents are the members of the list of Rgroups. You define the Rgroup substituents that you will allow to be found at specified positions in the molecules retrieved. Rgroup substituents can be any structural fragment, including functional groups and single atoms.

In the example below, the Rgroup substituents COOH, CN, or Ph are allowed at position 5 (R1) on the root structure and the Rgroup substituents OH or CH3 are allowed at position 2 (R2) on the root structure:

Attachment Points

An attachment point (marked with an arrow and an asterisk) designates the atom on the Rgroup substituent that is attached to the root structure:

You must designate an attachment point on an Rgroup substituent for each bond that is attached to the substituent.

If an Rgroup is attached to two bonds on the root structure, you must designate two attachment points:

In this example, one bond on the root structure is marked with a single quote that corresponds to the attachment point with a single quote on the Rgroup substituent. The other bond on the root structure is marked with a double quote that corresponds to the attachment point with a double quote on the Rgroup substituent.

Rule: To obtain the correct search results, be certain to assign the attachment point with a single quote on the Rgroup substituent to the corresponding atom on the root structure that contains the lower atom number of the two attachment sites. In the above example, you cannot see the atom numbers on the root structure, which are assigned automatically to the root structure during the drawing process.

Nested Rgroups

A nested Rgroup is an Rgroup that is a placeholder within another Rgroup rather than within the root structure. (You cannot nest an Rgroup any lower than this level.) In the following example, Rgroup R2 is nested within the Rgroup R1:

Nested Rgroups are equivalent to the following structures:

Note: You cannot specify more than one nested occurrence of a single Rgroup substituent (such as R2) within another (unnested) Rgroup substituent (such as R1). For example, you cannot specify that the nested Rgroup R2 be retrieved at both positions 1 and 2 within the R1 Rgroup substituent benzene. Instead, create a query in which a set of nested Rgroups (such as R2 and R3) contains identical substituents. Then specify the occurrence of each nested Rgroup only one time. For example, specify that the nested Rgroup R2 be retrieved at position 1 and that the nested Rgroup R3 be retrieved at position 2 within the R1 Rgroup substituent benzene.

29.1.3 Rgroup Conditions

You can apply restrictions to each Rgroup in your query after you assemble all the Rgroups. The set of restrictions is called the Rgroup conditions.

If you do not apply Rgroup conditions, ISIS assigns the default conditions: Occurrence > 0 and RestH off for each Rgroup.

Occurrence

With the Rgroup condition Occurrence, you can specify the number of Rgroup sites that must be occupied in the records retrieved. For example, the occurrence designation R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved. Type one of the following values in the Occurrence range text box:

Value	Explanation

0	All members of the Rgroup are excluded from the Rgroup site (such as R1). To allow any other Rgroup substituent at the Rgroup site, set RestH to off.

> 0	At least one Rgroup must be satisfied. If RestH is off, any other substituent can attach to unsatisfied sites. If RestH is on, unsatisfied sites must be filled solely by hydrogens.

n	Exactly n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

< n	Less than n number of sites (including zero) must be satisfied. RestH controls substitution at unsatisfied sites.

m - n	Any number of sites falling within the range of m to n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

m,n,...	Any combination of the above expressions, separated by commas. For example: 1, 3-5, 9, >12.

For example, the Rgroup condition R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved.

In another example, the Rgroup condition R1 > 0 and R2 > 0 specifies that an Rgroup substituent from the R1 list AND an Rgroup substituent from the R2 list must occupy at least one site on the root structure in the records retrieved.

Finally, the Rgroup conditions R1 = 1, 3-5, 9, >12 specify that either 1, 3, 4, 5, 9, or more than 12 sites must be satisfied:

RestH

With the Rgroup condition RestH, you can specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site.

An unsatisfied Rgroup site is an Rgroup site on the root structure that does not have an Rgroup member attached: If RestH is off, any functional group or atom may be attached at unsatisfied Rgroup sites on the root structure. If RestH is on, solely hydrogens are allowed to be attached at unsatisfied Rgroup sites on the root structure.

If/Then

With the Rgroup condition If/then, you can specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

For example, If R1 then R2 specifies that if the conditions for R1 are satisfied, then the conditions for R2 must also be satisfied. (If the conditions for R1 are not satisfied, then the conditions for R2 are ignored.) The If/then condition implies that a molecule may be retrieved even though R1 is not satisfied.

In the following query, R1 contains a nitro group and a sulfonic acid group. R2 contains a chlorine atom. The condition If R1 then R2 specifies that if a nitro group or a sulfonic acid group is attached at R1 on the root structure, then a chlorine must also be attached at R2. However, if the R1 site on the root structure does not have either the nitro or the sulfonic acid group (R1 is unsatisfied), then R2 can have any substituent (R2 is ignored):

29.2 Definition of Aromaticity

For remote databases: ISIS interprets the following ring systems as aromatic:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:

Note: The bonds of six-membered aromatic ring systems and the perimeter bonds of azulenes are stored as aromatic bonds in the database. The bonds of five-membered aromatic rings, however, are stored as single and double bonds and interpreted as aromatic during a search. The differences between five-membered rings and other types of aromatic rings can cause different search results for five- and six-membered rings/azulenes when you use the following bonds in queries: Single, Double, and Single/Double query bonds. For more information on the Single/Double query bond, see Section 29.3.7.

29.3 Specifying Query Features on Atoms and Bonds in Structures

A query feature on an atom and/or a bond in a molecule is a restriction that specifies the retrieval of certain types of molecule records from an ISIS/Base database.

If you do not use query features, the molecules retrieved contain solely your exact substructure query embedded wholly within them. For example:

29.3.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

29.3.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of hydrogens. For example:

29.3.3 Allowing an Unsaturated Atom

Use an atom query feature to specify that an atom is attached to at least one multiple bond (double, triple, or aromatic).

Atom Query Feature: Unsaturated Atom (u)

Specifies that the atom of your choice is attached to at least one multiple bond (double, triple, or aromatic). For example, the following query specifies both an unsaturated atom (u) and single or double bonds (the double dashed lines).

29.3.4 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

Atom Query Feature: Substitution Count of Zero, s0

Specifies that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of a single atom with attached hydrogens (if any).

Atom Query Feature: Substitution Count of One, s1

Specifies that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Two, s2

Specifies that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Three, s3

Specifies that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Four, s4

Specifies that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Five, s5

Specifies that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of at Least Six, s6

Specifies that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count as Drawn, s*

Specifies that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:

29.3.5 Allowing a Specific Number of Ring Bond Attachments

Use atom query features to specify the number of ring bond attachments.

Atom Query Feature: Ring Bond Count of Zero, r0

Specifies that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:

Atom Query Feature: Ring Bond Count of Two, r2

Specifies that the records retrieved have solely two ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of Three, r3

Specifies that the records retrieved have solely three ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of at Least Four, r4

Specifies that the records retrieved have at least four ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count as Drawn, r*

Specifies that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:

29.3.6 Allowing Additional Atoms and/or Bonds in a Chain or a Ring

Use a query feature that is for either atoms or bonds to specify the addition of atoms and/or bonds in a chain or a ring.

Atom or Bond Query Feature: Link Node

Use a link node to specify the addition of variable numbers repeating units (atoms and/or bonds) to a ring or chain. A repeating unit must be attached to two adjacent bonds. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the link node [L1-3]:

Or, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the link node [L1-3]:

29.3.7 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Note: An aromatic query bond hits any bond in all types of aromatic rings: 6-membered ring bonds, 5-membered ring bonds, and azulene perimeter bonds. For more information on the structures that ISIS interprets as aromatic, see Section 29.2.

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

Note: A Single/Double query bond does not hit bonds in 6-membered aromatic rings, or perimeter bonds of azulenes, because bonds in these structures are stored in the database as aromatic bonds. However, a Single/Double query bond does hit bonds in 5-membered rings that ISIS interprets as aromatic. For more information on the structures that ISIS interprets as aromatic, see Section 29.2.

Bond Query Feature: Single/Aromatic Bond

Specifies either a single or an aromatic bond at that position:

Bond Query Feature: Double/Aromatic Bond

Specifies either a double or an aromatic bond at that position:

29.3.8 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

29.3.9 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

29.4 Specifying Stereochemistry

For remote databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

An RGROUP search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve molecules with matching cis or trans stereochemistry. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An RGROUP search produces the following results:

Chiral Flags on Molecules

In a remote database, you can create a query with a chiral flag on a molecule with at least one asymmetric center or on a molecule that is asymmetric to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

29.5 Guidelines for Revising the Query

If your RGROUP search retrieved no records or too few records, you might want to:

*	Conduct an RGROUP search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the structural constraints in your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, remove substituent limits, or remove stereochemical requirements.

*	Make the Rgroup conditions in your query more general, and then search the same set of records. For example, you can decrease the number of Rgroup sites that must be satisfied or allow unsatisfied Rgroup sites to be filled with non-Rgroup substituents (instead of with hydrogens solely).

If your RGROUP search retrieved too many records, you might want to:

*	Refine the structural constraints of your query, and then search the same set of records. For example, you can limit substitution at specific positions, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Make the Rgroup conditions in your query more specific, and then search the same set of records. For example, you can increase the number of Rgroup sites that must be satisfied or restrict unsatisfied Rgroup sites to be filled solely with hydrogens.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

29.6 Searching Example 1: Basic RGROUP Search

The major advantage of an RGROUP search over a substructure (SSS) search is the ability to conduct a single search with a query that contains multiple structural variations. In an SSS search, you would have to conduct separate searches (with a different query for each search) to obtain the same results.

29.6.1 Problem

You want to find nitrogen-containing heteroaryl phenyl ethers.

29.6.2 Approach

Draw phenol as the root structure. Attach the Rgroup R1 to the oxygen, and then define the Rgroup substituents of R1 as all possible nitrogen-containing heteroaryl groups. To create the ether link, define a carbon atom on each heteroaryl group as the attachment point. Define the Rgroup conditions. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE.

Conduct an RGROUP search in the remote molecule database of your choice, such as the ISISMX demo database.

29.6.5 Query

The single N atom in each ring guarantees that the heteroaryl group contains at least one nitrogen. The three rings with the nitrogen at different positions are sufficient to define all possible nitrogen-containing heteroaryls.

The atom query feature A specifies any atom except hydrogen in the rings.

The Rgroup query features are as follows: The Rgroup R1 contains three Rgroup substituents. Each Rgroup substituent is a unique ring structure with an attachment point that is a carbon atom. This carbon atom replaces the R1 label on the root structure to form ether in the records retrieved.

29.6.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for RGROUP, how to/examples.

29.6.5 Results

Some of the molecules that might be retrieved from the remote molecule database of your choice are as follows:

29.7 Searching Example 2: Nesting Rgroups

This example shows you how to nest an Rgroup with an Rgroup substituent. You can only nest to one level.

29.7.1 Problem

You want to retrieve all 1-, 2-, and 3-carbon straight-chain alkyl esters and carboxylic acid anhydrides of benzoic, benzenesulfonic, and benzenephosphonic acids.

29.7.2 Approach

Draw benzene as the root structure. Attach the Rgroup R1 to the ring by a single bond, and then define the Rgroup substituents of R1 as the carboxylic, sulfonic, and phosphonic acid groups. Attach the nested Rgroup R2 to the single-bonded oxygen, and then define the Rgroup substituents of R2 as the 1-, 2-, and 3-carbon chains (to form esters) and as a carbonyl (to form the anhydride). Define the Rgroup conditions. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE.

Conduct an RGROUP search in the remote molecule database of your choice, such as the ISISMX demo database.

29.7.3 Query

The atom query feature s* on each atom specifies that solely those non-hydrogen attachments that you see are allowed at the specified positions.

The Rgroup query features are as follows: The Rgroup R1 contains three Rgroup substituents. Each Rgroup substituent in R1 is a unique structure with a nested Rgroup (R2) and contains a unique attachment point. The Rgroup R2 contains four Rgroup substituents. Each Rgroup substituent in R2 is a unique structure and contains a unique attachment point.

The four members of R2 may attach to the three R1 acids and form various combinations of alkyl esters and carboxylic acid anhydrides. For example, the members of R2 that attach to the R1 substituent carboxylic acid form the following functional groups:

29.7.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for RGROUP, how to/examples.

29.7.5 Results

Some of the molecules that might be retrieved from the remote molecule database of your choice are as follows:

29.8 Searching Example 3: Specifying Zero Occurrence for an Rgroup

This example shows you how to exclude all the members of the Rgroup from the Rgroup R1 on the root structure. You exclude Rgroup members with the Rgroup condition that specifies a zero occurrence.

29.8.1 Problem

You want to retrieve all alkyl diamines of up to ten atoms in length that are substituted solely at one nitrogen and that contain heteroaryl groups. You also want to exclude any aniline derivatives that involve the substituted nitrogen.

29.8.2 Approach

Draw the minimum structure for an alkyl diamine that can expand up to ten atoms in length as the root structure. On one nitrogen, prohibit substitution. On the other nitrogen, attach two Rgroups, R1 and R2. Define R1 as a phenyl group and R2 as a heteroaryl group. When R1 attaches to the root structure, an aniline derivative forms. Exclude the formation of aniline derivatives with the Rgroup condition zero occurrence, or R1 = 0. Ensure heteroaryl substitution with the Rgroup condition R2 > 0. In addition, ensure that unsatisfied sites must be filled solely by hydrogens with the Rgroup condition RestH on (since nitrogen has a valence of three or five).

Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE.

Conduct an RGROUP search in the remote molecule database of your choice, such as the ISISMX demo database.

29.8.3 Query

There are two atom query features: A on the Rgroup substituent in R2 specifies any atom except hydrogen. The s* specifies that solely those non-hydrogen attachments that you see are allowed at the specified position.

The bond query feature Ch allows solely an acyclic attachment (alkyl chain bonds) on the root structure.

The atom and/or bond query feature link node [L1-8] allows the 2-membered chain to expand to a 10-membered chain.

The Rgroup query features are as follows: The Rgroups R1 and R2 each contain one Rgroup substituent. Each Rgroup substituent is a unique structure and contains a unique attachment point. There is a restriction that R1 is not among the structures attached to the root structure in the molecules retrieved: Rgroup condition, R1: 0. Because benzene rings are eliminated by the zero occurrence of the R1 group, heteroaryl substitution is required.

29.8.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for RGROUP, how to/examples.

29.8.5 Results

Some of the molecules that might be retrieved from the remote molecule database of your choice are as follows:

29.9 Searching Example 4: Applying Conditional Logic

This example shows you how to use conditional, if/then logic to retrieve the correct set of molecules and to eliminate unwanted molecules in a single search.

29.9.1 Problem

You want to retrieve (2, 3, 5, 6)-nitro-, sulfonic acid-, and carboxylic acid-substituted phenols, but you do not want to retrieve nitro-cresols or nitro-4-ethylphenols.

29.9.2 Approach

Draw phenol as the root structure. To define the (2, 3, 5, 6)-nitro-, sulfonic acid-, and carboxylic acid-substituted phenols, attach R3 to positions 2, 3, 5, and 6 on the ring and specify the Rgroup condition R3 > 0.

Nitro-cresols and nitro-4-ethylphenols have nitro groups at positions 2, 3, 5, or 6 and a methyl or an ethyl group at position 4. For example:

To define the nitro-cresols or nitro-4-ethylphenols, attach R1 to position 4 and attach R2 to positions 2, 3, 5, and 6 on the ring. Then specify the Rgroup conditions R1 > 0, If R1 then R2, R2 = 0, and R3 > 0. The statement If R1 then R2 specifies that if R1 is satisfied (a methyl or an ethyl is at position 4), then R2 must also be satisfied (no nitro groups are allowed at positions 2, 3, 5, or 6).

Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE.

Conduct an RGROUP search in the remote molecule database of your choice, such as the ISISMX demo database.

29.9.3 Query

The atom query feature s* specifies that solely those non-hydrogen attachments that you see are allowed at the specified position. This feature prohibits any non-hydrogen substitutions on the methyl and ethyl groups.

The Rgroup query features are as follows: The Rgroups R1, R2, and R3 contain two, one, and three Rgroup substituents, respectively. Each Rgroup substituent is a unique structure and contains a unique attachment point. The Rgroup conditions are R1 > 0, If R1 then R2, R2 = 0, and R3 > 0.

29.9.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for RGROUP, how to/examples.

29.9.5 Results

Some of the molecules that might be retrieved from the remote molecule database of your choice are as follows:


Remote SSS: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote SSS Search	61.1

*	Definition of Aromaticity	61.2

*	Specifying Query Features on Atoms and Bonds in Structures	61.3

*	Specifying Stereochemistry	61.4

*	Guidelines for Revising the Query	61.5

*	Searching Example 1: General Classes of Compounds	61.6

*	Searching Example 2: Variable Ring Systems	61.7

*	Searching Example 3: Multiple Fragments in a Single Query	61.8

*	Searching Example 4: Unsubstituted Rings	61.9

*	Searching Example 5: Excluding Functional Groups	61.10

We recommend that you print this 26-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote SSS search, click here.

61.1 Definition of a Remote SSS Search

A remote Molecule Substructure (SSS) search finds reaction records in your remote database that contain your query as a substructure wholly within a larger reaction component. Your substructure query is a two-dimensional representation of a portion of a reaction component (a 2D substructure without a reaction arrow). For example:

You can also increase the power of an SSS search by the addition of specific restrictions (called query features) on atoms and/or bonds. There are a number of query features available for use.

In the following example, the ISIS atom-query feature (H0) prohibits the attachment of hydrogens on a specific atom in the records retrieved:

In addition, the hydrogens block substitutions at the specified positions.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

Note: If your query retrieves data that you perceive to be in the wrong place on the form, see your ISIS Administrator. (This might be the result of specifying the same name for multiple database fields on your form or in the Hview.)

61.2 Definition of Aromaticity

For remote databases: ISIS interprets the following ring systems as aromatic:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:

Note: The bonds of six-membered aromatic ring systems and the perimeter bonds of azulenes are stored as aromatic bonds in the database. The bonds of five-membered aromatic rings, however, are stored as single and double bonds and interpreted as aromatic during a search. The differences between five-membered rings and other types of aromatic rings can cause different search results for five- and six-membered rings/azulenes when you use the following bonds in queries: Single, Double, and Single/Double query bonds. For more information on the Single/Double query bond, see Section 61.3.7.

61.3 Specifying Query Features on Atoms and Bonds in Structures

A query feature on an atom and/or a bond in a reaction component is a restriction that specifies the retrieval of certain types of reaction records from an ISIS/Base database.

If you do not use query features, the records retrieved contain solely your exact substructure query embedded wholly within them. For example:

61.3.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

61.3.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of hydrogens. For example:

61.3.3 Allowing an Unsaturated Atom

Use an atom query feature to specify that an atom is attached to at least one multiple bond (double, triple, or aromatic).

Atom Query Feature: Unsaturated Atom (u)

Specifies that the atom of your choice is attached to at least one multiple bond (double, triple, or aromatic). For example, the following query specifies both an unsaturated atom (u) and single or double bonds (the double dashed lines).

61.3.4 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

Atom Query Feature: Substitution Count of Zero, s0

Specifies that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of a single atom with attached hydrogens (if any).

Atom Query Feature: Substitution Count of One, s1

Specifies that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Two, s2

Specifies that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Three, s3

Specifies that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Four, s4

Specifies that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Five, s5

Specifies that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of at Least Six, s6

Specifies that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count as Drawn, s*

Specifies that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:

61.3.5 Allowing a Specific Number of Ring Bond Attachments

Use atom query features to specify the number of ring bond attachments.

Atom Query Feature: Ring Bond Count of Zero, r0

Specifies that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:

Atom Query Feature: Ring Bond Count of Two, r2

Specifies that the records retrieved have solely two ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of Three, r3

Specifies that the records retrieved have solely three ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of at Least Four, r4

Specifies that the records retrieved have at least four ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count as Drawn, r*

Specifies that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:

61.3.6 Allowing Additional Atoms and/or Bonds in a Chain or a Ring

Use a query feature that is for either atoms or bonds to specify the addition of atoms and/or bonds in a chain or a ring.

Atom or Bond Query Feature: Link Node

Use a link node to specify the addition of variable numbers repeating units (atoms and/or bonds) to a ring or chain. A repeating unit must be attached to two adjacent bonds. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the link node [L1-3]:

Or, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the link node [L1-3]:

61.3.7 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Note: An aromatic query bond hits any bond in all types of aromatic rings: 6-membered ring bonds, 5-membered ring bonds, and azulene perimeter bonds. For more information on the structures that ISIS interprets as aromatic, see Section 61.2.

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

Note: An isolated Single/Double query bond does not hit bonds in 6-membered aromatic rings, or perimeter bonds of azulenes, because bonds in these structures are stored in the database as aromatic bonds. However, an isolated Single/Double query bond does hit bonds in 5-membered rings that ISIS interprets as aromatic. For more information on the structures that ISIS interprets as aromatic, see Section 61.2.

Bond Query Feature: Single/Aromatic Bond

Specifies either a single or an aromatic bond at that position:

Bond Query Feature: Double/Aromatic Bond

Specifies either a double or an aromatic bond at that position:

61.3.8 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

61.3.9 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

61.4 Specifying Stereochemistry

For remote databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve reactions with matching stereochemistry on the reaction components. For example:

An SSS search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve molecules with matching cis or trans stereochemistry. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An SSS search produces the following results:

Chiral Flags on Reaction Components

In a remote database, you can create a query with a chiral flag on a reaction component with at least one asymmetric center or on a reaction component that is asymmetric to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

61.5 Guidelines for Revising the Query

If your SSS search retrieved no records or too few records, you might want to:

*	Conduct an SSS search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, remove substituent limits, or remove stereochemical requirements.

If your SSS search retrieved too many records, you might want to:

*	Refine your query, and then search the same set of records. For example, you can limit substitution at specific positions, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	Conduct a different search on the same set of records with the same query. For example, you might conduct one of the following searches: Molecule Similarity (MSim) and Rgroup (RGROUP). For more information on these searches, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click the search of your choice. You will see the full definition of the search and how to do it.

*	First conduct a formula search to screen out large and complex molecules that are stored in your database, and then conduct a search on the less complex molecules. If your query is not able to map a stored molecule within a specific length of time, the molecule is added to the search results.

61.6 Searching Example 1: General Classes of Compounds

To retrieve a general class of compounds, draw a substructure query that contains the minimum structural features needed to define the compound class. If you draw too many specific features, you might unintentionally eliminate some molecules.

61.6.1 Problem

You want to retrieve all starting compounds that are nucleic acids.

61.6.2 Approach

Draw a substructure that generally defines nucleic acids (purines and pyrimidines). The minimum structural features include a hetero-substituted six-membered ring with two nitrogen atoms and variable bond types. Enter the query into the a box or table cell on the form in ISIS/Base that will hold your reaction component (without a reaction arrow). For example, enter a molecule that is a reactant into the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE.

Then conduct an SSS search in the remote reaction database of your choice, such as the ISISRX demo database.

61.6.3 Query

The atom query feature Q specifies the two heteroatoms.

There are two bond query features: ANY (dashed lines) allows any bond type and Ch allows solely an acyclic attachment.

61.6.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

61.6.5 Results

Some of the reaction components (reactants in this example) that might be retrieved from the remote reaction database of your choice are as follows:

61.7 Searching Example 2: Variable Ring Systems

To retrieve a class of compounds that contains variable ring sizes, draw a substructure query that contains the minimum structural features needed to define both compound class and the ring size. If you draw too many specific features, you might unintentionally eliminate some molecules.

61.7.1 Problem

You want to retrieve starting compounds that are isolated pairs of fused 5- or 6-membered rings, with heteroatoms in only one of the rings.

61.7.2 Approach

Draw the minimum structure and ring size for a class of compounds. Allow the rings to expand. Enter the query into the a box or table cell on the form in ISIS/Base that will hold your reaction component (without a reaction arrow). For example, enter a molecule that is a reactant into the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE.

Then conduct an SSS search in the remote reaction database of your choice, such as the ISISRX demo database.

61.7.3 Query

There are two atom query features: Q specifies the two heteroatoms. The r* on each atom specifies that solely those ring bonds drawn participate in a ring. (The r* allows the ring pair to be isolated from any other ring systems in the molecule.)

The bond query feature ANY (dashed lines) allows any bond type.

The atom and/or bond query feature link node [L1-2] allows each 5-membered ring to expand to a 6-membered ring.

61.7.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

61.7.5 Results

Some of the reaction components (reactants in this example) that might be retrieved from the remote reaction database of your choice are as follows:

61.8 Searching Example 3: Multiple Fragments in a Single Query

To retrieve molecules that contain all the fragments that you specify in your query, draw each fragment separately, and then group them. In the molecules retrieved, you see:

*	All the fragments in your query. You do not retrieve molecules that contain solely some of the fragments and not all of them.

*	No overlapping fragments. You do not retrieve molecules that contain fragments that share atoms or bonds.

61.8.1 Problem

Find all starting compounds that contain a halogen-substituted aromatic ring and a carboxylic acid group.

61.8.2 Approach

Draw a halogen-substituted aromatic ring fragment and a carboxylic acid fragment.

Select both fragments and enter them into the Structure box or table cell on the form in ISIS/Base that will hold your reaction component (without a reaction arrow). For example, enter a molecule that is a reactant into the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE.

Then conduct an SSS search in the remote reaction database of your choice, such as the ISISRX demo database.

61.8.3 Query

The atom query feature LIST specifies that solely those halogens in the bracketed listed be attached at the specified position.

The bond query feature AROMATIC (adjacent solid and dashed lines) allows solely an aromatic bond at the specified position. In ISIS/Base, aromatic bonds occur only in aromatic ring systems. Therefore, you can draw one aromatic bond to represent the entire aromatic ring.

61.8.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

61.8.5 Results

Some of the reaction components (reactants in this example) that might be retrieved from the remote reaction database of your choice are as follows:

Reaction components that are not retrieved are as follows:

61.9 Searching Example 4: Unsubstituted Rings

To retrieve a class of compounds that contains unsubstituted rings, draw a substructure query that contains the minimum structural features needed to define both compound class and the unsubstituted rings. If you draw too many specific features, you might unintentionally eliminate some molecules.

61.9.1 Problem

You want to retrieve starting compounds that contain unsubstituted 5- to 8-membered rings with at least one multiple bond (double, triple, or aromatic).

61.9.2 Approach

Draw the minimum structure and ring size for a class of compounds. Allow the rings to expand and specify at least one multiple bond. Enter the query into the a box or table cell on the form in ISIS/Base that will hold your reaction component (without a reaction arrow). For example, enter a molecule that is a reactant into the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE.

Then conduct an SSS search in the remote reaction database of your choice, such as the ISISRX demo database.

61.9.3 Query

There are two atom query features: A specifies any atom except hydrogen at the specified positions. The s* on each atom specifies that solely those non-hydrogen attachments that you see are allowed at the specified positions. (Because no other non-hydrogen attachments are allowed, the ring is unsubstituted.)

The bond query feature ANY (dashed lines) allows any bond type.

The atom and/or bond query feature link node [L1-4] allows the 5-membered ring to expand to an 8-membered ring.

61.9.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

61.9.5 Results

Some of the reaction components (reactants in this example) that might be retrieved from the remote reaction database of your choice are as follows:

61.10 Searching Example 5: Excluding Functional Groups

To exclude molecules with unwanted functional groups, you need to conduct two searches: Search 1 retrieves a general category of compounds. Search 2 searches the results of Search 1 to retrieve unwanted functional groups. You then subtract the results of Search 2 from the results of Search 1.

61.10.1 Problem

You want to find starting compounds that are benzoic acid derivatives but that are not acid anhydrides.

61.10.2 Approach

Search 1: Draw the benzoic acid query. Enter the query into the a box or table cell on the form in ISIS/Base that will hold your reaction component (without a reaction arrow). For example, enter a molecule that is a reactant into the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE. Then conduct an SSS search in the ISISRX demo database. Save the list of search results and name it List1.

Search 2: Draw the anhydride query. Enter the query into the a box or table cell on the form in ISIS/Base that will hold your reaction component (without a reaction arrow). Then conduct an SSS search in the ISISRX demo database. Save the list of search results and name it List2.

Subtract List2 from List1. You want the search results that remain.

61.10.3 Query 1

This query retrieves all reactants that contain benzoic acid embedded wholly within them, including some unwanted anhydrides.

61.10.4 Search 1

To execute Search 1 and save the results as List1, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

61.10. 5 Query 2

This query retrieves all reactants that contain anhydride embedded wholly within them.

61.10.6 Search 2

A search domain is the database or list of results that you search. To set the search domain to List1, execute Search 2, and save the results as List2, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

61.10.7 Results

To subtract List2 from List1 (to manipulate the search results), follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

The set of search results that remains contains benzoic acid structures as reactants that are not anhydrides. For example, some of the reactants retrieved from the remote reaction database of your choice are as follows:


Local SSS: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Local SSS Search	62.1

*	Definition of Aromaticity	62.2

*	Specifying Query Features on Atoms and Bonds in Structures	62.3

*	Specifying Stereochemistry	62.4

*	Guidelines for Revising the Query	62.5

*	Searching Example 1: General Classes of Compounds	62.6

*	Searching Example 2: Multiple Fragments in a Single Query	62.7

*	Searching Example 3: Excluding Functional Groups	62.8

We recommend that you print this 13-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a local SSS search, click here.

62.1 Definition of a Local SSS Search

A local Molecule Substructure (SSS) search finds reaction records in your local database that contain your query as a substructure wholly within a larger reaction component. Your substructure query is a two-dimensional representation of a portion of a reaction component (a 2D substructure without a reaction arrow). For example:

You can also increase the power of an SSS search by the addition of specific restrictions (called query features) on atoms and/or bonds. There are a number of query features available for use.

In the following example, the ISIS atom-query feature (H0) prohibits the attachment of hydrogens on a specific atom in the records retrieved:

In addition, the hydrogens block substitutions at the specified positions.

A local search is a search over a database that typically exists on your hard disk. To do a local search on your hard disk, you do not need to input network information.

Note: To do a local search that is accessed from a shared network, you need to input network information.

62.2 Definition of Aromaticity

For local databases: A bond is aromatic if it is in a six-membered ring with alternating double and single bonds, such as benzene.

Note: Aromaticity is not perceived for fused rings in which the double bonds are arranged in a way that cannot be defined as aromatic.

62.3 Specifying Query Features on Atoms and Bonds in Structures

A query feature on an atom and/or a bond in a reaction component is a restriction that specifies the retrieval of certain types of reaction records from an ISIS/Base database.

If you do not use query features, the records retrieved contain solely your exact substructure query embedded wholly within them. For example:

62.3.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

62.3.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of hydrogens. For example:

62.3.3 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

62.3.4 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

62.3.5 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

62.3.6 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

62.4 Specifying Stereochemistry

For local databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve reactions with matching stereochemistry on the reaction components. For example:

An SSS search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve molecules with matching cis or trans stereochemistry. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An SSS search produces the following results:

62.5 Guidelines for Revising the Query

If your SSS search retrieved no records or too few records, you might want to:

*	Conduct an SSS search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, or remove stereochemical requirements.

If your SSS search retrieved too many records, you might want to:

*	Refine your query, and then search the same set of records. For example, you can limit substitution at specific positions with explicit hydrogens, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	First conduct a formula search to screen out large and complex molecules that are stored in your database, and then conduct a search on the less complex molecules. If your query is not able to map a stored molecule within a specific length of time, the molecule is added to the search results.

62.6 Searching Example 1: General Classes of Compounds

To retrieve a general class of compounds, draw a substructure query that contains the minimum structural features needed to define the compound class. If you draw too many specific features, you might unintentionally eliminate some molecules.

62.6.1 Problem

You want to retrieve all starting compounds that are nucleic acids.

62.6.2 Approach

Draw a substructure that generally defines nucleic acids (purines and pyrimidines). The minimum structural features include a hetero-substituted six-membered ring with two nitrogen atoms and variable bond types. Enter the query into the a box or table cell on the form in ISIS/Base that will hold your reaction component (without a reaction arrow). For example, enter a molecule that is a reactant into the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE.

Then conduct an SSS search in the local reaction database of your choice, such as the LOCALRX demo database.

62.6.3 Query

The atom query feature Q specifies the two heteroatoms.

There are two bond query features: ANY (dashed lines) allows any bond type and Ch allows solely an acyclic attachment.

62.6.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

62.6.5 Results

Some of the reaction components (reactants in this example) that might be retrieved from the local reaction database of your choice are as follows:

62.7 Searching Example 2: Multiple Fragments in a Single Query

To retrieve molecules that contain all the fragments that you specify in your query, draw each fragment separately, and then group them. In the molecules retrieved, you see:

*	All the fragments in your query. You do not retrieve molecules that contain solely some of the fragments and not all of them.

*	No overlapping fragments. You do not retrieve molecules that contain fragments that share atoms or bonds.

62.7.1 Problem

Find all starting compounds that contain a halogen-substituted aromatic ring and a carboxylic acid group.

62.7.2 Approach

Draw a halogen-substituted aromatic ring fragment and a carboxylic acid fragment.

Select both fragments and enter them into the Structure box or table cell on the form in ISIS/Base that will hold your reaction component (without a reaction arrow). For example, enter a molecule that is a reactant into the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE.

Conduct an SSS search in the local reaction database of your choice, such as the LOCALRX demo database.

62.7.3 Query

The atom query feature LIST specifies that solely those halogens in the bracketed listed be attached at the specified position.

The bond query feature AROMATIC (adjacent solid and dashed lines) allows solely an aromatic bond at the specified position. In ISIS/Base, aromatic bonds occur only in aromatic ring systems. Therefore, you can draw one aromatic bond to represent the entire aromatic ring.

62.7.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

62.7.5 Results

Some of the reaction components (reactants in this example) that might be retrieved from the local reaction database of your choice are as follows:

Reaction components that are not retrieved are as follows:

62.8 Searching Example 3: Excluding Functional Groups

To exclude molecules with unwanted functional groups, you need to conduct two searches: Search 1 retrieves a general category of compounds. Search 2 searches the results of Search 1 to retrieve unwanted functional groups. You then subtract the results of Search 2 from the results of Search 1.

62.8.1 Problem

You want to find starting compounds that are benzoic acid derivatives but that are not acid anhydrides.

62.8.2 Approach

Search 1: Draw the benzoic acid query. Enter the query into the a box or table cell on the form in ISIS/Base that will hold your reaction component (without a reaction arrow). For example, enter a molecule that is a reactant into the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE. Then conduct an SSS search in the LOCALRX demo database. Save the list of search results and name it List1.

Search 2: Draw the anhydride query. Enter the query into the a box or table cell on the form in ISIS/Base that will hold your reaction component (without a reaction arrow). Then conduct an SSS search in the LOCALRX demo database. Save the list of search results and name it List2.

Subtract List2 from List1. You want the search results that remain.

62.8.3 Query 1

This query retrieves all reactants that contain benzoic acid embedded wholly within them, including some unwanted anhydrides.

62.8.4 Search 1

To execute Search 1 and save the results as List1, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

62.8. 5 Query 2

This query retrieves all reactants that contain anhydride embedded wholly within them.

62.8.6 Search 2

A search domain is the database or list of results that you search. To set the search domain to List1, execute Search 2, and save the results as List2, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

62.8.7 Results

To subtract List2 from List1 (to manipulate the search results), follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SSS, how to/examples.

The set of search results that remains contains benzoic acid structures but no anhydrides. For example, some of the reactants retrieved from the local reaction database of your choice are as follows:


Remote RSS/Rxn: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote RSS/Rxn Search	33.1

*	Definition of Aromaticity	33.2

*	Specifying Query Features on Atoms and Bonds in Structures	33.3

*	Specifying Stereochemistry	33.4

*	Specifying Query Features on a Reaction	33.5

*	Specifying an Atom-Atom Map on a Reaction	33.6

*	Guidelines for Revising the Query	33.7

*	Searching Example 1: Preparing m-Hetero-Substituted Benzaldehydes	33.8

*	Searching Example 2: Selective Reduction of Ketones	33.9

*	Searching Example 3: Ring-Opening of Oxiranes	33.10

We recommend that you print this 24-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote RSS/Rxn search, click here.

33.1 Definition of a Remote RSS/Rxn Search

A remote Reaction Substructure for Reactions (RSS/Rxn) search finds reaction records in your remote database that contain your query as a reaction substructure wholly within a larger reaction. Your reaction substructure query is a two-dimensional representation of a portion of a reaction (a 2D reaction substructure) with mapped atoms and your choice of restrictions on the reacting centers. For example:

Your query can also contain restrictions (called query features) on the atoms, bonds and the reaction. In this example, the ISIS reaction-query feature CHANGE (/) specifies that the bond type in the reactant must change in the product at the specified position. For more information on restricting a reacting center bond, see Section 33.5.1.

An atom-atom map on the reaction components in a query specifies exactly which atoms in the reactants correspond to the atoms in the products. For more information on atom-atom maps, see Section 33.6.

You can also add hydrogens with visible bonds (called explicit hydrogens) to your query to block substituents on specific atoms.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

Note: If your query retrieves data that you perceive to be in the wrong place on the form, see your ISIS Administrator. (This might be the result of specifying the same name for multiple database fields on your form or in the Hview.)

33.2 Definition of Aromaticity

For remote databases: ISIS interprets the following ring systems as aromatic:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:

Note: The bonds of six-membered aromatic ring systems and the perimeter bonds of azulenes are stored as aromatic bonds in the database. The bonds of five-membered aromatic rings, however, are stored as single and double bonds and interpreted as aromatic during a search. The differences between five-membered rings and other types of aromatic rings can cause different search results for five- and six-membered rings/azulenes when you use the following bonds in queries: Single, Double, and Single/Double query bonds. For more information on the Single/Double query bond, see Section 33.3.7.

33.3 Specifying Query Features on Atoms and Bonds in Structures

A query feature on an atom and/or a bond in a reaction component is a restriction that specifies the retrieval of certain types of reaction records from an ISIS/Base database.

If you do not use query features, the records retrieved contain solely your exact substructure query embedded wholly within them. For example:

33.3.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

33.3.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of hydrogens. For example:

33.3.3 Allowing an Unsaturated Atom

Use an atom query feature to specify that an atom is attached to at least one multiple bond (double, triple, or aromatic).

Atom Query Feature: Unsaturated Atom (u)

Specifies that the atom of your choice is attached to at least one multiple bond (double, triple, or aromatic). For example, the following query specifies both an unsaturated atom (u) and single or double bonds (the double dashed lines).

33.3.4 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

Atom Query Feature: Substitution Count of Zero, s0

Specifies that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of a single atom with attached hydrogens (if any).

Atom Query Feature: Substitution Count of One, s1

Specifies that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Two, s2

Specifies that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Three, s3

Specifies that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Four, s4

Specifies that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Five, s5

Specifies that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of at Least Six, s6

Specifies that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count as Drawn, s*

Specifies that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:

33.3.5 Allowing a Specific Number of Ring Bond Attachments

Use atom query features to specify the number of ring bond attachments.

Atom Query Feature: Ring Bond Count of Zero, r0

Specifies that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:

Atom Query Feature: Ring Bond Count of Two, r2

Specifies that the records retrieved have solely two ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of Three, r3

Specifies that the records retrieved have solely three ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of at Least Four, r4

Specifies that the records retrieved have at least four ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count as Drawn, r*

Specifies that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:

33.3.6 Allowing Additional Atoms and/or Bonds in a Chain or a Ring

Use a query feature that is for either atoms or bonds to specify the addition of atoms and/or bonds in a chain or a ring.

Atom or Bond Query Feature: Link Node

Use a link node to specify the addition of variable numbers repeating units (atoms and/or bonds) to a ring or chain. A repeating unit must be attached to two adjacent bonds. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the link node [L1-3]:

Or, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the link node [L1-3]:

33.3.7 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Note: An aromatic query bond hits any bond in all types of aromatic rings: 6-membered ring bonds, 5-membered ring bonds, and azulene perimeter bonds. For more information on the structures that ISIS interprets as aromatic, see Section 33.2.

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

Note: A Single/Double query bond does not hit bonds in 6-membered aromatic rings, or perimeter bonds of azulenes, because bonds in these structures are stored in the database as aromatic bonds. However, a Single/Double query bond does hit bonds in 5-membered rings that ISIS interprets as aromatic. For more information on the structures that ISIS interprets as aromatic, see Section 33.2.

Bond Query Feature: Single/Aromatic Bond

Specifies either a single or an aromatic bond at that position:

Bond Query Feature: Double/Aromatic Bond

Specifies either a double or an aromatic bond at that position:

33.3.8 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

33.3.9 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

33.4 Specifying Stereochemistry of Reaction Components

For remote databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve reactions with matching stereochemistry on the reaction components. For example:

An RSS/Rxn search produces the following results for each reaction component:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve reactions with matching cis or trans stereochemistry on the reaction components. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An RSS/Rxn search produces the following results for each reaction component:

Chiral Flags on Reaction Components

In a remote database, you can create a query with a chiral flag on a reaction component with at least one asymmetric center or on a reaction component that is asymmetric to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

33.5 Specifying Query Features on a Reaction

A query feature on a reaction is a restriction on reacting-center bonds that specifies the retrieval of certain types of reaction records from an ISIS/Base database.

You can restrict a reacting center bond to form, break, change its bond type, or change in an unspecified way or you can restrict a stereo bond to invert or retain its stereochemistry.

You can restrict an atom in a reaction to change exactly to your specifications.

33.5.1 Specifying Query Features on a Reacting Center

Use query features to specify whether a bond in a reacting center changes at all, changes in an unspecified way, or whether the bond specifically forms, breaks, or changes its bond type.

If you do not use a query feature on a reacting center, the transformations retrieved contain solely your exact substructure query embedded wholly within them, without regard to the chemistry that is involved in the reacting center.

For example, you want to retrieve solely indoles. Without a query feature on a reacting center, you might retrieve additional, unwanted transformations:

Reacting Center Query Feature: Not Center (X)

Specifies that a bond must not change in the records retrieved. For example, to specify the reduction of a carbonyl to an alcohol, the adjacent double bonds must not change as a result of the transformation:

Reacting Center Query Feature: Center (#)

Specifies that a bond changes in an unspecified way (can form, break, or change its bond type) in the records retrieved. For example, to specify the reduction of a nitrile to a primary amine:

Reacting Center Query Feature: Change (/)

Specifies that a bond changes solely its bond type in the records retrieved. For example, to change the bond type of all bonds in a cyclohexane reactant:

Reacting Center Query Feature: Make/Break (//)

Specifies that a bond is either formed or broken in the records retrieved. For example, to specify the formation of indoles (without also retrieving additional, unwanted results that are not indoles):

Reacting Center Query Feature: Make & Change (///)

Specifies that a bond is either formed or broken and that it changes its bond type in the records retrieved.

33.5.2 Specifying Query Features on a Stereo Bond

A stereo bond is an Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of any of the following atoms: C, N, O, P, S, or Si. Use query features on a stereo bond in the reactants and products of a transformation to specify whether the stereo bond inverts or retains its position.

If you do not use a query feature on a stereo bond, the transformations retrieved contain your exact substructure query embedded wholly within them.

Stereo Bond Query Feature: .Inv.

Specifies that the stereo bond is inverted in the records retrieved. For example:

Stereo Bond Query Feature: .Ret.

Specifies that the stereo is retained (does not invert) in the records retrieved. For example:

33.5.3 Specifying Exact Changes on an Atom in the Reaction

Atom Query Feature: .Ext.

Specifies that an atom changes exactly as you specify it in the reactants and products. (Mark at least one reactant and at least one product with this query feature.) No other changes may occur.

You must specify any changes in the number of hydrogens that are attached to this atom. For example, to show the chlorination of an ethyl group, draw a chlorine in the product that replaces an explicit hydrogen in the reactant. (Either draw the explicit hydrogen or specify a hydrogen count on the reactant at the site of chlorination.)

Note: You must apply atom-atom maps to the reaction before you use this query feature. (If you do not atom-atom map your reaction, this query feature is ignored during the search.

33.6 Specifying an Atom-Atom Map on a Reaction

An atom-atom map on the reaction components in a query specifies exactly which atoms in the reactants correspond to the atoms in the products. You can specify the atoms that must (or must not) change in the transformations that you retrieve.

For example, the following query allows you to see exactly which C-O bond is cleaved to form the product:

An atom-atom map eliminates additional, unwanted results. In this example, the atom-atom map eliminates transformations that produce an alcohol group that is not the result of the demethylation process.

33.6.1 Atom-Atom Map Automatically or Manually

To obtain the correct search results, you need to atom-atom map a reaction query. In ISIS, you can map either automatically or manually.

Automapping a Reaction Query (in ISIS/Base)

If you atom-atom map a reaction automatically, you execute the automap process in ISIS/Base. This process both maps your reaction query and adds any relevant reacting centers and any relevant stereo bond inversion and/or retention marks automatically.

Mapping a Reaction Query Manually (in ISIS/Draw)

If you atom-atom map a reaction manually (in ISIS/Draw), you can choose your own correspondence between the atoms in the reactants and the atoms in the products. However, the reacting centers (and stereo bond inversion and/or retention marks) are not added to your query automatically.

Note: After you atom-atom map a reaction query manually, if you want to add the reacting centers and/or stereo bond markings, you can either add them manually or you can automap the reaction query.

Guidelines for Mapping a Reaction Query

Use the following guidelines to help you to atom-atom map your query correctly:

Always atom-atom map a query that contains an entire reaction (at least a portion of a reactant and at least a portion of a product). Do not attempt to atom-atom map a query that contains solely a reaction component and a reaction arrow.

Note: We strongly recommend that you draw solely the reacting fragments (and use query features where relevant) rather than draw each reactant and product in detail.

Only map those specific atoms that you see in both the reactants and the products. For example, do not map the oxygen atom that you see only in the product:

To simplify the atom-atom mapping process, map your query automatically with the automap feature. However, there are specific times when you need to map a portion of your query manually, and then apply the automap feature to finish the task. For example, map a portion of your query manually if it is unbalanced or if it is mapped incorrectly with the automap feature.

An unbalanced reaction query is a reaction query that contains multiple mappings of a single atom. You need to manually map enough of the atoms to allow the automap feature to map your query correctly. Then select the entire query and automap it. For example:

*	Select a reactant atom and a product atom that you want to specify as Atom 1 and map them manually.

*	Select the same atom in the reactant and another atom in the product that you want to specify as Atom 1 (a multiple mapping of Atom 1) and map them manually. For example, you see the following:

*	Select the entire query and automap it.

Inspect the atom-atom maps on a reaction query before you use the query to conduct a search. If you notice that a map is incorrect, delete it entirely. You need to manually map enough of the atoms to allow the automap feature to map your query correctly. Then select the entire query and re-automap it.

Always atom-atom map a reaction query last, after you add all other structures, stereochemistry, and/or query features to your query.

33.7 Guidelines for Revising the Query

If your RSS/Rxn search retrieved no records or too few records, you might want to:

*	Conduct an RSS/Rxn search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the structural constraints in your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, remove substituent limits, or remove stereochemical requirements.

Note: To retrieve structures that contain Inversion (.Inv.), Retention (.Ret.), Exact Changes (.Ext.), and atom-atom maps, the structures in your database must contain these query features.

If your RSS/Rxn search retrieved too many records, you might want to:

*	Refine your query, and then search the same set of records. For example, you can limit substitution at specific positions, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Mark the reacting centers in your query, and then search the same set of records.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	Conduct a different search on the same set of records with the same query. For example, you might conduct a Reaction Similarity (RSim) search. For more information on this search, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click RSim. You will see the full definition of the search and how to do it.

If your RSS/Rxn search retrieved incorrect records, you might want to:

*	Remap the atoms in your reaction query.

33.8 Searching Example 1: Preparing m-Hetero-Substituted Benzaldehydes

To retrieve synthetic methods for a general class of compounds, draw a reaction substructure query that contains the minimum structural features needed to define the reactant and the product. If you draw too many specific features, you might unintentionally eliminate some synthetic methods.

33.8.1 Problem

You want to retrieve all reactions that prepare m-hetero-substituted benzaldehydes from unsubstituted benzaldehydes.

33.8.2 Approach

Draw a reaction substructure that contains the unsubstituted benzaldehyde as the reactant and the m-hetero-substituted benzaldehyde as the product. Specify the bonds that must be formed or broken for heteroatom substitution to occur.

Specify with an atom-atom map exactly which atoms in the reactants correspond to the atoms in the products. (Always use atom-atom maps in a reaction substructure query. In addition, if you atom-atom map your reaction substructure query automatically, or automap your query, all reacting centers in your query are marked for you automatically.)

Enter the query into the Reaction Structure box or table cell on the form in ISIS/Base that connects to the database field RXNSTRUCTURE.

Conduct an RSS/Rxn search in the remote reaction database of your choice, such as the ISISRX demo database.

33.8.3 Query

The atom query feature Q specifies the heteroatom. The bond query feature Make/Break (bond marked with //) specifies that the bond at the specified position is formed or broken. The numbers that you see are the atom-atom maps.

33.8.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for RSS/Rxn, how to/examples.

33.8.5 Results

Some of the reactions that might be retrieved from the remote reaction database of your choice are as follows:

33.9 Searching Example 2: Selective Reduction of Ketones

To retrieve reactions that transform a specific functional group while avoiding unwanted side reactions, draw a reaction substructure query that contains the minimum structural features needed to define the reactant and the product. If you draw too many specific features, you might unintentionally eliminate some synthetic methods.

33.9.1 Problem

You want to retrieve reactions that reduce the ketone to the alcohol without affecting any aldehydes present. For example:

33.9.2 Approach

Draw the minimum structures in the reaction, and then specify with an atom-atom map exactly which atoms in the reactants correspond to the atoms in the products. (Always use atom-atom maps in a reaction substructure query.)

Before you add the reaction arrow, you must group the reactant fragments, and then you must group the product fragments. (To group a set of fragments, select the fragments to be grouped, and then choose Object > Group.)

Enter the query into the Reaction Structure box or table cell on the form in ISIS/Base that connects to the database field RXNSTRUCTURE.

Conduct an RSS/Rxn search in the remote reaction database of your choice, such as the ISISRX demo database.

33.9.3 Query

The numbers that you see are the atom-atom maps.

33.9.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for RSS/Rxn, how to/examples.

33.9.5 Results

Some of the reactions that might be retrieved from the remote reaction database of your choice are as follows:

33.10 Searching Example 3: Ring-Opening of Oxiranes

To retrieve SN2 displacement reactions with their characteristic stereo inversion, draw a reaction substructure that contains the minimum structural features needed to define the reactant and the product and add the specific stereo bonds. If you draw too many specific features, you might unintentionally eliminate some synthetic methods.

33.10.1 Problem

You want to retrieve all reactions that open oxiranes with halogens in an SN2 reaction:

33.10.2 Approach

Draw a reaction substructure that opens an oxirane. Mark the Up and Down stereo bonds, and specify those bonds that are inverted and retained. Specify the bonds that must be formed or broken for the displacement reaction to occur.

Specify with an atom-atom map exactly which atoms in the reactants correspond to the atoms in the products. (Always use atom-atom maps in a reaction substructure query. In addition, if you atom-atom map your reaction substructure query automatically, or automap your query, all reacting centers in your query are marked for you automatically.)

Enter the query into the Reaction Structure box or table cell on the form in ISIS/Base that connects to the database field RXNSTRUCTURE.

Conduct an RSS/Rxn search in the remote reaction database of your choice, such as the ISISRX demo database.

33.10.3 Query

The atom query feature LIST specifies that solely those halogens in the bracketed listed be attached at the specified position.

The stereo bond query features .Inv. and .Ret. specify that the stereo bonds are inverted and retained, respectively.

The bond query feature Make/Break (bond marked with //) specifies that the bond at the specified position is formed or broken.

The numbers that you see are the atom-atom maps.

33.10.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for RSS/Rxn, how to/examples.

33.10.5 Results

One of the reactions that might be retrieved from the remote reaction database of your choice is as follows:


Local RSS/Rxn: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Local RSS/Rxn Search	34.1

*	Definition of Aromaticity	34.2

*	Specifying Query Features on Atoms and Bonds in Structures	34.3

*	Specifying Stereochemistry	34.4

*	Guidelines for Revising the Query	34.5

*	Searching Example 1: Preparing m-Hetero-Substituted Benzaldehydes	34.6

We recommend that you print this 10-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a local RSS/Rxn search, click here.

34.1 Definition of a Local RSS/Rxn Search

A local Reaction Substructure for Reactions (RSS/Rxn) search finds reaction records in your local database that contain your query as a reaction substructure wholly within a larger reaction. Your reaction substructure query is a two-dimensional representation of a portion of a reaction (a 2D reaction substructure). For example:

Your query can also contain restrictions (called query features) on atoms and bonds. For example, you can use the atom query feature (H0) to prohibit the attachment of hydrogens on a specific atom in the records retrieved. You can also add hydrogens with visible bonds (called explicit hydrogens) to your query to block substituents on specific atoms.

A local search is a search over a database that typically exists on your hard disk. To do a local search on your hard disk, you do not need to input network information.

Note: To do a local search that is accessed from a shared network, you need to input network information.

34.2 Definition of Aromaticity

For local databases: A bond is aromatic if it is in a six-membered ring with alternating double and single bonds, such as benzene.

Note: Aromaticity is not perceived for fused rings in which the double bonds are arranged in a way that cannot be defined as aromatic.

34.3 Specifying Query Features on Atoms and Bonds in Structures

A query feature on an atom and/or a bond in a reaction component is a restriction that specifies the retrieval of certain types of reaction records from an ISIS/Base database.

If you do not use query features, the records retrieved contain solely your exact substructure query embedded wholly within them. For example:

34.3.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

34.3.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of hydrogens. For example:

34.3.3 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

34.3.4 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

34.3.5 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

34.3.6 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

34.4 Specifying Stereochemistry of Reaction Components

For local databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve reactions with matching stereochemistry on the reaction components. For example:

An RSS/Rxn search produces the following results for each reaction component:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve reactions with matching cis or trans stereochemistry on the reaction components. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An RSS/Rxn search produces the following results for each reaction component:

34.5 Guidelines for Revising the Query

If your RSS/Rxn search retrieved no records or too few records, you might want to:

*	Conduct an RSS/Rxn search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the structural constraints in your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, or remove stereochemical requirements.

If your RSS/Rxn search retrieved too many records, you might want to:

*	Refine your query, and then search the same set of records. For example, you can limit substitution at specific positions with explicit hydrogens, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

34.6 Searching Example 1: Preparing m-Hetero-Substituted Benzaldehydes

To retrieve synthetic methods for a general class of compounds, draw a reaction substructure query that contains the minimum structural features needed to define the reactant and the product. If you draw too many specific features, you might unintentionally eliminate some synthetic methods.

34.6.1 Problem

You want to retrieve all reactions that prepare m-hetero-substituted benzaldehydes from unsubstituted benzaldehydes.

34.6.2 Approach

Draw a reaction substructure that contains the unsubstituted benzaldehyde as the reactant and the m-hetero-substituted benzaldehyde as the product.

Enter the query into the Reaction Structure box or table cell on the form in ISIS/Base that connects to the database field RXNSTRUCTURE.

Conduct an RSS/Rxn search in the local reaction database of your choice, such as the LOCALRX demo database.

34.6.3 Query

The atom query feature Q specifies the heteroatom.

34.6.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for RSS/Rxn, how to/examples.

34.6.5 Results

Some of the reactions that might be retrieved from the local reaction database of your choice are as follows:


Remote RSS/Comp: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote RSS/Comp Search	35.1

*	Definition of Aromaticity	35.2

*	Specifying Query Features on Atoms and Bonds in Structures	35.3

*	Specifying Stereochemistry	35.4

*	Specifying Reaction Query Features on a Reaction Component	35.5

*	Guidelines for Revising the Query	35.6

*	Searching Example 1: Preparing m-Substituted Benzaldehydes	35.7

We recommend that you print this 19-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote RSS/Comp search, click here.

35.1 Definition of a Remote RSS/Comp Search

A remote Reaction Substructure for Reaction Components (RSS/Comp) search finds reaction records in your remote database that contain your query as a substructure wholly within a larger reactant or product (with a reaction arrow). Your reaction component substructure query is a two-dimensional representation of a portion of a reactant or a product (a 2D reaction component substructure) with your choice of restrictions on the reacting centers. For example, a reactant substructure query is as follows:

Your query can also contain restrictions (called query features) on the atoms, bonds, and the reaction. In this example, the ISIS reaction-query feature CHANGE (/) specifies that the bond type in the reactant must change in the product at the specified position. For more information on restricting a reacting center bond, see Section 35.5.1.

You can also add hydrogens with visible bonds (called explicit hydrogens) to your query to block substituents on specific atoms.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

Note: If your query retrieves data that you perceive to be in the wrong place on the form, see your ISIS Administrator. (This might be the result of specifying the same name for multiple database fields on your form or in the Hview.)

35.2 Definition of Aromaticity

For remote databases: ISIS interprets the following ring systems as aromatic:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:

Note: The bonds of six-membered aromatic ring systems and the perimeter bonds of azulenes are stored as aromatic bonds in the database. The bonds of five-membered aromatic rings, however, are stored as single and double bonds and interpreted as aromatic during a search. The differences between five-membered rings and other types of aromatic rings can cause different search results for five- and six-membered rings/azulenes when you use the following bonds in queries: Single, Double, and Single/Double query bonds. For more information on the Single/Double query bond, see Section 35.3.7.

35.3 Specifying Query Features on Atoms and Bonds in Structures

A query feature on an atom and/or a bond in a reaction component is a restriction that specifies the retrieval of certain types of reaction records from an ISIS/Base database.

If you do not use query features, the records retrieved contain solely your exact substructure query embedded wholly within them. For example:

35.3.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

35.3.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of hydrogens. For example:

35.3.3 Allowing an Unsaturated Atom

Use an atom query feature to specify that an atom is attached to at least one multiple bond (double, triple, or aromatic).

Atom Query Feature: Unsaturated Atom (u)

Specifies that the atom of your choice is attached to at least one multiple bond (double, triple, or aromatic). For example, the following query specifies both an unsaturated atom (u) and single or double bonds (the double dashed lines).

35.3.4 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

Atom Query Feature: Substitution Count of Zero, s0

Specifies that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of a single atom with attached hydrogens (if any).

Atom Query Feature: Substitution Count of One, s1

Specifies that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Two, s2

Specifies that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Three, s3

Specifies that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Four, s4

Specifies that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Five, s5

Specifies that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of at Least Six, s6

Specifies that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count as Drawn, s*

Specifies that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:

35.3.5 Allowing a Specific Number of Ring Bond Attachments

Use atom query features to specify the number of ring bond attachments.

Atom Query Feature: Ring Bond Count of Zero, r0

Specifies that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:

Atom Query Feature: Ring Bond Count of Two, r2

Specifies that the records retrieved have solely two ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of Three, r3

Specifies that the records retrieved have solely three ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of at Least Four, r4

Specifies that the records retrieved have at least four ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count as Drawn, r*

Specifies that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:

35.3.6 Allowing Additional Atoms and/or Bonds in a Chain or a Ring

Use a query feature that is for either atoms or bonds to specify the addition of atoms and/or bonds in a chain or a ring.

Atom or Bond Query Feature: Link Node

Use a link node to specify the addition of variable numbers repeating units (atoms and/or bonds) to a ring or chain. A repeating unit must be attached to two adjacent bonds. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the link node [L1-3]:

Or, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the link node [L1-3]:

35.3.7 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Note: An aromatic query bond hits any bond in all types of aromatic rings: 6-membered ring bonds, 5-membered ring bonds, and azulene perimeter bonds. For more information on the structures that ISIS interprets as aromatic, see Section 35.2.

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

Note: A Single/Double query bond does not hit bonds in 6-membered aromatic rings, or perimeter bonds of azulenes, because bonds in these structures are stored in the database as aromatic bonds. However, a Single/Double query bond does hit bonds in 5-membered rings that ISIS interprets as aromatic. For more information on the structures that ISIS interprets as aromatic, see Section 35.2.

Bond Query Feature: Single/Aromatic Bond

Specifies either a single or an aromatic bond at that position:

Bond Query Feature: Double/Aromatic Bond

Specifies either a double or an aromatic bond at that position:

35.3.8 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

35.3.9 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

35.4 Specifying Stereochemistry

For remote databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve reactions with matching stereochemistry on the reaction components. For example:

An RSS/Comp search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve reactions with matching cis or trans stereochemistry on the reaction components. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An RSS/Comp search produces the following results:

Chiral Flags on Reaction Components

In a remote database, you can create a query with a chiral flag on a reaction component with at least one asymmetric center or on a reaction component that is asymmetric to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

35.5 Specifying Reaction Query Features on a Reaction Component

A reaction query feature on a reaction component is a restriction on reacting center bonds in a reactant or a product that specifies the retrieval of certain types of reaction records from an ISIS/Base database.

You can restrict a reacting center bond to form, break, change its bond type, or change in an unspecified way or you can restrict a stereo bond to invert or retain its stereochemistry.

You can restrict an atom in a reaction to change exactly to your specifications.

35.5.1 Specifying Query Features on a Reacting Center

Use query features to specify whether a bond in a reacting center changes at all, changes in an unspecified way, or whether the bond specifically forms, breaks, or changes its bond type.

If you do not use a query feature on a reacting center, the transformations retrieved contain solely your exact substructure query embedded wholly within them, without regard to the chemistry that is involved in the reacting center.

For example, you want to retrieve solely indoles. Without a query feature on a reacting center, you might retrieve additional, unwanted transformations:

Reacting Center Query Feature: Not Center (X)

Specifies that a bond must not change in the records retrieved. For example, to specify the reduction of a carbonyl to an alcohol, the adjacent double bonds must not change as a result of the transformation:

Reacting Center Query Feature: Center (#)

Specifies that a bond changes in an unspecified way (can form, break, or change its bond type) in the records retrieved. For example, to specify the reduction of a nitrile to a primary amine:

Reacting Center Query Feature: Change (/)

Specifies that a bond changes solely its bond type in the records retrieved. For example, to change the bond type of all bonds in a cyclohexane reactant:

Reacting Center Query Feature: Make/Break (//)

Specifies that a bond is either formed or broken in the records retrieved. For example, to specify the formation of indoles (without also retrieving additional, unwanted results that are not indoles):

Reacting Center Query Feature: Make & Change (///)

Specifies that a bond is either formed or broken and that it changes its bond type in the records retrieved.

35.5.2 Specifying Query Features on a Stereo Bond

A stereo bond is an Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of any of the following atoms: C, N, O, P, S, or Si. Use query features on a stereo bond on a reaction component to specify whether the stereo bond inverts or retains its position in the records retrieved.

If you do not use a query feature on a stereo bond, the transformations retrieved contain your exact substructure query embedded wholly within them.

Stereo Bond Query Feature: .Inv.

Specifies that the stereo bond is inverted in the records retrieved. For example:

Stereo Bond Query Feature: .Ret.

Specifies that the stereo bond is retained (does not invert) in the records retrieved. For example:

35.5.3 Reaction Query Features That you Cannot Use

An RSS/Comp search contains solely reactants or solely products, entire reactions (in which there is at least one reactant and at least one product). The following query features are for entire reactions only and cannot be used in an RSS/Comp search:

*	Atom-atom maps

*	Atom query feature: .Ext.

To use these query features, you must have an entire reaction as your query and conduct an RSS/Rxn search.

35.6 Guidelines for Revising the Query

If your RSS/Comp search retrieved no records or too few records, you might want to:

*	Conduct an RSS/Comp search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the structural constraints in your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, remove substituent limits, or remove stereochemical requirements.

Note: To retrieve structures that contain Inversion (.Inv.), Retention (.Ret.), Exact Changes (.Ext.), and atom-atom maps, the structures in your database must contain these query features.

If your RSS/Comp search retrieved too many records, you might want to:

*	Refine your query, and then search the same set of records. For example, you can limit substitution at specific positions, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Mark the reacting centers in your query, and then search the same set of records.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	Conduct a different search on the same set of records with the same query. For example, you might conduct a Reaction Similarity (RSim) search. For more information on this search, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click RSim. You will see the full definition of the search and how to do it.

35.7 Searching Example 1: Preparing m-Substituted Benzaldehydes

To retrieve synthetic methods for a general class of compounds from any starting material, draw a substructure query that contains the minimum structural features needed to define the product. If you draw too many specific features, you might unintentionally eliminate some synthetic methods.

35.7.1 Problem

You want to retrieve all reactions that prepare m-substituted benzaldehydes (but not o- or p-substituted benzaldehydes) from any starting material.

35.7.2 Approach

Draw a product substructure (with a reaction arrow) that contains the benzaldehyde as the product. Add explicit hydrogen atoms to block all sites where substitution might occur (but do not add an explicit hydrogen at the meta position).

Enter the query into the Reaction Structure box or table cell on the form in ISIS/Base that connects to the database field RXNSTRUCTURE.

Conduct an RSS/Comp search in the remote reaction database of your choice, such as the ISISRX demo database.

35.7.3 Query

35.7.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for RSS/Comp, how to/examples.

35.7.5 Results

One of the reactions that might be retrieved from the remote reaction database of your choice is as follows:


Local RSS/Comp: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Local RSS/Comp Search	36.1

*	Definition of Aromaticity	36.2

*	Specifying Query Features on Atoms and Bonds in Structures	36.3

*	Specifying Stereochemistry	36.4

*	Guidelines for Revising the Query	36.5

*	Searching Example 1: Preparing m-Substituted Benzaldehydes	36.6

We recommend that you print this 9-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a local RSS/Comp search, click here.

36.1 Definition of a Local RSS/Comp Search

A local Reaction Substructure for Reaction Components (RSS/Comp) search finds reaction records in your local database that contain your query as a substructure wholly within a larger reactant or product (with a reaction arrow). Your reaction component substructure query is a two-dimensional representation of a portion of a reactant or a product (a 2D reaction component substructure). For example, a reactant substructure query is as follows:

Your query can also contain restrictions (called query features) on atoms and bonds. For example, you can use the atom query feature (H0) to prohibit the attachment of hydrogens on a specific atom in the records retrieved. You can also add hydrogens with visible bonds (called explicit hydrogens) to your query to block substituents on specific atoms.

A local search is a search over a database that typically exists on your hard disk. To do a local search on your hard disk, you do not need to input network information.

Note: To do a local search that is accessed from a shared network, you need to input network information.

36.2 Definition of Aromaticity

For local databases: A bond is aromatic if it is in a six-membered ring with alternating double and single bonds, such as benzene.

Note: Aromaticity is not perceived for fused rings in which the double bonds are arranged in a way that cannot be defined as aromatic.

36.3 Specifying Query Features on Atoms and Bonds in Structures

A query feature on an atom and/or a bond in a reaction component is a restriction that specifies the retrieval of certain types of reaction records from an ISIS/Base database.

If you do not use query features, the records retrieved contain solely your exact substructure query embedded wholly within them. For example:

36.3.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

36.3.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of hydrogens. For example:

36.3.3 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

36.3.4 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

36.3.5 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

36.3.6 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

36.4 Specifying Stereochemistry

For local databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve reactions with matching stereochemistry on the reaction components. For example:

An RSS/Comp search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve reactions with matching cis or trans stereochemistry on the reaction components. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An RSS/Comp search produces the following results:

36.5 Guidelines for Revising the Query

If your RSS/Comp search retrieved no records or too few records, you might want to:

*	Conduct an RSS/Comp search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, or remove stereochemical requirements.

If your RSS/Comp search retrieved too many records, you might want to:

*	Refine your query, and then search the same set of records. For example, you can limit substitution at specific positions with explicit hydrogens, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

36.6 Searching Example 1: Preparing m-Substituted Benzaldehydes

To retrieve synthetic methods for a general class of compounds from any starting material, draw a substructure query that contains the minimum structural features needed to define the product. If you draw too many specific features, you might unintentionally eliminate some synthetic methods.

36.6.1 Problem

You want to retrieve all reactions that prepare m-substituted benzaldehydes (but not o- or p-substituted benzaldehydes) from any starting material.

36.6.2 Approach

Draw a product substructure (with a reaction arrow) that contains the benzaldehyde as the product. Add explicit hydrogen atoms to block all sites where substitution might occur (but do not add an explicit hydrogen at the meta position).

Enter the query into the Reaction Structure box or table cell on the form in ISIS/Base that connects to the database field RXNSTRUCTURE.

Conduct an RSS/Comp search in the local reaction database of your choice, such as the LOCALRX demo database.

36.6.3 Query

36.6.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for RSS/Comp, how to/examples.

36.6.5 Results

One of the reactions that might be retrieved from the local reaction database of your choice is as follows:


Remote SBF in a Molecule Database: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote SBF Search in a Molecule Database	37.1

*	Definition of Aromaticity	37.2

*	Specifying Query Features on Atoms and Bonds in Structures	37.3

*	Specifying Rgroup Query Features	37.4

*	Specifying Stereochemistry	37.5

*	Guidelines for Revising the Query	37.6

*	Searching Example 1: Combining Text/Numeric Queries	37.7

*	Searching Example 2: Combining Text/Numeric and Graphical Queries	37.8

We recommend that you print this 27-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote SBF search in a molecule database, click here.

37.1 Definition of a Remote SBF Search in a Molecule Database

A remote Search By Form (SBF) search in a molecule database search finds molecule records in your remote database that contain your text/numeric query exactly as you specify it or your graphical query as a substructure wholly within a larger structure.

Note: If your database contains the exact match of your substructure query, you also retrieve the exact match.

In addition, you can combine text/numeric and graphical queries. For example, you want to find all molecules that contain a specific steroid substructure wholly within them and that have a melting point that is greater than 220 degrees Centigrade and that contain a compound name that ends in "one" (You can enter as many as 25 queries into different cells of the same table.):

Your text/numeric query can also contain wildcards. A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: (The wildcard % is a placeholder for at least one unspecified character.) To find the exact match of the data of interest, enter the search operator LIKE and place your target text in double quotes. A search operator is the command that specifies the type of search.

Your graphical query can also contain restrictions (called query features) on atoms and bonds. For example, you can use the ISIS bond-query feature Ch to specify that a bond is part of an acyclic structure in the records retrieved. You can also add hydrogens with visible bonds (called explicit hydrogens) to your query to block substituents on specific atoms.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

37.1.1 Specifying a Text/Numeric String as a Query

A text/numeric string as an SBF query is a phrase in a box or column on the form that specifies the retrieval of data. For example, to find structures with a molecular weight greater than 350, enter the text/numeric string > 350 into the Molecular Weight box on the form.

Each phrase in a text/numeric string contains:

*	A search operator that specifies the type of search. For example, the search operators = (equal sign) and LIKE specify the retrieval of the exact match of your query. Use = when you want to retrieve data with numeric values. Use LIKE when you want to retrieve data with text. For details on search operators, see Section 37.1.2.

*	A text or numeric target value that you want to find (such as 350 for the molecular weight or ANTIBIOTIC for the activity).

Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

Specifying Numeric String Queries

Do not include the units, such as a percent sign (%) or the degrees Centigrade (C). For example, to retrieve all compounds with a molecular weight greater than 350, enter:

> 350

where the search operator is > and the target value is 350.

Specifying Text/Numeric String Queries

Always use a wildcard, such as %, in queries that contain text (with or without numeric values). Double quotes around the text string are optional. For example, to retrieve all compounds from the author Smythe, enter one of the following:

LIKE %Smythe%
LIKE "%Smythe%"

where the search operator is LIKE and the target value is Smythe.

A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. The wildcard _ is a placeholder for solely one unspecified character. Without a wildcard, you retrieve solely those records that contain exactly the target value that you specified. For example:

Query Without a Wildcard	Example of a Record Retrieved

LIKE "antibiotic"	Antibiotic

Query With the Wildcard %	Examples of Records Retrieved

LIKE "%antibiotic%"	Antibiotic

ANTIBIOTIC

Antibiotic activity

Resistance to extracellular products such as antibiotics

Note: If you want to retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

37.1.2 The Search Operators

<, <=, >, >=, and <>

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Search Operator	Definition	Examples

=	equal (numeric)	= 350

<	less than (numeric)	< 350

<=	less than or equal to (numeric)	= 350

>	greater than (numeric)	> 350

>=	greater than or equal to (numeric)	>= 350

<>	not equal to (text or numeric)	<> 350

<> "initiator"

LIKE

Use LIKE with text enclosed in double quotation marks. Enter your query as follows:

Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. For example:

Query	Examples of Records Retrieved

LIKE "methane"	Methane

LIKE "benzoic acid"	Benzoic Acid

LIKE "%acid"	Benzoic Acid

Acetic Acid

LIKE "%acid%"	Benzoic Acid Sodium Salt

Acetic Acid Sodium Salt

LIKE "%but_ne"	Trans 2-Butene

2-Butene

N-Butane

Butane

Butene

LIKE "_ethyl"	Methyl

Ethyl

LIKE "antibiotic"	Antibiotic

LIKE "%antibiotic%"	Antibiotic activity

Resistance to extracellular products such as antibiotics

Note: To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice. To retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

BETWEEN

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks. For example:

BETWEEN "XR11" "XZ15"

BETWEEN 95 100

EXISTS

Use EXISTS to retrieve all records in the database that contain data in a specific database field. For example:

EXISTS

Note: You can only use the EXISTS search operator for database fields that do not give you an error message.

37.1.3 Specifying a Molecular Formula as a Query

To search the data in Formula box (that is, a box that is connected to a MOLFORMULA field), you can specify the following text/numeric queries:

*	An exact formula. Use an exact formula query to find records that contain solely the exact atoms that you specify.

*	A subformula. Use a subformula query to find records that contain the specific atoms that you specify, and any additional atoms.

Exact Formula Query

To specify an exact formula query, specify the target value for the formula. The target value must include all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required. The equals operator (=) and quotes are optional. For example:

Exact Formula Query	Examples of Records Retrieved

c6 h6 O	Phenol

c6h6o

C20 H12 Na2 O4	Sodium salt of phenolphthalein

C20H12Na2O4

= C20 H12 Na2 O4

= C20H12Na2O4

= "C20 H12 Na2 O4"

= "C20H12Na2O4"

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Exact Formula Query	Examples of Records Retrieved

C17 H19 N 03	Piperine

C17H19N 03	Piperine

C17H19N103	Piperine

C17H19N03	No molecules retrieved. ISIS interprets "NO3" as 3 Nobelium atoms.

Subformula Query

To specify a subformula query, use the LIKE operator with a target value for the subformula. The target value can include a range of atom counts, and typically excludes the hydrogens. To exclude specific atoms from the molecules that you retrieve, specify zero for that atom. You can use a single space to separate atoms. Capital letters are not required. Quotes are optional.

Subformula Query	Examples of Records Retrieved

LIKE Na	All sodium salts

LIKE c12 Br(1-2) S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE "C12Br(1-2)S2"	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE c6 h6	All molecules that contain six carbon atoms, six hydrogen atoms, and any number of other atoms

LIKE C5 H10 N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

LIKE C5H10N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Subformula Query	Examples of Records Retrieved

LIKE C12 Br S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12Br1S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12BrS2	No molecules retrieved. ISIS interprets "BrS" as an atom symbol, and gives an error message.

37.1.4 Specifying a Graphical Substructure as a Query

A graphical substructure query retrieves records that contain your graphical query embedded wholly within them. For example:

You can also increase the power of an SBF search by the addition of specific restrictions (called query features) on atoms and/or bonds. There are a number of query features available for use.

In the following example, the ISIS atom-query feature (H0) prohibits the attachment of hydrogens on a specific atom in the records retrieved:

In addition, the hydrogens block substitutions at the specified positions.

To use a graphical query, you must have a Structure box or table cell on the form that connects to the database field MOLSTRUCTURE.

Notes: (1) You can enter multiple graphical queries onto the form in ISIS/Base. (2) You do not use a search operator with a graphical query.

37.1.5 Specifying Multiple Queries in a Single SBF Search

When you combine two or more queries of any type into a single SBF search, the search results that you obtain depend on both the specifications and accuracy of your query and the way that information is stored in your database. For more information on how to create an adequate query, see Section 37.1.1 through Section 37.1.4.

Information in a database is stored either in a single level (called a flat database) or in multiple levels (called a hierarchical database). Storage in a hierarchical database is more efficient, but it requires you to enter your queries in the correct location on the form to obtain the search results that you want.

For example, the following hierarchical database stores data for multiple decomposition tests that are conducted under different atmospheric conditions:

(In this database, structures are stored at the top (or root) level, and the percentage of oxygen and the number of peaks are stored at a lower level, under the parent field Decomposition. A parent field is a branch in the hierarchy that contains a set of child fields, such as percent O2 and number of peaks.)

You want specific decomposition data from different tests. Your multiple query in a single SBF search specifies that you want all compounds within a single test that contain: Query 1, greater than 65% O2; Query 2, less than three peaks.

To obtain search results that match all queries (Query 1 AND Query 2), you can either (a) enter each search query into separate boxes or (b) enter each search query into the same row in a single table. This search gives you all compounds within a single test that meet both requirements in your query:

Caution: For all versions of ISIS before 2.0, multiple queries in boxes might give different results than multiple queries in tables. In the previous example, the SBF query in the box on the form at the left retrieves records in which at least one decomposition test that matches both conditions. The SBF query in the table on the form at the right, however, retrieves additional records in which one decomposition test matches one condition, and another decomposition test matches the other condition. In ISIS 2.0, both queries retrieve only those records in which both conditions are met within the same decomposition test.

To obtain search results that match either one query or the other (Query 1 OR Query 2), you must enter each search query into different rows of a single table. You must be certain that the first column in the table is a field at the same database level that you want to search. This search gives you all compounds within a single test that meet either requirement in your query (but not necessarily both requirements):

When you filter your search results, you see solely those lower-level records that meet your search requirements.

Note: A box retrieves data from a single database field. A table retrieves data from multiple database fields. Also, you can enter as many as 25 queries into the same table.

37.1.6 Specifying Searchable Keys as a Query

If your database contains the database field MOLSKEYS, you can use numbered keys to retrieve specific substructures or chemical representations. Separate multiple keys with a comma (with no spaces):

*	Use parentheses to specify the retrieval of all the keys in your query. Example: To specify the retrieval of molecules that contain 6-membered rings and bromine, enter (163,46) into the box or table cell on the form in ISIS/Base that connects to the database field MOLSKEYS.

*	Use square brackets to specify the retrieval of one ore more keys in your query. Example: To specify the retrieval of molecules that contain 6-membered rings or bromine, enter [163,46] into the box or table cell on the form in ISIS/Base that connects to the database field MOLSKEYS.

*	Use angle brackets to specify the retrieval of none of the keys in your query. Example: To specify the retrieval of molecules that do not contain 6-membered rings or bromine, enter <163,46> into the box or table cell on the form in ISIS/Base that connects to the database field MOLSKEYS.

*	Use braces to specify the retrieval of solely one of the keys in your query but not any others in your query. Example: To specify the retrieval of molecules that contain either 6-membered rings or bromine but not both 6-membered rings and bromine, enter {163,46} into the box or table cell on the form in ISIS/Base that connects to the database field MOLSKEYS.

*	Use no restrictors to specify the retrieval of one and/or any other keys in your query. Example: To specify the retrieval of molecules that contain 6-membered rings and/or bromine, enter 163,46 into the box or table cell on the form in ISIS/Base that connects to the database field MOLSKEYS.

Additional Examples

The query 161,[11,96] specifies the retrieval of N and a 4- or 5-membered ring.

The query [(161,96),(164,163)] specifies the retrieval of N and a 5-membered ring or O and a 6-membered ring. Both sets of molecules can be retrieved.

The query [42,46,103],<27> specifies the retrieval of at least one halogen, which cannot be iodine.

The List of Searchable Keys

If you search a MACCS-II database, there are 166 numbered keys that you can use. If you do not recognize the words for a specific key, the words might be in a special type of language called query language. The list of searchable keys is as follows:

Key	Description	Key	Description

1	ISOTOPE	84	NH2

2	103 < ATOMIC NO. < 256	85	CN(C)C

3	GROUP IVA,VA,VIA PERIODS 4-6 (GE..)	86	CH2QCH2

4	ACTINIDE	87	X!A$A

5	GROUP IIIB,IVB (SC..)	88	S

6	LANTHANIDE	89	OAAAO

7	GROUP VB,VIB,VIIB (V..)	90	QHAACH2A

8	QAAA@1	91	QHAAACH2A

9	GROUP VIII (FE..)	92	OC(N)C

10	GROUP IIA (ALKALINE EARTH)	93	QCH3

11	4M RING	94	QN

12	GROUP IB,IIB (CU..)	95	NAAO

13	ON(C)C	96	5M RING

14	S-S	97	NAAAO

15	OC(O)O	98	QAAAAA@1

16	QAA@1	99	C=C

17	CTC	100	ACH2N

18	GROUP IIIA (B..)	101	8M RING OR LARGER

19	7M RING	102	QO

20	Si	103	CL

21	C=C(Q)Q	104	QHACH2A

22	3M RING	105	A$A($A)$A

23	NC(O)O	106	QA(Q)Q

24	N-O	107	XA(A)A

25	NC(N)N	108	CH3AAACH2A

26	C$=C($A)$A	109	ACH2O

27	I	110	NCO

28	QCH2Q	111	NACH2A

29	P	112	AA(A)(A)A

30	CQ(C)(C)A	113	Onot%A%A

31	QX	114	CH3CH2A

32	CSN	115	CH3ACH2A

33	NS	116	CH3AACH2A

34	CH2=A	117	NAO

35	GROUP IA (ALKALI METAL)	118	ACH2CH2A>1

36	S HETEROCYCLE	119	N=A

37	NC(O)N	120	HETEROCYCLIC ATOM>1 (&..)

38	NC(C)N	121	N HETEROCYCLE

39	OS(O)O	122	AN(A)A

40	S-O	123	OCO

41	CTN	124	QQ

42	F	125	AROMATIC RING>1

43	QHAQH	126	A!O!A

44	OTHER	127	A$A!O>1 (&..)

45	C=CN	128	ACH2AAACH2A

46	BR	129	ACH2AACH2A

47	SAN	130	QQ>1 (&..)

48	OQ(O)O	131	QH>1

49	CHARGE	132	OACH2A

50	C=C(C)C	133	A$A!N

51	CSO	134	X (HALOGEN)

52	NN	135	Nnot%A%A

53	QHAAAQH	136	O=A.1

54	QHAAQH	137	HETEROCYCLE

55	OSO	138	QCH2A>1 (&..)

56	ON(O)C	139	OH

57	O HETEROCYCLE	140	O>3 (&..)

58	QSQ	141	CH3>2 (&..)

59	Snot%A%A	142	N>1

60	S=O	143	A$A!O

61	AS(A)A	144	Anot%A%Anot%A

62	A$A!A$A	145	6M RING>1

63	N=O	146	O>2

64	A$A!S	147	ACH2CH2A

65	C%N	148	AQ(A)A

66	CC(C)(C)A	149	CH3>1

67	QS	150	A!A$A!A

68	QHQH (&..)	151	NH

69	QQH	152	OC(C)C

70	QNQ	153	QCH2A

71	NO	154	C=O

72	OAAO	155	A!CH2!A

73	S=A	156	NA(A)A

74	CH3ACH3	157	C-O

75	A!N$A	158	C-N

76	C=C(A)A	159	O>1

77	NAN	160	CH3

78	C=N	161	N

79	NAAN	162	AROMATIC

80	NAAAN	163	6M RING

81	SA(A)A	164	O

82	ACH2QH	165	RING

83	QAAAA@1	166	FRAGMENTS

Where (&..) is equivalent to "and other rare features;" and Key 166 Key 166 corresponds to molecules that consist of more than one fragment. (A molecule has more than one fragment if its structure cannot be drawn in one connected set of bonds.)

Some of the keys that you see are encoded in a substructure-search query language, such as QAAAA@1 for Key 83. This language allows atoms to be expressed as follows:

*	Unbracketed for C, N, O, P, and S; but bracketed for all other single element symbols, such as [CL] for chlorine, or multiple element symbols in lists, such as [N,O] for nitrogen and oxygen, or [F,CL,BR,I] for halogens.

*	A for any atom except hydrogen, and Q for any atom except carbon or hydrogen.

*	Substituted with a specific number of hydrogens: H0 on an atom prohibits hydrogens at that position, such as CH0; and Hn allows at least that number (n) of hydrogens, such as CH2 (methyl or methylene).

*	Charged: A plus sign (+) on an atom is a positive charge, such as +, +2, or +3; a single quote (') is a monoradical; a double quote (") is a negative charge; and an asterisk (*) is a neutral atom.

*	Variable in mass: The isotopic label M+n indicates a difference of n from the standard mass, such as CM+1 to indicate the isotope carbon 13, or OM-1 to indicate the isotope oxygen 15.

*	Variable in atom number: The notation @n at the end of the atom to which it refers indicates that atom number (n) is attached here. Atoms (except hydrogen) are numbered from left to right, such as C-C-C-@1 (but not @3-C-C-C) to indicate a three-membered ring, or CH3-C-C-C-@2 to indicate (methyl or methylene).

*	Branched: The parentheses around an atom or group indicates that the atom or group branches from the atom at its left (but not its right) in the string. For example, C-C-C-C is butane, while C-C(C)-C-C is 2-methyl butane. N+(-C)(-C)(-C)(-C) is a quaternary ammonium salt.

This language allows bonds to be expressed as follows:

*	Variable bond type: A hyphen (-) is a single bond; an equal sign (=) is a double bond; a (T) is a triple bond; a percent sign (%) is an aromatic bond; a tilde (~) is either a single or a double bond; and an unspecified bond type is the omission a bond marker. For example, the two carbon chain CC contains any type of bond.

*	Variable numbers of fragments: A space between strings indicates that there is no connection between the groups. For example, C=O C-OH retrieves a carbonyl and a hydroxyl, but the groups cannot be centered on the same carbon (the fragments cannot overlap).

*	Part of a ring: A dollar sign ($) that precedes a bond indicates that the bond is part of a ring.

*	Part of a chain: An exclamation sign (!) that precedes a bond indicates that the bond is part of a chain.

37.2 Definition of Aromaticity

For remote databases: ISIS interprets the following ring systems as aromatic:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:

Note: The bonds of six-membered aromatic ring systems and the perimeter bonds of azulenes are stored as aromatic bonds in the database. The bonds of five-membered aromatic rings, however, are stored as single and double bonds and interpreted as aromatic during a search. The differences between five-membered rings and other types of aromatic rings can cause different search results for five- and six-membered rings/azulenes when you use the following bonds in queries: Single, Double, and Single/Double query bonds. For more information on the Single/Double query bond, see Section 37.3.7.

37.3 Specifying Query Features on Atoms and Bonds in Structures

A query feature on an atom and/or a bond in a molecule is a restriction that specifies the retrieval of certain types of molecule records from an ISIS/Base database.

If you do not use query features, the molecules retrieved contain solely your exact substructure query embedded wholly within them. For example:

37.3.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

37.3.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of hydrogens. For example:

37.3.3 Allowing an Unsaturated Atom

Use an atom query feature to specify that an atom is attached to at least one multiple bond (double, triple, or aromatic).

Atom Query Feature: Unsaturated Atom (u)

Specifies that the atom of your choice is attached to at least one multiple bond (double, triple, or aromatic). For example, the following query specifies both an unsaturated atom (u) and single or double bonds (the double dashed lines).

37.3.4 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

Atom Query Feature: Substitution Count of Zero, s0

Specifies that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of a single atom with attached hydrogens (if any).

Atom Query Feature: Substitution Count of One, s1

Specifies that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Two, s2

Specifies that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Three, s3

Specifies that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Four, s4

Specifies that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Five, s5

Specifies that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of at Least Six, s6

Specifies that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count as Drawn, s*

Specifies that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:

37.3.5 Allowing a Specific Number of Ring Bond Attachments

Use atom query features to specify the number of ring bond attachments.

Atom Query Feature: Ring Bond Count of Zero, r0

Specifies that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:

Atom Query Feature: Ring Bond Count of Two, r2

Specifies that the records retrieved have solely two ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of Three, r3

Specifies that the records retrieved have solely three ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of at Least Four, r4

Specifies that the records retrieved have at least four ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count as Drawn, r*

Specifies that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:

37.3.6 Allowing Additional Atoms and/or Bonds in a Chain or a Ring

Use a query feature that is for either atoms or bonds to specify the addition of atoms and/or bonds in a chain or a ring.

Atom or Bond Query Feature: Link Node

Use a link node to specify the addition of variable numbers repeating units (atoms and/or bonds) to a ring or chain. A repeating unit must be attached to two adjacent bonds. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the link node [L1-3]:

Or, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the link node [L1-3]:

37.3.7 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Note: An aromatic query bond hits any bond in all types of aromatic rings: 6-membered ring bonds, 5-membered ring bonds, and azulene perimeter bonds. For more information on the structures that ISIS interprets as aromatic, see Section 37.2.

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

Note: A Single/Double query bond does not hit bonds in 6-membered aromatic rings, or perimeter bonds of azulenes, because bonds in these structures are stored in the database as aromatic bonds. However, a Single/Double query bond does hit bonds in 5-membered rings that ISIS interprets as aromatic. For more information on the structures that ISIS interprets as aromatic, see Section 37.2.

Bond Query Feature: Single/Aromatic Bond

Specifies either a single or an aromatic bond at that position:

Bond Query Feature: Double/Aromatic Bond

Specifies either a double or an aromatic bond at that position:

37.3.8 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

37.3.9 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

37.4 Specifying Rgroup Query Features

An Rgroup query finds structures that contain your query as a root structure with defined Rgroup substituents attached to it at specific positions. Your query can contain restrictions on the Rgroup substituents, called Rgroup conditions: You can specify the number of Rgroup sites that must be occupied in the records retrieved, specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site, or specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

Your Rgroup query can also contain restrictions on atoms and bonds of the root structure and Rgroup substituents. For example, you can use the atom query feature H(0) to prohibit the attachment of implicit hydrogens on a specific atom in the structures retrieved.

An example of an Rgroup query is as follows:

37.4.1 The Root Structure

The root structure contains the portion of the structure that does not vary among the structures retrieved. For example, if you want to find 2, 5-Dihydroxypyridine in which the substituent at position 2 can be COOH, CN, or Ph, and the substituent at position 5 can be OH or CH3, the root structure is 2, 5-Dihydroxypyridine with Rgroups (such as R1 and R2):

Rgroups

On the root structure, Rgroups (R1 through R32) are placeholders that designate where the lists of functional groups and atoms that can attach to the root structure. In the example above, the Rgroup R1 designates that the members of the list R1 (the Rgroup substituents) are allowed at position 5 on the root structure. The Rgroup R2 designates that the members of the list R2 (the Rgroup substituents) are allowed at position 2 on the root structure.

Multiple Rgroups at One Position

You can specify multiple Rgroups at a single site on the root structure. For example:

One Rgroup at Multiple Positions

You can specify a single Rgroup (such as R1) at multiple positions on the root structure. For example:

Note: For information on how to restrict the number of Rgroups that must be occupied in the records retrieved, See Section 37.4.3, "Rgroup Conditions." A molecule need not satisfy all the Rgroup sites on the root structure to be retrieved. For example, the Rgroup condition R1 > 0 specifies that any molecule in which at least one of the R1 sites is filled by an R1 member will be retrieved. In addition, the Rgroup condition RestH determines whether the unsatisfied sites must be filled with hydrogen atoms or if other molecule fragments are allowed to be attached if they are not on the list.

37.4.2 Rgroup Substituents

Rgroup substituents are the members of the list of Rgroups. You define the Rgroup substituents that you will allow to be found at specified positions in the molecules retrieved. Rgroup substituents can be any structural fragment, including functional groups and single atoms.

In the example below, the Rgroup substituents COOH, CN, or Ph are allowed at position 5 (R1) on the root structure and the Rgroup substituents OH or CH3 are allowed at position 2 (R2) on the root structure:

Attachment Points

An attachment point (marked with an arrow and an asterisk) designates the atom on the Rgroup substituent that is attached to the root structure:

You must designate an attachment point on an Rgroup substituent for each bond that is attached to the substituent. If an Rgroup is attached to two bonds on the root structure, you must designate two attachment points. The bond on the root structure that is marked with double quotes corresponds to the attachment point on the Rgroup substituent that is marked with double quotes. The other attachment point on the Rgroup substituent is marked with a single quote:

Nested Rgroups

A nested Rgroup is an Rgroup that is a placeholder within another Rgroup rather than within the root structure. (You cannot nest an Rgroup any lower than this level.) In the following example, Rgroup R2 is nested within the Rgroup R1:

Nested Rgroups are equivalent to the following structures:

37.4.3 Rgroup Conditions

You can apply restrictions to each Rgroup in your query after you assemble all the Rgroups. The set of restrictions is called the Rgroup conditions.

If you do not apply Rgroup conditions, ISIS assigns the default conditions: Occurrence > 0 and RestH off for each Rgroup.

Occurrence

With the Rgroup condition Occurrence, you can specify the number of Rgroup sites that must be occupied in the records retrieved. For example, the occurrence designation R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved. Type one of the following values in the Occurrence range text box:

Value	Explanation

0	All members of the Rgroup are excluded from the Rgroup site (such as R1). To allow any other Rgroup substituent at the Rgroup site, set RestH to off.

> 0	At least one Rgroup must be satisfied. If RestH is off, any other substituent can attach to unsatisfied sites. If RestH is on, unsatisfied sites must be filled solely by hydrogens.

n	Exactly n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

< n	Less than n number of sites (including zero) must be satisfied. RestH controls substitution at unsatisfied sites.

m - n	Any number of sites falling within the range of m to n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

m,n,...	Any combination of the above expressions, separated by commas. For example: 1, 3-5, 9, >12.

For example, the Rgroup condition R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved.

In another example, the Rgroup condition R1 > 0 and R2 > 0 specifies that an Rgroup substituent from the R1 list AND an Rgroup substituent from the R2 list must occupy at least one site on the root structure in the records retrieved.

Finally, the Rgroup conditions R1 = 1, 3-5, 9, >12 specify that either 1, 3, 4, 5, 9, or more than 12 sites must be satisfied:

RestH

With the Rgroup condition RestH, you can specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site.

An unsatisfied Rgroup site is an Rgroup site on the root structure that does not have an Rgroup member attached: If RestH is off, any functional group or atom may be attached at unsatisfied Rgroup sites on the root structure. If RestH is on, solely hydrogens are allowed to be attached at unsatisfied Rgroup sites on the root structure.

If/Then

With the Rgroup condition If/then, you can specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

For example, If R1 then R2 specifies that if the conditions for R1 are satisfied, then the conditions for R2 must also be satisfied. (If the conditions for R1 are not satisfied, then the conditions for R2 are ignored.) The If/then condition implies that a molecule may be retrieved even though R1 is not satisfied.

In the following query, R1 contains a nitro group and a sulfonic acid group. R2 contains a chlorine atom. The condition If R1 then R2 specifies that if a nitro group or a sulfonic acid group is attached at R1 on the root structure, then a chlorine must also be attached at R2. However, if the R1 site on the root structure does not have either the nitro or the sulfonic acid group (R1 is unsatisfied), then R2 can have any substituent (R2 is ignored):

37.5 Specifying Stereochemistry

For remote databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

An SBF search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve molecules with matching cis or trans stereochemistry. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An SBF search produces the following results:

Chiral Flags on Molecules

In a remote database, you can create a query with a chiral flag on a molecule with at least one asymmetric center or on a molecule that is asymmetric to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

37.6 Guidelines for Revising the Query

If your SBF search retrieved no records or too few records, you might want to:

*	Conduct an SBF search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the structural constraints in your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, remove substituent limits, or remove stereochemical requirements.

*	Make the text/numeric strings in your query more general, and then search the same set of records. For example, you can apply operators that partially restrict, such as > or between instead of =, or you can apply wildcards. (A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters.)

If your SBF search retrieved too many records, you might want to:

*	Refine the structural constraints in your query, and then search the same set of records. For example, you can limit substitution at specific positions, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Make the text/numeric strings in your query more restrictive, and then search the same set of records. For example, you can use the operator = instead of >.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	First conduct a formula search to screen out large and complex molecules that are stored in your database, and then conduct a search on the less complex molecules. If your query is not able to map a stored molecule within a specific length of time, the molecule is added to the search results.

*	Filter your search results so that you view solely the lower-level records. (This assumes that you are viewing both upper- and lower-level records.)

37.7 Searching Example 1: Combining Text/Numeric Queries

This searching example shows you how to conduct a single SBF search with a query that contains two text/numeric strings.

37.7.1 Problem

You want to retrieve all molecules that meet both of the following requirements:

*	Have a molecular weight greater than 250

*	Contain two or three oxygen atoms

37.7.2 Approach

Enter the numeric string query > 250 into the Molecular Weight box or table cell on the form in ISIS/Base that connects to the database field MOLECULAR.WEIGHT. This string contains the search operator > and the target value 250.

Enter the text/numeric string query LIKE "O(2-3)" into the Formula box or table cell on the form that connects to the database field MOL>MOLFORMULA. This string contains the search operator LIKE and the target value o(2-3) in double quotation marks, where o is either in upper- or lower-case characters.

Note: If you enter both queries into different rows in a single table, you retrieve those molecules that meet either requirement (but not necessarily both).

Conduct an SBF search in the remote molecule database of your choice, such as the ISISMX demo database.

37.7.3 Query

Note: Your form in ISIS/Base might be entirely different from the one in this example.

37.7.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SBF, how to/examples.

37.7.5 Results

You retrieve records with molecules that have a molecular weight greater than 250 and records with molecules that contain two or three oxygens.

37.8 Searching Example 2: Combining Text/Numeric and Graphical Queries

This searching example shows you how to conduct a single SBF search with a query that contains a text/numeric string and a graphical query.

37.8.1 Problem

You want to retrieve all molecules that meet both of the following requirements:

*	Contain a steroid substructure embedded wholly within them

*	Have a melting point that is greater than 220 degrees Centigrade

37.8.2 Approach

Enter the numeric string query > 220 into the Temperature box or table cell on the form in ISIS/Base that connects to the database field TEMPERATURE (or to an equivalent field with another name). This string contains the search operator > and the target value 220.

Draw the following steroid as your graphical query:

Enter the steroid query into the Structure box or table cell on the form that connects to the database field MOLSTRUCTURE.

Conduct an SBF search in the remote molecule database of your choice, such as the ISISMX demo database.

37.8.3 Query

Note: Your form in ISIS/Base might be entirely different from the one in this example.

37.8.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SBF, how to/examples.

37.8.5 Results

You retrieve records with molecules that have a melting point greater than 220 and all records that contain the steroid substructure in your query.


Local SBF in a Molecule Database: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Local SBF Search in a Molecule Database	38.1

*	Definition of Aromaticity	38.2

*	Specifying Query Features on Atoms and Bonds in Structures	38.3

*	Specifying Stereochemistry	38.4

*	Guidelines for Revising the Query	38.5

*	Searching Example 1: Combining Text/Numeric Queries	38.6

*	Searching Example 2: Combining Text/Numeric and Graphical Queries	38.7

We recommend that you print this 15-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a local SBF search in a molecule database, click here.

38.1 Definition of a Local SBF Search in a Molecule Database

A local Search By Form (SBF) search in a molecule database search finds molecule records in your local database that contain your text/numeric query exactly as you specify it or your graphical query as a substructure wholly within a larger structure.

Note: If your database contains the exact match of your substructure query, you also retrieve the exact match.

In addition, you can combine text/numeric and graphical queries. For example, you want to find all molecules that contain a specific steroid substructure wholly within them and that have a melting point that is greater than 220 degrees Centigrade and that contain a compound name that ends in "one" (You can enter as many as 25 queries into different cells of the same table.):

Your text/numeric query can also contain wildcards. A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: (The wildcard % is a placeholder for at least one unspecified character.) To find the exact match of the data of interest, enter the search operator LIKE and place your target text in double quotes. A search operator is the command that specifies the type of search.

Your graphical query can also contain restrictions (called query features) on atoms and bonds. For example, you can use the ISIS bond-query feature Ch to specify that a bond is part of an acyclic structure in the records retrieved. You can also add hydrogens with visible bonds (called explicit hydrogens) to your query to block substituents on specific atoms.

A local search is a search over a database that typically exists on your hard disk. To do a local search on your hard disk, you do not need to input network information.

Note: To do a local search that is accessed from a shared network, you need to input network information.

38.1.1 Specifying a Text/Numeric String as a Query

A text/numeric string as an SBF query is a phrase in a box or column on the form that specifies the retrieval of data. For example, to find structures with a molecular weight greater than 350, enter the text/numeric string > 350 into the Molecular Weight box on the form.

Each phrase in a text/numeric string contains:

*	A search operator that specifies the type of search. For example, the search operators = (equal sign) and LIKE specify the retrieval of the exact match of your query. Use = when you want to retrieve data with numeric values. Use LIKE when you want to retrieve data with text. For details on search operators, see Section 38.1.2.

*	A text or numeric target value that you want to find (such as 350 for the molecular weight or ANTIBIOTIC for the activity).

Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

Specifying Numeric String Queries

Do not include the units, such as a percent sign (%) or the degrees Centigrade (C). For example, to retrieve all compounds with a molecular weight greater than 350, enter:

> 350

where the search operator is > and the target value is 350.

Specifying Text/Numeric String Queries

Enclose queries that contain text (with or without numeric values) in double quotes and always use a wildcard, such as %. For example, to retrieve all compounds from the author Smythe, enter:

LIKE "%Smythe%"

where the search operator is LIKE and the target value is Smythe.

A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. The wildcard _ is a placeholder for solely one unspecified character. Without a wildcard, you retrieve solely those records that contain exactly the target value that you specified. For example:

Query Without a Wildcard	Example of a Record Retrieved

LIKE "antibiotic"	Antibiotic
ANTIBIOTIC

Query With the Wildcard %	Examples of Records Retrieved

LIKE "%antibiotic%"	Antibiotic
ANTIBIOTIC

Antibiotic activity

Resistance to extracellular products such as antibiotics

Note: If you want to retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

38.1.2 The Search Operators

<, <=, >, >=, and <>

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Search Operator	Definition	Examples

=	equal (numeric)	= 350

<	less than (numeric)	< 350

<=	less than or equal to (numeric)	= 350

>	greater than (numeric)	> 350

>=	greater than or equal to (numeric)	>= 350

<>	not equal to (text or numeric)	<> 350

<> "initiator"

LIKE

Use LIKE with text enclosed in double quotation marks. Enter your query as follows:

Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. For example:

Query	Examples of Records Retrieved

LIKE "methane"	Methane

LIKE "benzoic acid"	Benzoic Acid

LIKE "%acid"	Benzoic Acid

Acetic Acid

LIKE "%acid%"	Benzoic Acid Sodium Salt

Acetic Acid Sodium Salt

LIKE "%but_ne"	Trans 2-Butene

2-Butene

N-Butane

Butane

Butene

LIKE "_ethyl"	Methyl

Ethyl

LIKE "antibiotic"	Antibiotic

LIKE "%antibiotic%"	Antibiotic activity

Resistance to extracellular products such as antibiotics

Note: To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice. To retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

BETWEEN

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks. For example:

BETWEEN "XR11" "XZ15"

BETWEEN 95 100

EXISTS

Use EXISTS to retrieve all records in the database that contain data in a specific database field. For example:

EXISTS

Note: You can only use the EXISTS search operator for database fields that do not give you an error message.

38.1.3 Specifying a Molecular Formula as a Query

To search the data in Formula box (that is, a box that is connected to a MOLFORMULA field), you can specify the following text/numeric queries:

*	An exact formula. Use an exact formula query to find records that contain solely the exact atoms that you specify.

*	A subformula. Use a subformula query to find records that contain the specific atoms that you specify, and any additional atoms.

Exact Formula Query

To specify an exact formula query, specify the target value for the formula. The target value must include all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required. The equals operator (=) and quotes are optional. For example:

Exact Formula Query	Examples of Records Retrieved

c6 h6 O	Phenol

c6h6o

C20 H12 Na2 O4	Sodium salt of phenolphthalein

C20H12Na2O4

= C20 H12 Na2 O4

= C20H12Na2O4

= "C20 H12 Na2 O4"

= "C20H12Na2O4"

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Exact Formula Query	Examples of Records Retrieved

C17 H19 N 03	Piperine

C17H19N 03	Piperine

C17H19N103	Piperine

C17H19N03	No molecules retrieved. ISIS interprets "NO3" as 3 Nobelium atoms.

Subformula Query

To specify a subformula query, use the LIKE operator with a target value for the subformula. The target value can include a range of atom counts, and typically excludes the hydrogens. To exclude specific atoms from the molecules that you retrieve, specify zero for that atom. You can use a single space to separate atoms. Capital letters are not required. Quotes are optional.

Subformula Query	Examples of Records Retrieved

LIKE Na	All sodium salts

LIKE c12 Br(1-2) S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE "C12Br(1-2)S2"	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE c6 h6	All molecules that contain six carbon atoms, six hydrogen atoms, and any number of other atoms

LIKE C5 H10 N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

LIKE C5H10N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Subformula Query	Examples of Records Retrieved

LIKE C12 Br S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12Br1S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12BrS2	No molecules retrieved. ISIS interprets "BrS" as an atom symbol, and gives an error message.

38.1.4 Specifying a Graphical Substructure as a Query

A graphical substructure query retrieves records that contain your graphical query embedded wholly within them. For example:

You can also increase the power of an SBF search by the addition of specific restrictions (called query features) on atoms and/or bonds. There are a number of query features available for use.

In the following example, the ISIS atom-query feature (H0) prohibits the attachment of hydrogens on a specific atom in the records retrieved:

In addition, the hydrogens block substitutions at the specified positions.

To use a graphical query, you must have a Structure box or table cell on the form that connects to the database field MOLSTRUCTURE.

Notes: (1) You can enter multiple graphical queries onto the form in ISIS/Base. (2) You do not use a search operator with a graphical query.

38.1.5 Specifying Multiple Queries in a Single SBF Search

When you combine two or more queries of any type into a single SBF search, the search results that you obtain depend on both the specifications and accuracy of your query and the way that information is stored in your database. For more information on how to create an adequate query, see Section 38.1.1 through Section 38.1.4.

Information in a database is stored either in a single level (called a flat database) or in multiple levels (called a hierarchical database). Storage in a hierarchical database is more efficient, but it requires you to enter your queries in the correct location on the form to obtain the search results that you want.

For example, the following hierarchical database stores data for multiple decomposition tests that are conducted under different atmospheric conditions:

(In this database, structures are stored at the top (or root) level, and the percentage of oxygen and the number of peaks are stored at a lower level, under the parent field Decomposition. A parent field is a branch in the hierarchy that contains a set of child fields, such as percent O2 and number of peaks.)

You want specific decomposition data from different tests. Your multiple query in a single SBF search specifies that you want all compounds within a single test that contain: Query 1, greater than 65% O2; Query 2, less than three peaks.

To obtain search results that match all queries (Query 1 AND Query 2), you can either (a) enter each search query into separate boxes or (b) enter each search query into the same row in a single table. This search gives you all compounds within a single test that meet both requirements in your query:

Caution: For all versions of ISIS before 2.0, multiple queries in boxes might give different results than multiple queries in tables. In the previous example, the SBF query in the box on the form at the left retrieves records in which at least one decomposition test that matches both conditions. The SBF query in the table on the form at the right, however, retrieves additional records in which one decomposition test matches one condition, and another decomposition test matches the other condition. In ISIS 2.0, both queries retrieve only those records in which both conditions are met within the same decomposition test.

To obtain search results that match either one query or the other (Query 1 OR Query 2), you must enter each search query into different rows of a single table. You must be certain that the first column in the table is a field at the same database level that you want to search. This search gives you all compounds within a single test that meet either requirement in your query (but not necessarily both requirements):

When you filter your search results, you see solely those lower-level records that meet your search requirements.

Note: A box retrieves data from a single database field. A table retrieves data from multiple database fields. Also, you can enter as many as 25 queries into the same table.

38.2 Definition of Aromaticity

For local databases: A bond is aromatic if it is in a six-membered ring with alternating double and single bonds, such as benzene.

Note: Aromaticity is not perceived for fused rings in which the double bonds are arranged in a way that cannot be defined as aromatic.

38.3 Specifying Query Features on Atoms and Bonds in Structures

A query feature on an atom and/or a bond in a molecule is a restriction that specifies the retrieval of certain types of molecule records from an ISIS/Base database.

If you do not use query features, the molecules retrieved contain solely your exact substructure query embedded wholly within them. For example:

38.3.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

38.3.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of hydrogens. For example:

38.3.3 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

38.3.4 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

38.3.5 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

38.3.6 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

38.4 Specifying Stereochemistry

For local databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

An SBF search produces the following results:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve molecules with matching cis or trans stereochemistry. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An SBF search produces the following results:

38.5 Guidelines for Revising the Query

If your SBF search retrieved no records or too few records, you might want to:

*	Conduct an SBF search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the structural constraints in your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, or remove stereochemical requirements.

*	Make the text/numeric strings in your query more general, and then search the same set of records. For example, you can apply operators that partially restrict, such as > or between instead of =, or you can apply wildcards. (A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters.)

If your SBF search retrieved too many records, you might want to:

*	Refine the structural constraints in your query, and then search the same set of records. For example, you can limit substitution at specific positions with explicit hydrogens, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Make the text/numeric strings in your query more restrictive, and then search the same set of records. For example, you can use the operator = instead of >.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	First conduct a formula search to screen out large and complex molecules that are stored in your database, and then conduct a search on the less complex molecules. If your query is not able to map a stored molecule within a specific length of time, the molecule is added to the search results.

*	Filter your search results so that you view solely the lower-level records. (This assumes that you are viewing both upper- and lower-level records.)

38.6 Searching Example 1: Combining Text/Numeric Queries

This searching example shows you how to conduct a single SBF search with a query that contains two text/numeric strings.

38.6.1 Problem

You want to retrieve all molecules that meet both of the following requirements:

*	Have a molecular weight greater than 250

*	Contain two or three oxygen atoms

38.6.2 Approach

Enter the numeric string query > 250 into the Molecular Weight box or table cell on the form in ISIS/Base that connects to the database field MOLECULAR.WEIGHT. This string contains the search operator > and the target value 250.

Enter the text/numeric string query LIKE "O(2-3)" into the Formula box or table cell on the form that connects to the database field MOL>MOLFORMULA. This string contains the search operator LIKE and the target value o(2-3) in double quotation marks, where o is either in upper- or lower-case characters.

Note: If you enter both queries into different rows in a single table, you retrieve only those molecules that meet one requirement (but not necessarily both).

Conduct an SBF search in the local molecule database of your choice, such as the LOCALMX demo database.

38.6.3 Query

Note: Your form in ISIS/Base might be entirely different from the one in this example.

38.6.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SBF, how to/examples.

38.6.5 Results

You retrieve records with molecules that have a molecular weight greater than 250 and records with molecules that contain two or three oxygens.

38.7 Searching Example 2: Combining Text/Numeric and Graphical Queries

This searching example shows you how to conduct a single SBF search with a query that contains a text/numeric string and a graphical query.

38.7.1 Problem

You want to retrieve all molecules that meet both of the following requirements:

*	Contain a steroid substructure embedded wholly within them

*	Have a melting point that is greater than 220 degrees Centigrade

38.7.2 Approach

Enter the numeric string query > 220 into the Temperature box or table cell on the form in ISIS/Base that connects to the database field TEMPERATURE (or to an equivalent field with another name). This string contains the search operator > and the target value 220.

Draw the following steroid as your graphical query:

Enter the steroid query into the Structure box or table cell on the form that connects to the database field MOLSTRUCTURE.

Conduct an SBF search in the local molecule database of your choice, such as the LOCALMX demo database.

38.7.3 Query

Note: Your form in ISIS/Base might be entirely different from the one in this example.

38.7.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SBF, how to/examples.

38.7.5 Results

You retrieve records with molecules that have a melting point greater than 220 and all records that contain the steroid substructure in your query.


Remote SBF in a Reaction Database: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote SBF Search in a Reaction Database	39.1

*	Definition of Aromaticity	39.2

*	Specifying Query Features on Atoms and Bonds in Structures	39.3

*	Specifying Rgroup Query Features	39.4

*	Specifying Stereochemistry	39.5

*	Specifying Query Features on a Reaction	39.6

*	Specifying an Atom-Atom Map on a Reaction	39.7

*	Guidelines for Revising the Query	39.8

*	Searching Example 1: Combining Text/Numeric Queries	39.9

*	Searching Example 2: Combining Text/Numeric and Graphical Queries	39.10

We recommend that you print this 31-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote SBF search in a reaction database, click here.

39.1 Definition of a Remote SBF Search in a Reaction Database

A remote Search By Form (SBF) search in a reaction database search finds reaction records in your remote database that contain your text/numeric query exactly as you specify it or your graphical query as a substructure wholly within a larger structure.

Note: If your database contains the exact match of your substructure query, you also retrieve the exact match.

In addition, you can combine text/numeric and graphical queries. For example, you want to find all transformations with a specific reaction substructure wholly within them and that have a product yield that is greater than 95 percent and that have a REGNO that begins with the letter T (You can enter as many as 25 queries into different cells of the same table.):

In this example, one of the text/numeric queries contains the search operator LIKE (to specify the retrieval of an exact match of the target text), double quotes around the target text, and a wildcard. A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters. A search operator is the command that specifies the type of search.

Your graphical query can also contain restrictions (called query features) on the atoms, bonds, and on the reaction. In this example, the ISIS reaction-query feature CHANGE (/) specifies that the bond order in the reactant must change in the product at the specified position.

The atom-atom maps (numbers on the atoms) specify which atoms in the reactants correspond to the atoms in the products.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

39.1.1 Specifying a Text/Numeric String as a Query

A text/numeric string as an SBF query is a phrase in a box or column on the form that specifies the retrieval of data. For example, to find structures with a molecular weight greater than 350, enter the text/numeric string > 350 into the Molecular Weight box on the form.

Each phrase in a text/numeric string contains:

*	A search operator that specifies the type of search. For example, the search operators = (equal sign) and LIKE specify the retrieval of the exact match of your query. Use = when you want to retrieve data with numeric values. Use LIKE when you want to retrieve data with text. For details on search operators, see Section 38.1.2.

*	A text or numeric target value that you want to find (such as 350 for the molecular weight or ANTIBIOTIC for the activity).

Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

Specifying Numeric String Queries

Do not include the units, such as a percent sign (%) or the degrees Centigrade (C). For example, to retrieve all compounds with a molecular weight greater than 350, enter:

> 350

where the search operator is > and the target value is 350.

Specifying Text/Numeric String Queries

Always use a wildcard, such as %, in queries that contain text (with or without numeric values). Double quotes around the text string are optional. For example, to retrieve all compounds from the author Smythe, enter one of the following:

LIKE %Smythe%
LIKE "%Smythe%"

where the search operator is LIKE and the target value is Smythe.

A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. The wildcard _ is a placeholder for solely one unspecified character. Without a wildcard, you retrieve solely those records that contain exactly the target value that you specified. For example:

Query Without a Wildcard	Example of a Record Retrieved

LIKE "antibiotic"	Antibiotic
ANTIBIOTIC

Query With the Wildcard %	Examples of Records Retrieved

LIKE "%antibiotic%"	Antibiotic
ANTIBIOTIC

Antibiotic activity

Resistance to extracellular products such as antibiotics

Note: If you want to retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

39.1.2 The Search Operators

<, <=, >, >=, and <>

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Search Operator	Definition	Examples

=	equal (numeric)	= 350

<	less than (numeric)	< 350

<=	less than or equal to (numeric)	= 350

>	greater than (numeric)	> 350

>=	greater than or equal to (numeric)	>= 350

<>	not equal to (text or numeric)	<> 350

<> "initiator"

LIKE

Use LIKE with text enclosed in double quotation marks. Enter your query as follows:

Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. For example:

Query	Examples of Records Retrieved

LIKE "methane"	Methane

LIKE "benzoic acid"	Benzoic Acid

LIKE "%acid"	Benzoic Acid

Acetic Acid

LIKE "%acid%"	Benzoic Acid Sodium Salt

Acetic Acid Sodium Salt

LIKE "%but_ne"	Trans 2-Butene

2-Butene

N-Butane

Butane

Butene

LIKE "_ethyl"	Methyl

Ethyl

LIKE "antibiotic"	Antibiotic

LIKE "%antibiotic%"	Antibiotic activity

Resistance to extracellular products such as antibiotics

Note: To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice. To retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

BETWEEN

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks. For example:

BETWEEN "XR11" "XZ15"

BETWEEN 95 100

EXISTS

Use EXISTS to retrieve all records in the database that contain data in a specific database field. For example:

EXISTS

Note: You can only use the EXISTS search operator for database fields that do not give you an error message.

39.1.3 Specifying a Molecular Formula as a Query

To search the data in Formula box (that is, a box that is connected to a MOLFORMULA field), you can specify the following text/numeric queries:

*	An exact formula. Use an exact formula query to find records that contain solely the exact atoms that you specify.

*	A subformula. Use a subformula query to find records that contain the specific atoms that you specify, and any additional atoms.

Exact Formula Query

To specify an exact formula query, specify the target value for the formula. The target value must include all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required. The equals operator (=) and quotes are optional. For example:

Exact Formula Query	Examples of Records Retrieved

c6 h6 O	Phenol

c6h6o

C20 H12 Na2 O4	Sodium salt of phenolphthalein

C20H12Na2O4

= C20 H12 Na2 O4

= C20H12Na2O4

= "C20 H12 Na2 O4"

= "C20H12Na2O4"

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Exact Formula Query	Examples of Records Retrieved

C17 H19 N 03	Piperine

C17H19N 03	Piperine

C17H19N103	Piperine

C17H19N03	No molecules retrieved. ISIS interprets "NO3" as 3 Nobelium atoms.

Subformula Query

To specify a subformula query, use the LIKE operator with a target value for the subformula. The target value can include a range of atom counts, and typically excludes the hydrogens. To exclude specific atoms from the molecules that you retrieve, specify zero for that atom. You can use a single space to separate atoms. Capital letters are not required. Quotes are optional.

Subformula Query	Examples of Records Retrieved

LIKE Na	All sodium salts

LIKE c12 Br(1-2) S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE "C12Br(1-2)S2"	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE c6 h6	All molecules that contain six carbon atoms, six hydrogen atoms, and any number of other atoms

LIKE C5 H10 N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

LIKE C5H10N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Subformula Query	Examples of Records Retrieved

LIKE C12 Br S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12Br1S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12BrS2	No molecules retrieved. ISIS interprets "BrS" as an atom symbol, and gives an error message.

39.1.4 Specifying a Graphical Substructure as a Query

A graphical substructure query retrieves records that contain your graphical query embedded wholly within them. For example:

You can also increase the power of an SBF search by the addition of specific restrictions (called query features) on atoms and/or bonds. There are a number of query features available for use.

In the following example, the ISIS atom-query feature (H0) prohibits the attachment of hydrogens on a specific atom in the records retrieved:

In addition, the hydrogens block substitutions at the specified positions.

To use a graphical query, you must have a structure box on the form in ISIS/Base that will hold your query:

*	A Reaction Structure box holds any structure with a reaction arrow. For example, enter a transformation into the Reaction Structure box on the form, or enter a product (or a reactant) with a reaction arrow into the Reaction Structure box on the form.

*	All other structure boxes hold a specific type of structure without a reaction arrow. For example, enter a product without a reaction arrow into the Product Structure box on the form, or enter a reactant without a reaction arrow into the Reactant Structure box on the form.

Notes: (1) You can enter multiple graphical queries onto the form in ISIS/Base. (2) You do not use a search operator with a graphical query.

39.1.5 Specifying Multiple Queries in a Single SBF Search

When you combine two or more queries of any type into a single SBF search, the search results that you obtain depend on both the specifications and accuracy of your query and the way that information is stored in your database. For more information on how to create an adequate query, see Section 39.1.1 through Section 39.1.4.

How Information Can Be Stored

Information in a database is stored either in a single level (called a flat database) or in multiple levels (called a hierarchical database). Storage in a hierarchical database is more efficient, but it requires you to enter your queries in the correct location on the form to obtain the search results that you want.

A typical hierarchical database is as follows:

The top (or root) level in the hierarchy stores the reaction structure and ID number for each reaction record, and the lower level in the hierarchy stores the literature references and variations for each reaction structure. LITREF is the parent field for the database fields journal and author, and VARIATION is the parent field for the database fields variation number (varno), solvent, and yield. Each reaction record might have multiple literature references and multiple variation subrecords associated with it.

Obtaining the Correct Search Results From a Hierarchical Database

If you search a hierarchical database for lower level records with multiple queries in a single SBF search, where you enter your queries on the form is significant.

For example, the following hierarchical database stores data for multiple decomposition tests that are conducted under different atmospheric conditions:

(In this database, structures are stored at the top (or root) level, and the percentage of oxygen and the number of peaks are stored at a lower level, under the parent field Decomposition. A parent field is a branch in the hierarchy that contains a set of child fields, such as percent O2 and number of peaks.)

You want specific decomposition data from different tests. Your multiple query in a single SBF search specifies that you want all compounds within a single test that contain: Query 1, greater than 65% O2; Query 2, less than three peaks.

To obtain search results that match all queries (Query 1 AND Query 2), you can either (a) enter each search query into separate boxes or (b) enter each search query into the same row in a single table. This search gives you all compounds within a single test that meet both requirements in your query:

Caution: For all versions of ISIS before 2.0, multiple queries in boxes might give different results than multiple queries in tables. In the previous example, the SBF query in the box on the form at the left retrieves records in which at least one decomposition test that matches both conditions. The SBF query in the table on the form at the right, however, retrieves additional records in which one decomposition test matches one condition, and another decomposition test matches the other condition. In ISIS 2.0, both queries retrieve only those records in which both conditions are met within the same decomposition test.

To obtain search results that match either one query or the other (Query 1 OR Query 2), you must enter each search query into different rows of a single table. You must be certain that the first column in the table is a field at the same database level that you want to search. This search gives you all compounds within a single test that meet either requirement in your query (but not necessarily both requirements):

When you filter your search results, you see solely those lower-level records that meet your search requirements.

Note: A box retrieves data from a single database field. A table retrieves data from multiple database fields. Also, you can enter as many as 25 queries into the same table.

39.2 Definition of Aromaticity

For remote databases: ISIS interprets the following ring systems as aromatic:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:

Note: The bonds of six-membered aromatic ring systems and the perimeter bonds of azulenes are stored as aromatic bonds in the database. The bonds of five-membered aromatic rings, however, are stored as single and double bonds and interpreted as aromatic during a search. The differences between five-membered rings and other types of aromatic rings can cause different search results for five- and six-membered rings/azulenes when you use the following bonds in queries: Single, Double, and Single/Double query bonds. For more information on the Single/Double query bond, see Section 39.3.7.

39.3 Specifying Query Features on Atoms and Bonds in Structures

A query feature on an atom and/or a bond in a reaction component is a restriction that specifies the retrieval of certain types of reaction records from an ISIS/Base database.

If you do not use query features, the records retrieved contain solely your exact substructure query embedded wholly within them. For example:

39.3.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

39.3.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of hydrogens. For example:

39.3.3 Allowing an Unsaturated Atom

Use an atom query feature to specify that an atom is attached to at least one multiple bond (double, triple, or aromatic).

Atom Query Feature: Unsaturated Atom (u)

Specifies that the atom of your choice is attached to at least one multiple bond (double, triple, or aromatic). For example, the following query specifies both an unsaturated atom (u) and single or double bonds (the double dashed lines).

39.3.4 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

Atom Query Feature: Substitution Count of Zero, s0

Specifies that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of a single atom with attached hydrogens (if any).

Atom Query Feature: Substitution Count of One, s1

Specifies that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Two, s2

Specifies that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Three, s3

Specifies that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Four, s4

Specifies that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Five, s5

Specifies that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of at Least Six, s6

Specifies that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count as Drawn, s*

Specifies that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:

39.3.5 Allowing a Specific Number of Ring Bond Attachments

Use atom query features to specify the number of ring bond attachments.

Atom Query Feature: Ring Bond Count of Zero, r0

Specifies that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:

Atom Query Feature: Ring Bond Count of Two, r2

Specifies that the records retrieved have solely two ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of Three, r3

Specifies that the records retrieved have solely three ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of at Least Four, r4

Specifies that the records retrieved have at least four ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count as Drawn, r*

Specifies that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:

39.3.6 Allowing Additional Atoms and/or Bonds in a Chain or a Ring

Use a query feature that is for either atoms or bonds to specify the addition of atoms and/or bonds in a chain or a ring.

Atom or Bond Query Feature: Link Node

Use a link node to specify the addition of variable numbers repeating units (atoms and/or bonds) to a ring or chain. A repeating unit must be attached to two adjacent bonds. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the link node [L1-3]:

Or, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the link node [L1-3]:

39.3.7 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Note: An aromatic query bond hits any bond in all types of aromatic rings: 6-membered ring bonds, 5-membered ring bonds, and azulene perimeter bonds. For more information on the structures that ISIS interprets as aromatic, see Section 39.2.

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

Note: A Single/Double query bond does not hit bonds in 6-membered aromatic rings, or perimeter bonds of azulenes, because bonds in these structures are stored in the database as aromatic bonds. However, a Single/Double query bond does hit bonds in 5-membered rings that ISIS interprets as aromatic. For more information on the structures that ISIS interprets as aromatic, see Section 39.2.

Bond Query Feature: Single/Aromatic Bond

Specifies either a single or an aromatic bond at that position:

Bond Query Feature: Double/Aromatic Bond

Specifies either a double or an aromatic bond at that position:

39.3.8 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

39.3.9 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

39.4 Specifying Rgroup Query Features

An Rgroup query finds structures that contain your query as a root structure with defined Rgroup substituents attached to it at specific positions. Your query can contain restrictions on the Rgroup substituents, called Rgroup conditions: You can specify the number of Rgroup sites that must be occupied in the records retrieved, specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site, or specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

Your Rgroup query can also contain restrictions on atoms and bonds of the root structure and Rgroup substituents. For example, you can use the atom query feature H(0) to prohibit the attachment of implicit hydrogens on a specific atom in the structures retrieved.

An example of an Rgroup query is as follows:

39.4.1 The Root Structure

The root structure contains the portion of the structure that does not vary among the structures retrieved. For example, if you want to find 2, 5-Dihydroxypyridine in which the substituent at position 2 can be COOH, CN, or Ph, and the substituent at position 5 can be OH or CH3, the root structure is 2, 5-Dihydroxypyridine with Rgroups (such as R1 and R2):

Rgroups

On the root structure, Rgroups (R1 through R32) are placeholders that designate where the lists of functional groups and atoms that can attach to the root structure. In the example above, the Rgroup R1 designates that the members of the list R1 (the Rgroup substituents) are allowed at position 5 on the root structure. The Rgroup R2 designates that the members of the list R2 (the Rgroup substituents) are allowed at position 2 on the root structure.

Multiple Rgroups at One Position

You can specify multiple Rgroups at a single site on the root structure. For example:

One Rgroup at Multiple Positions

You can specify a single Rgroup (such as R1) at multiple positions on the root structure. For example:

Note: For information on how to restrict the number of Rgroups that must be occupied in the records retrieved, See Section 39.4.3, "Rgroup Conditions." A molecule need not satisfy all the Rgroup sites on the root structure to be retrieved. For example, the Rgroup condition R1 > 0 specifies that any molecule in which at least one of the R1 sites is filled by an R1 member will be retrieved. In addition, the Rgroup condition RestH determines whether the unsatisfied sites must be filled with hydrogen atoms or if other molecule fragments are allowed to be attached if they are not on the list.

39.4.2 Rgroup Substituents

Rgroup substituents are the members of the list of Rgroups. You define the Rgroup substituents that you will allow to be found at specified positions in the molecules retrieved. Rgroup substituents can be any structural fragment, including functional groups and single atoms.

In the example below, the Rgroup substituents COOH, CN, or Ph are allowed at position 5 (R1) on the root structure and the Rgroup substituents OH or CH3 are allowed at position 2 (R2) on the root structure:

Attachment Points

An attachment point (marked with an arrow and an asterisk) designates the atom on the Rgroup substituent that is attached to the root structure:

You must designate an attachment point on an Rgroup substituent for each bond that is attached to the substituent. If an Rgroup is attached to two bonds on the root structure, you must designate two attachment points. The bond on the root structure that is marked with double quotes corresponds to the attachment point on the Rgroup substituent that is marked with double quotes. The other attachment point on the Rgroup substituent is marked with a single quote:

Nested Rgroups

A nested Rgroup is an Rgroup that is a placeholder within another Rgroup rather than within the root structure. (You cannot nest an Rgroup any lower than this level.) In the following example, Rgroup R2 is nested within the Rgroup R1:

Nested Rgroups are equivalent to the following structures:

39.4.3 Rgroup Conditions

You can apply restrictions to each Rgroup in your query after you assemble all the Rgroups. The set of restrictions is called the Rgroup conditions.

If you do not apply Rgroup conditions, ISIS assigns the default conditions: Occurrence > 0 and RestH off for each Rgroup.

Occurrence

With the Rgroup condition Occurrence, you can specify the number of Rgroup sites that must be occupied in the records retrieved. For example, the occurrence designation R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved. Type one of the following values in the Occurrence range text box:

Value	Explanation

0	All members of the Rgroup are excluded from the Rgroup site (such as R1). To allow any other Rgroup substituent at the Rgroup site, set RestH to off.

> 0	At least one Rgroup must be satisfied. If RestH is off, any other substituent can attach to unsatisfied sites. If RestH is on, unsatisfied sites must be filled solely by hydrogens.

n	Exactly n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

< n	Less than n number of sites (including zero) must be satisfied. RestH controls substitution at unsatisfied sites.

m - n	Any number of sites falling within the range of m to n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

m,n,...	Any combination of the above expressions, separated by commas. For example: 1, 3-5, 9, >12.

For example, the Rgroup condition R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved.

In another example, the Rgroup condition R1 > 0 and R2 > 0 specifies that an Rgroup substituent from the R1 list AND an Rgroup substituent from the R2 list must occupy at least one site on the root structure in the records retrieved.

Finally, the Rgroup conditions R1 = 1, 3-5, 9, >12 specify that either 1, 3, 4, 5, 9, or more than 12 sites must be satisfied:

RestH

With the Rgroup condition RestH, you can specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site.

An unsatisfied Rgroup site is an Rgroup site on the root structure that does not have an Rgroup member attached: If RestH is off, any functional group or atom may be attached at unsatisfied Rgroup sites on the root structure. If RestH is on, solely hydrogens are allowed to be attached at unsatisfied Rgroup sites on the root structure.

If/Then

With the Rgroup condition If/then, you can specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

For example, If R1 then R2 specifies that if the conditions for R1 are satisfied, then the conditions for R2 must also be satisfied. (If the conditions for R1 are not satisfied, then the conditions for R2 are ignored.) The If/then condition implies that a molecule may be retrieved even though R1 is not satisfied.

In the following query, R1 contains a nitro group and a sulfonic acid group. R2 contains a chlorine atom. The condition If R1 then R2 specifies that if a nitro group or a sulfonic acid group is attached at R1 on the root structure, then a chlorine must also be attached at R2. However, if the R1 site on the root structure does not have either the nitro or the sulfonic acid group (R1 is unsatisfied), then R2 can have any substituent (R2 is ignored):

39.5 Specifying Stereochemistry

For remote databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve reactions with matching stereochemistry on the reaction components. For example:

An SBF search produces the following results for each reaction component:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve reactions with matching cis or trans stereochemistry on the reaction components. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An SBF search produces the following results for each reaction component:

Chiral Flags on Reaction Components

In a remote database, you can create a query with a chiral flag on a reaction component with at least one asymmetric center or on a reaction component that is asymmetric to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

39.6 Specifying Query Features on a Reaction

A query feature on a reaction is a restriction on reacting-center bonds that specifies the retrieval of certain types of reaction records from an ISIS/Base database.

You can restrict a reacting center bond to form, break, change its bond type, or change in an unspecified way or you can restrict a stereo bond to invert or retain its stereochemistry.

You can restrict an atom in a reaction to change exactly to your specifications.

39.6.1 Specifying Query Features on a Reacting Center

Use query features to specify whether a bond in a reacting center changes at all, changes in an unspecified way, or whether the bond specifically forms, breaks, or changes its bond type.

If you do not use a query feature on a reacting center, the transformations retrieved contain solely your exact substructure query embedded wholly within them, without regard to the chemistry that is involved in the reacting center.

For example, you want to retrieve solely indoles. Without a query feature on a reacting center, you might retrieve additional, unwanted transformations:

Reacting Center Query Feature: Not Center (X)

Specifies that a bond must not change in the records retrieved. For example, to specify the reduction of a carbonyl to an alcohol, the adjacent double bonds must not change as a result of the transformation:

Reacting Center Query Feature: Center (#)

Specifies that a bond changes in an unspecified way (can form, break, or change its bond type) in the records retrieved. For example, to specify the reduction of a nitrile to a primary amine:

Reacting Center Query Feature: Change (/)

Specifies that a bond changes solely its bond type in the records retrieved. For example, to change the bond type of all bonds in a cyclohexane reactant:

Reacting Center Query Feature: Make/Break (//)

Specifies that a bond is either formed or broken in the records retrieved. For example, to specify the formation of indoles (without also retrieving additional, unwanted results that are not indoles):

Reacting Center Query Feature: Make & Change (///)

Specifies that a bond is either formed or broken and that it changes its bond type in the records retrieved.

39.6.2 Specifying Query Features on a Stereo Bond

A stereo bond is an Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of any of the following atoms: C, N, O, P, S, or Si. Use query features on a stereo bond in the reactants and products of a transformation to specify whether the stereo bond inverts or retains its position.

If you do not use a query feature on a stereo bond, the transformations retrieved contain your exact substructure query embedded wholly within them.

Stereo Bond Query Feature: .Inv.

Specifies that the stereo bond is inverted in the records retrieved. For example:

Stereo Bond Query Feature: .Ret.

Specifies that the stereo is retained (does not invert) in the records retrieved. For example:

39.6.3 Specifying Exact Changes on an Atom in the Reaction

Atom Query Feature: .Ext.

Specifies that an atom changes exactly as you specify it in the reactants and products. (Mark at least one reactant and at least one product with this query feature.) No other changes may occur.

You must specify any changes in the number of hydrogens that are attached to this atom. For example, to show the chlorination of an ethyl group, draw a chlorine in the product that replaces an explicit hydrogen in the reactant. (Either draw the explicit hydrogen or specify a hydrogen count on the reactant at the site of chlorination.)

Note: You must apply atom-atom maps to the reaction before you use this query feature. (If you do not atom-atom map your reaction, this query feature is ignored during the search.

39.7 Specifying an Atom-Atom Map on a Reaction

An atom-atom map on the reaction components in a query specifies exactly which atoms in the reactants correspond to the atoms in the products. You can specify the atoms that must (or must not) change in the transformations that you retrieve.

For example, the following query allows you to see exactly which C-O bond is cleaved to form the product:

An atom-atom map eliminates additional, unwanted results. In this example, the atom-atom map eliminates transformations that produce an alcohol group that is not the result of the demethylation process.

39.7.1 Atom-Atom Map Automatically or Manually

To obtain the correct search results, you need to atom-atom map a reaction query. In ISIS, you can map either automatically or manually.

Automapping a Reaction Query (in ISIS/Base)

If you atom-atom map a reaction automatically, you execute the automap process in ISIS/Base. This process both maps your reaction query and adds any relevant reacting centers and any relevant stereo bond inversion and/or retention marks automatically.

Mapping a Reaction Query Manually (in ISIS/Draw)

If you atom-atom map a reaction manually (in ISIS/Draw), you can choose your own correspondence between the atoms in the reactants and the atoms in the products. However, the reacting centers (and stereo bond inversion and/or retention marks) are not added to your query automatically.

Note: After you atom-atom map a reaction query manually, if you want to add the reacting centers and/or stereo bond markings, you can either add them manually or you can automap the reaction query.

Guidelines for Mapping a Reaction Query

Use the following guidelines to help you to atom-atom map your query correctly:

Always atom-atom map a query that contains an entire reaction (at least a reactant and a product). Do not attempt to atom-atom map a query that contains solely a reaction component and a reaction arrow.

Note: We strongly recommend that you draw solely the reacting fragments (and use query features where relevant) rather than draw each reactant and product in detail.

Only map those specific atoms that you see in both the reactants and the products. For example, do not map the oxygen atom that you see only in the product:

To simplify the atom-atom mapping process, map your query automatically with the automap feature. However, there are specific times when you need to map a portion of your query manually, and then apply the automap feature to finish the task. For example, map a portion of your query manually if it is unbalanced or if it is mapped incorrectly with the automap feature.

An unbalanced reaction query is a reaction query that contains multiple mappings of a single atom. You need to manually map enough of the atoms to allow the automap feature to map your query correctly. Then select the entire query and automap it. For example:

*	Select a reactant atom and a product atom that you want to specify as Atom 1 and map them manually.

*	Select the same atom in the reactant and another atom in the product that you want to specify as Atom 1 (a multiple mapping of Atom 1) and map them manually. For example, you see the following:

*	Select the entire query and automap it.

Inspect the atom-atom maps on a reaction query before you use the query to conduct a search. If you notice that a map is incorrect, delete it entirely. You need to manually map enough of the atoms to allow the automap feature to map your query correctly. Then select the entire query and re-automap it.

Always atom-atom map a reaction query last, after you add all other structures, stereochemistry, and/or query features to your query.

39.8 Guidelines for Revising the Query

If your SBF search retrieved no records or too few records, you might want to:

*	Conduct an SBF search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the structural constraints in your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, remove substituent limits, or remove stereochemical requirements.

*	Make the text/numeric strings in your query more general, and then search the same set of records. For example, you can apply operators that partially restrict, such as > or between instead of =, or you can apply wildcards. (A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters.)

Note: To retrieve structures that contain Inversion (.Inv.), Retention (.Ret.), Exact Changes (.Ext.), and atom-atom maps, the structures in your database must contain these query features.

If your SBF search retrieved too many records, you might want to:

*	Refine the structural constraints in your query, and then search the same set of records. For example, you can limit substitution at specific positions, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Mark the reacting centers in your query, and then search the same set of records.

*	Make the text/numeric strings in your query more restrictive, and then search the same set of records. For example, you can use the operator = instead of >.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	Filter your search results so that you view solely the lower-level records. (This assumes that you are viewing both upper- and lower-level records.)

If your SBF search retrieved incorrect records and your graphical query contained a transformation with atom-atom maps, you might want to:

*	Remap the atoms in your reaction substructure query.

39.9 Searching Example 1: Combining Text/Numeric Queries

This searching example shows you how to conduct a single SBF search with a query that contains two text/numeric strings.

39.9.1 Problem

You want to retrieve all records that meet both of the following requirements:

*	Have a product yield that is greater than %95 percent

*	Contains two or three oxygen atoms

39.9.2 Approach

Enter the numeric string query > 95 into the Product Yield box or table cell on the form in ISIS/Base (or an equivalent label) that connects to the database field RXN>VARIATION>PRODUCT>YIELD. This string contains the search operator > and the target value 95.

Enter the text/numeric string query LIKE "O(2-3)" into the Formula box or table cell on the form that connects to the database field MOL>MOLFORMULA. This string contains the search operator LIKE and the target value o(2-3) in double quotation marks, where o is either in upper- or lower-case characters.

Note: If you enter both queries into different rows in a single table, you retrieve those molecules that meet one requirement (but not necessarily both).

Then conduct an SBF search in the remote reaction database of your choice, such as the ISISRX demo database. (This is a hierarchical database.)

39.9.3 Query

Note: Your form in ISIS/Base might be entirely different from the one in this example.

39.9.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SBF, how to/examples.

39.9.5 Results

For Versions of ISIS Before 2.0

If you entered your queries into separate boxes, you retrieve records that meet both requirements.

If you entered your queries into the same row within a single table, you retrieve records that meet either (but not necessarily both) requirement.

(If you filter your search results, you see solely those lower-level records that meet your search requirements.)

For ISIS 2.0 and Later

If you entered your queries either into separate boxes or into the same row within a single table, you retrieve records that meet both requirements.

If you entered your queries into different rows within a single table, you retrieve records that meet either (but not necessarily both) requirement.

(If you filter your search results, you see solely those lower-level records that meet your search requirements.)

39.10 Searching Example 2: Combining Text/Numeric and Graphical Queries

This searching example shows you how to conduct a single SBF search with both a text/numeric string as a query and a graphical query.

39.10.1 Problem

You want to retrieve all records that meet both of the following requirements:

*	Have a reactant with a molecular weight that is greater than 250

*	Contain a specific reaction substructure embedded wholly within them (the conversion of benzaldehydes to benzyl alcohols)

39.10.2 Approach

Enter the numeric string query > 250 into the Reactant Molecular Weight box or table cell on the form in ISIS/Base that connects to the database field RXN>VARIATION>REACTANT>MOLECULAR.WEIGHT (or an equivalent database field name). In this example, this field is at a lower level in the database. The string contains the search operator > and the target value 250.

Create the graphical query as follows: Draw the minimum structures in the reaction, specify that the bond type must change at a specific position, and then specify with an atom-atom map exactly which atoms in the reactants correspond to the atoms in the products. (Always use atom-atom maps in a reaction substructure query. In addition, if you atom-atom map your reaction substructure query automatically, or automap your query, all reacting centers in your query are marked for you automatically.) Enter this query into the Reaction Structure box or table cell on the form in ISIS/Base that connects to the database field RXNSTRUCTURE. In this example, this field is at the top level of the database.

Conduct an SBF search in the remote reaction database of your choice, such as the ISISRX demo database. (This is a hierarchical database.)

39.10.3 Query

Note: Your form in ISIS/Base might be entirely different from the one in this example.

The Change bonds (bonds marked with /) specify that the bond types are changed at the specified positions. The numbers that you see on the reaction substructure query are the atom-atom maps.

39.10.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SBF, how to/examples.

39.10.5 Results

You retrieve all reaction records that contain a specific reaction substructure embedded wholly within them (the conversion of benzaldehye to benzyl alcohol) and all records in which a reactant has a molecular weight that is greater than 250.


Local SBF in a Reaction Database: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Local SBF Search in a Reaction Database	40.1

*	Definition of Aromaticity	40.2

*	Specifying Query Features on Atoms and Bonds in Structures	40.3

*	Specifying Stereochemistry	40.4

*	Guidelines for Revising the Query	40.5

*	Searching Example 1: Combining Text/Numeric Queries	40.6

*	Searching Example 2: Combining Text/Numeric and Graphical Queries	40.7

We recommend that you print this 16-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a local SBF search in a reaction database, click here.

40.1 Definition of a Local SBF Search in a Reaction Database

A local Search By Form (SBF) search in a reaction database search finds reaction records in your local database that contain your text/numeric query exactly as you specify it or your graphical query as a substructure wholly within a larger structure.

Note: If your database contains the exact match of your substructure query, you also retrieve the exact match.

In addition, you can combine text/numeric and graphical queries. For example, you want to find all transformations with a specific reaction substructure wholly within them and that have a product yield that is greater than 95 percent and that have a REGNO that begins with the letter T (You can enter as many as 25 queries into different cells of the same table.):

In this example, one of the text/numeric queries contains the search operator LIKE (to specify the retrieval of an exact match of the target text), double quotes around the target text, and a wildcard. A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters. A search operator is the command that specifies the type of search.

Your graphical query can also contain restrictions (called query features) on atoms and bonds. For example, you can use the ISIS atom-query feature (H0) to prohibit the attachment of hydrogens on a specific atom. You can also add hydrogens with visible bonds (called explicit hydrogens) to your query to block substituents on specific atoms.

A local search is a search over a database that typically exists on your hard disk. To do a local search on your hard disk, you do not need to input network information.

Note: To do a local search that is accessed from a shared network, you need to input network information.

40.1.1 Specifying a Text/Numeric String as a Query

A text/numeric string as an SBF query is a phrase in a box or column on the form that specifies the retrieval of data. For example, to find structures with a molecular weight greater than 350, enter the text/numeric string > 350 into the Molecular Weight box on the form.

Each phrase in a text/numeric string contains:

*	A search operator that specifies the type of search. For example, the search operators = (equal sign) and LIKE specify the retrieval of the exact match of your query. Use = when you want to retrieve data with numeric values. Use LIKE when you want to retrieve data with text. For details on search operators, see Section 40.1.2.

*	A text or numeric target value that you want to find (such as 350 for the molecular weight or ANTIBIOTIC for the activity).

Your text/numeric string is case-sensitive solely when you use a relational database or a UNIX platform.

Specifying Numeric String Queries

Do not include the units, such as a percent sign (%) or the degrees Centigrade (C). For example, to retrieve all compounds with a molecular weight greater than 350, enter:

> 350

where the search operator is > and the target value is 350.

Specifying Text/Numeric String Queries

Enclose queries that contain text (with or without numeric values) in double quotes and always use a wildcard, such as %. For example, to retrieve all compounds from the author Smythe, enter:

LIKE "%Smythe%"

where the search operator is LIKE and the target value is Smythe.

A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. The wildcard _ is a placeholder for solely one unspecified character. Without a wildcard, you retrieve solely those records that contain exactly the target value that you specified. For example:

Query Without a Wildcard	Example of a Record Retrieved

LIKE "antibiotic"	Antibiotic
ANTIBIOTIC

Query With the Wildcard %	Examples of Records Retrieved

LIKE "%antibiotic%"	Antibiotic

Antibiotic activity

Resistance to extracellular products such as antibiotics

Note: If you want to retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

40.1.2 The Search Operators

<, <=, >, >=, and <>

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Search Operator	Definition	Examples

=	equal (numeric)	= 350

<	less than (numeric)	< 350

<=	less than or equal to (numeric)	= 350

>	greater than (numeric)	> 350

>=	greater than or equal to (numeric)	>= 350

<>	not equal to (text or numeric)	<> 350

<> "initiator"

LIKE

Use LIKE with text enclosed in double quotation marks. Enter your query as follows:

Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. For example:

Query	Examples of Records Retrieved

LIKE "methane"	Methane

LIKE "benzoic acid"	Benzoic Acid

LIKE "%acid"	Benzoic Acid

Acetic Acid

LIKE "%acid%"	Benzoic Acid Sodium Salt

Acetic Acid Sodium Salt

LIKE "%but_ne"	Trans 2-Butene

2-Butene

N-Butane

Butane

Butene

LIKE "_ethyl"	Methyl

Ethyl

LIKE "antibiotic"	Antibiotic

LIKE "%antibiotic%"	Antibiotic activity

Resistance to extracellular products such as antibiotics

Note: To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice. To retrieve data that contains double quotes within it, such as aa"a, you need to enter additional double quotes as follows: LIKE "aa""a" or LIKE"%aa""a%".

BETWEEN

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks. For example:

BETWEEN "XR11" "XZ15"

BETWEEN 95 100

EXISTS

Use EXISTS to retrieve all records in the database that contain data in a specific database field. For example:

EXISTS

Note: You can only use the EXISTS search operator for database fields that do not give you an error message.

40.1.3 Specifying a Molecular Formula as a Query

To search the data in Formula box (that is, a box that is connected to a MOLFORMULA field), you can specify the following text/numeric queries:

*	An exact formula. Use an exact formula query to find records that contain solely the exact atoms that you specify.

*	A subformula. Use a subformula query to find records that contain the specific atoms that you specify, and any additional atoms.

Exact Formula Query

To specify an exact formula query, specify the target value for the formula. The target value must include all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required. The equals operator (=) and quotes are optional. For example:

Exact Formula Query	Examples of Records Retrieved

c6 h6 O	Phenol

c6h6o

C20 H12 Na2 O4	Sodium salt of phenolphthalein

C20H12Na2O4

= C20 H12 Na2 O4

= C20H12Na2O4

= "C20 H12 Na2 O4"

= "C20H12Na2O4"

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Exact Formula Query	Examples of Records Retrieved

C17 H19 N 03	Piperine

C17H19N 03	Piperine

C17H19N103	Piperine

C17H19N03	No molecules retrieved. ISIS interprets "NO3" as 3 Nobelium atoms.

Subformula Query

To specify a subformula query, use the LIKE operator with a target value for the subformula. The target value can include a range of atom counts, and typically excludes the hydrogens. To exclude specific atoms from the molecules that you retrieve, specify zero for that atom. You can use a single space to separate atoms. Capital letters are not required. Quotes are optional.

Subformula Query	Examples of Records Retrieved

LIKE Na	All sodium salts

LIKE c12 Br(1-2) S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE "C12Br(1-2)S2"	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE c6 h6	All molecules that contain six carbon atoms, six hydrogen atoms, and any number of other atoms

LIKE C5 H10 N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

LIKE C5H10N0	All molecules that contain five carbon atoms, ten hydrogen atoms, and zero nitrogen atoms.

If you enter a single atom within your query you must enter a value of 1 or a space after the symbol. If you do not, ISIS cannot interpret the query correctly. For example:

Subformula Query	Examples of Records Retrieved

LIKE C12 Br S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12Br1S2	All molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms

LIKE C12BrS2	No molecules retrieved. ISIS interprets "BrS" as an atom symbol, and gives an error message.

40.1.4 Specifying a Graphical Substructure as a Query

A graphical substructure query retrieves records that contain your graphical query embedded wholly within them. For example:

You can also increase the power of an SBF search by the addition of specific restrictions (called query features) on atoms and/or bonds. There are a number of query features available for use.

In the following example, the ISIS atom-query feature (H0) prohibits the attachment of hydrogens on a specific atom in the records retrieved:

In addition, the hydrogens block substitutions at the specified positions.

To use a graphical query, you must have a structure box on the form in ISIS/Base that will hold your query:

*	A Reaction Structure box holds any structure with a reaction arrow. For example, enter a transformation into the Reaction Structure box on the form, or enter a product (or a reactant) with a reaction arrow into the Reaction Structure box on the form.

*	All other structure boxes hold a specific type of structure without a reaction arrow. For example, enter a product without a reaction arrow into the Product Structure box on the form, or enter a reactant without a reaction arrow into the Reactant Structure box on the form.

Notes: (1) You can enter multiple graphical queries onto the form in ISIS/Base. (2) You do not use a search operator with a graphical query.

40.1.5 Specifying Multiple Queries in a Single SBF Search

When you combine two or more queries of any type into a single SBF search, the search results that you obtain depend on both the specifications and accuracy of your query and the way that information is stored in your database. For more information on how to create an adequate query, see Section 40.1.1 through Section 40.1.4.

How Information Can Be Stored

Information in a database is stored either in a single level (called a flat database) or in multiple levels (called a hierarchical database). Storage in a hierarchical database is more efficient, but it requires you to enter your queries in the correct location on the form to obtain the search results that you want.

A typical hierarchical database is as follows:

The top level in the hierarchy stores the reaction structure and ID number for each reaction record, and the lower level in the hierarchy stores the literature references and variations for each reaction structure. LITREF is the parent field for the database fields journal and author, and VARIATION is the parent field for the database fields variation number (varno), solvent, and yield. Each reaction record might have multiple literature references and multiple variation subrecords associated with it.

Obtaining the Correct Search Results From a Hierarchical Database

If you search a hierarchical database for lower level records with multiple queries in a single SBF search, where you enter your queries on the form is significant.

For example, the following hierarchical database stores data for multiple decomposition tests that are conducted under different atmospheric conditions:

(In this database, structures are stored at the top (or root) level, and the percentage of oxygen and the number of peaks are stored at a lower level, under the parent field Decomposition. A parent field is a branch in the hierarchy that contains a set of child fields, such as percent O2 and number of peaks.)

You want specific decomposition data from different tests. Your multiple query in a single SBF search specifies that you want all compounds within a single test that contain: Query 1, greater than 65% O2; Query 2, less than three peaks.

To obtain search results that match all queries (Query 1 AND Query 2), you can either (a) enter each search query into separate boxes or (b) enter each search query into the same row in a single table. This search gives you all compounds within a single test that meet both requirements in your query:

Caution: For all versions of ISIS before 2.0, multiple queries in boxes might give different results than multiple queries in tables. In the previous example, the SBF query in the box on the form at the left retrieves records in which at least one decomposition test that matches both conditions. The SBF query in the table on the form at the right, however, retrieves additional records in which one decomposition test matches one condition, and another decomposition test matches the other condition. In ISIS 2.0, both queries retrieve only those records in which both conditions are met within the same decomposition test.

To obtain search results that match either one query or the other (Query 1 OR Query 2), you must enter each search query into different rows of a single table. You must be certain that the first column in the table is a field at the same database level that you want to search. This search gives you all compounds within a single test that meet either requirement in your query (but not necessarily both requirements):

When you filter your search results, you see solely those lower-level records that meet your search requirements.

Note: A box retrieves data from a single database field. A table retrieves data from multiple database fields. Also, you can enter as many as 25 queries into the same table.

40.2 Definition of Aromaticity

For local databases: A bond is aromatic if it is in a six-membered ring with alternating double and single bonds, such as benzene.

Note: Aromaticity is not perceived for fused rings in which the double bonds are arranged in a way that cannot be defined as aromatic.

40.3 Specifying Query Features on Atoms and Bonds in Structures

A query feature on an atom and/or a bond in a reaction component is a restriction that specifies the retrieval of certain types of reaction records from an ISIS/Base database.

If you do not use query features, the records retrieved contain solely your exact substructure query embedded wholly within them. For example:

40.3.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

40.3.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of hydrogens. For example:

40.3.3 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

40.3.4 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

40.3.5 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

40.3.6 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

40.4 Specifying Stereochemistry

For local databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve reactions with matching stereochemistry on the reaction components. For example:

An SBF search produces the following results for each reaction component:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve reactions with matching cis or trans stereochemistry on the reaction components. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An SBF search produces the following results for each reaction component:

40.5 Guidelines for Revising the Query

If your SBF search retrieved no records or too few records, you might want to:

*	Conduct an SBF search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the structural constraints in your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, or remove stereochemical requirements.

*	Make the text/numeric strings in your query more general, and then search the same set of records. For example, you can apply operators that partially restrict, such as > or between instead of =, or you can apply wildcards. (A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters.)

If your SBF search retrieved too many records, you might want to:

*	Refine the structural constraints in your query, and then search the same set of records. For example, you can limit substitution at specific positions with explicit hydrogens, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Make the text/numeric strings in your query more restrictive, and then search the same set of records. For example, you can use the operator = instead of >.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

*	Filter your search results so that you view solely the lower-level records. (This assumes that you are viewing both upper- and lower-level records.)

40.6 Searching Example 1: Combining Text/Numeric Queries

This searching example shows you how to conduct a single SBF search with a query that contains two text/numeric strings.

40.6.1 Problem

You want to retrieve all records that meet both of the following requirements:

*	Have a product yield that is greater than %95 percent

*	Contains two or three oxygen atoms

40.6.2 Approach

Enter the numeric string query > 95 into the Product Yield box or table cell on the form in ISIS/Base (or an equivalent label) that connects to the database field RXN>VARIATION>PRODUCT>YIELD. This string contains the search operator > and the target value 95.

Enter the text/numeric string query LIKE "O(2-3)" into the Formula box or table cell on the form that connects to the database field MOL>MOLFORMULA. This string contains the search operator LIKE and the target value o(2-3) in double quotation marks, where o is either in upper- or lower-case characters.

Note: If you enter both queries into different rows in a single table, you retrieve only those molecules that meet one requirement (but not necessarily both).

Then conduct an SBF search in the local reaction database of your choice, such as the LOCALRX demo database. (This is a hierarchical database.)

40.6.3 Query

Note: Your form in ISIS/Base might be entirely different from the one in this example.

40.6.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SBF, how to/examples.

40.6.5 Results

For Versions of ISIS Before 2.0

If you entered your queries into separate boxes, you retrieve records that meet both requirements.

If you entered your queries into the same row within a single table, you retrieve records that meet either (but not necessarily both) requirement.

(If you filter your search results, you see solely those lower-level records that meet your search requirements.)

For ISIS 2.0 and Later

If you entered your queries either into separate boxes or into the same row within a single table, you retrieve records that meet both requirements. (If you filter your search results, you see solely those lower-level records that meet your search requirements.)

If you entered your queries into different rows within a single table, you retrieve records that meet either (but not necessarily both) requirement.

(If you filter your search results, you see solely those lower-level records that meet your search requirements.)

40.7 Searching Example 2: Combining Text/Numeric and Graphical Queries

This searching example shows you how to conduct a single SBF search with both a text/numeric string as a query and a graphical query.

40.7.1 Problem

You want to retrieve all records that meet both of the following requirements:

*	Have a reactant with a molecular weight that is greater than 250

*	Contain a specific reaction substructure embedded wholly within them (the conversion of benzaldehydes to benzyl alcohols)

40.7.2 Approach

Enter the numeric string query > 250 into the Reactant Molecular Weight box or table cell on the form in ISIS/Base that connects to the database field RXN>VARIATION>REACTANT>MOLECULAR.WEIGHT (or an equivalent database field name). In this example, this field is at a lower level in the database. The string contains the search operator > and the target value 250.

Create the graphical query as follows: Draw the minimum structures in the reaction, specify that the bond type must change at a specific position, and then specify with an atom-atom map exactly which atoms in the reactants correspond to the atoms in the products. (Always use atom-atom maps in a reaction substructure query. In addition, if you atom-atom map your reaction substructure query automatically, or automap your query, all reacting centers in your query are marked for you automatically.) Enter this query into the Reaction Structure box or table cell on the form in ISIS/Base that connects to the database field RXNSTRUCTURE. In this example, this field is at the top level of the database.

Then conduct an SBF search in the local reaction database of your choice, such as the LOCALRX demo database. (This is a hierarchical database.)

40.7.3 Query

Note: Your form in ISIS/Base might be entirely different from the one in this example.

40.7.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for SBF, how to/examples.

40.7.5 Results

You retrieve all reaction records that contain benzyl alcohol and all records in which a reactant has a molecular weight that is greater than 250.


Remote RSim: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote RSim Search	43.1

*	Guidelines for Revising the Query	43.2

*	Searching Example 1: Similar Reactions to Michael Addition	43.3

We recommend that you print this 4-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote RSim search, click here.

43.1 Definition of a Remote RSim Search

A remote Similarity (RSim) search finds reaction records in your remote database that are similar to your query structurally (with varying structural complexities) and/or transformationally. You can define both the type and degree of similarity in your query.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

Note: If your query retrieves data that you perceive to be in the wrong place on the form, see your ISIS Administrator. (This might be the result of specifying the same name for multiple database fields on your form or in the Hview.)

43.1.1 Types of Similarity and Structural Complexity

The type of similarity can be:

a) Structural Similarity -- physical resemblance to the substrate molecules in your query. In addition, if you specify structural similarity, you can also specify that the reaction components that are retrieved contain:

*	The same structural complexity as your query. (Your query is not a substructure or a superstructure.) Click Normal.

*	More structural complexity than your query. (Your query is a substructure.) Click Subsimilar.

*	Less structural complexity than your query. (Your query is a superstructure.) Click Supersimilar.

b) Transformational Similarity -- similar reacting centers

43.1.2 Degrees of Similarity

The degree of structural similarity depends on the number of searchable structural keys that a stored reaction component has in common with the query compared to the total number of searchable structural keys (MDL sets approximately 960 searchable keys in the database). A searchable key defines a specific structural feature, such as a ring structure or the arrangement of a heteroatom in a molecule.

The degree of transformational similarity depends on number of searchable reacting center keys that a stored reaction has in common with the query compared to the total number of searchable reacting center keys (MDL sets approximately 231 searchable reacting center keys in the database).

The degree of both types of similarity can be arbitrary values between 0 and 100 (these are not actual units). The higher the value, the more similarity.

Note: You might need to conduct a series of RSim searches to retrieve the records that you want.

43.2 Guidelines for Revising the Query

If your RSim search retrieved no records or too few records, you might want to:

*	Conduct an RSim search with lower similarity values for structure and/or reacting centers.

*	Conduct an RSim search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

If your RSim search retrieved too many records, you might want to:

*	Conduct an RSim search with higher similarity values for structure and/or reacting centers.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

43.3 Searching Example 1: Similar Reactions to Michael Addition

The following searching example shows you how to retrieve all reactions that are similar to a specific Michael reaction.

43.3.1 Problem

You want to retrieve reactions with similar reacting centers to the Michael reaction in which the reactants cyclohexanone and trans-(2-nitro) phenylethylene are added together to produce the product 1-cyclohexanyl-2-nitro phenylethylane.

Thus, you want the reactions retrieved to have transformational similarities to your reaction query in that there are similar changes between the reactants and product in the reactions retrieved. However, you are not concerned about retrieving similar chemical systems.

43.3.2 Approach

Either draw the reaction or retrieve the query as the rxnfile SIMILARQ.RXN. Enter the query into the Reaction Structure box or table cell on the form in ISIS/Base that connects to the database field RXN>RXNSTRUCTURE. Then conduct an RSim search in the remote reaction database of your choice, such as the ISISRX database.

During the search, you are prompted to enter both a structural similarity value and a reacting center similarity value. Your similarity values can be between 0 and 100 (these are not actual units). The higher the value, the more similarity.

Enter a low structural similarity value ( such as 20) so that the search can retrieve a wide variety of chemical systems. Enter a high reacting center similarity value (such as 70) so that the transformations retrieved are nearly identical to the query. You might need to conduct a series of RSim searches with different similarity values to obtain a set of search results that is easy to browse.

43.3.1 Query

The Make/Break (bonds marked with //) specifies that the bonds at the specified position is formed or broken. The Change bonds (bonds marked with /) specify that the bond types are changed at the specified positions.

43.3.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for RSim, how to/examples.

43.3.4 Results

This example retrieves Michael reactions that have widely different substrates and reaction conditions. For example, you might retrieve reactions like these from your database:

You also retrieve reactions with "Michael-like" reactions that include the radical reaction and the olefin addition to a carbonyl group. For example, you might retrieve reactions like these from your database:


Remote MSim: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote MSim Search	44.1

*	Guidelines for Revising the Query	44.2

*	Searching Example 1: Structurally Similar Molecules	44.3

We recommend that you print this 3-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote MSim search, click here.

44.1 Definition of a Remote MSim Search

A remote Molecule Similarity (MSim) search finds molecules in your remote database that are structurally similar to your query. You can define the degree of similarity in your query to be an arbitrary value between 0 and 100 (these are not actual units). The higher the value, the more similarity. For example:

The degree of structural similarity depends on the number of searchable keys that a stored structure has in common with the query compared to the total number of searchable keys (MDL sets approximately 960 searchable keys in the database). A searchable key defines a specific structural feature, such as a ring structure or the arrangement of a heteroatom in a molecule.

You can also specify that the retrieved molecules contain:

*	The same structural complexity as your query. (Your query is not a substructure or a superstructure.) Click Normal.

*	More structural complexity than your query. (Your query is a substructure.) Click Subsimilar.

*	Less structural complexity than your query. (Your query is a superstructure.) Click Supersimilar.

3D Database Users: An MSim search uses solely the 2D information on a molecule, such as atom types, bond types, and connectivity.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

44.2 Guidelines for Revising the Query

If your MSim search retrieved no records or too few records, you might want to:

*	Conduct an MSim search with lower similarity values for structure and/or reacting centers.

*	Conduct an MSim search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

If your MSim search retrieved too many records, you might want to:

*	Conduct an MSim search with higher similarity values for structure and/or reacting centers.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

44.3 Searching Example 1: Structurally Similar Molecules

The following searching example shows you how to retrieve all molecules that are structurally similar to your structure query.

44.3.1 Problem

You want to retrieve molecules that are structurally similar to Meperidine:

44.3.2 Approach

Draw the structure. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE. Then conduct an MSim search in the remote molecule database of your choice, such as the ISISMX demo database.

During the search, you are prompted to enter a structural similarity value between 0 and 100 (these are not actual units). The higher the value, the more similarity. Enter a value of 50 for your first search. If you retrieve too many molecules, redo the search with a higher structural similarity value. Or, if you retrieve too few molecules, redo the search with a lower structural similarity value.

44.3.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for MSim, how to/examples.

44.3.4 Results

Some of the molecules that might be retrieved from the remote molecule database of your choice is as follows:


Remote FLEX: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote FLEX Search	45.1

*	Specifying Flexmatch Parameters	45.2

*	Specifying Stereochemistry	45.3

*	Specifying Mixtures and Attached Data	45.4

*	Guidelines for Revising the Query	45.5

*	Searching Example 1: Structural Representations in the Database	45.6

*	Searching Example 2: All Salt Forms of a Structure	45.7

*	Searching Example 3: All Sodium Salts in the Database	45.8

We recommend that you print this 16-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote FLEX search, click here.

45.1 Definition of a Remote FLEX Search

A remote Flexible Match (Flexmatch or FLEX) search finds molecule records in your remote database that are an exact match of your query, except in the ways that you can specify with any of the flexmatch parameters. For example, you can specify in your structure query that all bond types in the molecule records do not have to match, or that the radical value on each atom does not have to match.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

45.2 Specifying Flexmatch Parameters

Flexmatch parameters define the features of retrieved molecules that must match your query molecule. If you change the default values of these parameters, you loosen the definition of an exact match. For the set of default parameters, see Section 45.2.3. (If you turn off all flexmatch parameters, you retrieve the loosest fit that is possible for an exact match.)

45.2.1 Parameters for Polymer and Non-Polymer Structures

The parameters in this section apply to both polymer and non-polymer structures. You specify these parameters in one of two ways:

*	Choosing options in the Flexmatch Parameters dialog box. You see the three-letter codes for the parameters that you specify in the Flexmatch switches box on the Current Mol dialog.

*	Typing the three-letter codes directly into the Flexmatch switches box on the Current Mol dialog.

Bond Type (BON)

You can specify that all bond types must match. By default, this parameter is ON (checked).

Tautomer (TAU)

You can specify that tautomer groups must contain the same number of hydrogens in the tautomeric region, within a tolerance limit. By default, this parameter is OFF (unchecked).

The tolerance limit is the sum of the absolute values of charges plus the sum of the number of radicals plus the number of metal bonds. Diradicals count as two radicals. (If you specify this feature with the hydrogen count on, the tolerance limit is zero.)

A tautomer is a group of atoms with any of the following patterns:

Where	Q = O, N, S, Se, or Te

X = C, O, N, S, Se, or Te

Y = C, I, P, As, Sb, Cl, or Br

You can have multiple tautomeric groups in a single molecule. For example:

In addition, any bonds in the tautomeric region can be aromatic. For example:

Atom charges (CHA)

You can specify that the charge on each atom must match those in your query. This automatically ensures that the sum of the charges on each fragment must match. By default, this parameter is ON (checked).

Ion charges (ION)

You can specify that the total charge for each fragment in the query must match. By default, this parameter is OFF (unchecked).

Fragments must match (FRA)

You can specify that all fragments must match your query, and that no additional fragments are allowed. By default, this parameter is ON (checked).

For example, a single query that contains solely fragments A and B retrieves molecules that contain solely fragments A and B. However, the same query does not retrieve molecules that contain solely fragment A, solely fragment B, or fragments A, B, and C (where C is any fragment that is not in the query).

Note: Salt queries that contain fragment B as the counterion retrieve solely Fragment A, where A is the parent of the salt.

For monomer and structural repeating unit (SRU) brackets, the settings of POL and TYP influence how ISIS perceives fragments. For example, ISIS perceives the following source-based representation of a polymer as a single fragment when you specify both POL and TYP in the query, but perceives two fragments when you do not specify POL and TYP:

With POL and TYP specified, ISIS sees the polymer as a single chemical species, and therefore as a single fragment.

Hydrogen count must match (HYD)

You can specify that hydrogen count must match for each fragment in your query. By default, this parameter is ON (checked).

If you do not specify that hydrogen count must match on each fragment in your query, the hydrogen count within a tolerance limit for each of the fragments must match. The tolerance limit is the sum of the absolute values of charges plus the sum of the number of radicals plus the number of metal bonds. Diradicals count as two radicals.

If you specify this feature with Tautomer selected, the hydrogen count must match exactly in both the tautomeric regions and in the individual atoms of non-tautomeric regions.

If you do not specify hydrogen count in your query with Tautomer selected, the hydrogen count must match within the tolerance limit in both the tautomeric regions and in the individual atoms of non-tautomeric regions.

Isotopes must match (MAS)

You can specify that the isotopic labels on each atom must match those in your query. (Isotopic labels include H, D, and T.) By default, this parameter is ON (checked).

If you do not specify this feature, you retrieve molecules in the database that have different isotopic labels, and H, D, and T are equivalent to each other.

Metal bonds must match (MET)

You can specify that the connectivity of all metals must match your query. A metal is any atom other than H, D, T, He, B through Ne, Si through Ar, As through Kr, Te, I, Xe, At, and Rn. By default, this parameter is ON (checked).

If you do not specify this feature, you retrieve all the different representations. For example, to retrieve all representations of ferrocene even though the pi-metal bonds are represented in different ways in your database, turn this feature OFF.

If you do not specify this feature and you also do not specify Salts must match, any counterions that are attached to the metal are removed.

Radicals must match (RAD)

You can specify that the radical value on each atom must match those in your query. By default, this parameter is ON (checked).

Salts must match (SAL)

You can specify that the counterions in the structures retrieved must match the counterion in your query. A counterion is any fragment or single atom in the SALTS.DAT file (or equivalent). This file is customizable. For more information, see your ISIS Administrator. By default, this parameter is ON (checked).

If you do not specify this feature, you retrieve molecules with different counterions than those in your salt query.

If you do not specify this feature and also specify Fragments must match, you retrieve solely the parent structures of salts. For a searching example, see Section 45.7.

Stereoconfiguration must match (STE)

You can specify that the configuration of stereo centers (in geometric and optical stereoisomers) must match. You can only use this feature if you also select Bond Type.

If your query contains unspecified stereo centers, you retrieve solely those structures with unspecified stereo centers. An unspecified stereo center is the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si, that is connected to one of the following: No stereo bonds, an EITHER query bond that specifies either the Up or Down stereoconfiguration, or a DOUBLE EITHER bond that specifies either the cis or trans stereoconfiguration. By default, this parameter is ON (checked).

Valence must match (VAL)

You can specify that the valence on each atom must match those in your query. By default, this parameter is ON (checked).

Notes: (1) If no valence is specified, an implicit valence is calculated from the structure. A query with an unspecified valence (with a calculated implicit valence) might retrieve a structure that contains the matching explicit valence. Or, a query with a specified valence might retrieve a structure that does not contain an explicit valences (that contains a calculated implicit valence). (2) Some valences are illegal. For transition metals, a valence is illegal if it is smaller than the number of bonds to the atom. For other real atom types, an illegal valence is ignored in a FLEX search and the query retrieves any valence.

45.2.2 Parameters for Polymers, Mixtures, and Attached Data

Use these parameters to specify features on structures that contain polymers, mixtures, and attached data. You specify these parameters solely by typing the three-letter codes directly into the Flexmatch switches box on the Current Mol dialog.

Note: The POLY/Exact, POLY/Both, and POLY/Co searches use combinations of flexmatch switches that are especially useful for polymer queries. We recommend that you use one of these searches for searching polymer structures. For more information on these searches, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click the search of your choice. You will see the full definition of the search and how to do it.

Polymer End Groups (END)

END specifies that polymer end groups must match those in your query. A polymer end group is a connected set of atom and bonds that:

*	is connected to the rest of the structure by just one crossing bond (a crossing bond is a bond that crosses a bracket)

*	contains no brackets.

END depends on POL. END can be on solely when POL is also on.

Attached Data (DAT)

DAT specifies that attached data must match the attached data in your query. For example:

Mixtures (MIX)

MIX specifies that the type of mixture (ordered or unordered), and the order of components in an ordered mixture, must match the corresponding structures in your query.

Monomer/SRU Uniqueness (MSU)

MSU specifies that the source-based and structure-based representations of the same polymer are considered distinct structures. When MSU is OFF (not specified), the source-based and structure-based representations of a polymer find each other. For example:

MSU depends on both POL and TYP. POL and TYP must be on for MSU to function.

When MSU is off (not specified), ISIS ignores the settings of BON and HYD for structures within monomer and SRU brackets.

Polymers (POL)

POL specifies that all polymer definitions must match. (The polymer definition is the set of atoms and bonds that is associated with a set of polymer brackets).

The TYP, END, and MSU switches depend on POL. That is, turning off POL automatically turns off TYP, END, and MSU. For monomer and SRU brackets, the setting of POL also determines how ISIS perceives fragments within the polymer. For more information, see FRA.

Polymer Type (TYP)

TYP specifies that the polymer bracket type (for example, monomer, SRU, crosslink, block copolymer, and other bracket types) and polymer connectivity must match your query.

TYP depends upon the setting of POL. That is, POL must be on for TYP to be on. MSU also depends on TYP; TYP must be on for MSU to be on. For monomer and SRU brackets, the setting of TYP also influences how ISIS perceives fragments in the polymer. For more information, see FRA.

45.2.3 The Default Flexmatch Parameters

When you begin an ISIS/Base session, you see the following default flexmatch parameters that retrieve the most restricted exact match of your FLEX query from the database:

Type of Bond Match: Bond Order

Type of Charge Match: Atom Charges

Fragments must match

Hydrogen count must match

Isotopes must match

Metal bonds must match

Radicals must match

Salts must match

Stereoconfiguration must match

Valence must match

If your structure contains polymers, mixtures, and/or attached data, you also need to specify the following parameters in the Flexmatch switches box in the Current Mol dialog: DAT, MIX, POL, TYP, END, MSU. You see the following in the Flexmatch switches box:

FRA/HYD/MAS/MET/RAD/SAL/STE/VAL/BON/TAU/ION/CHA/MIX/DAT/END/POL
/TYP/MSU

To retrieve the least restricted exact match of your FLEX query from the database, you require the following flexmatch parameters:

Type of Bond Match: Both Off

Type of Charge Match: Both Off

Fragments must match

Hydrogen count must match

Isotopes must match

Metal bonds must match

Radicals must match

Salts must match

Stereoconfiguration must match

Valence must match

If your structure contains polymers, mixtures, and/or attached data, you also need to remove any parameters that you specified in the Flexmatch switches box in the Current Mol dialog. For the loosest possible match, the Flexmatch switches box contains no three-letter codes.

45.2.4 Examples of the Interactivity of Flexmatch Parameters

The flexmatch parameters are typically interactive. To obtain the correct results, you need to know which flexmatch parameters require other flexmatch parameters to function correctly. With the correct interactive settings, you can retrieve closely related structures that are represented in a variety of ways in your database. For example:

Sulfones

MDL depicts sulfones with undisplayed charges in which two of the four bonds on the sulfur atom are double bonds. In your database, these compounds might be displayed with charges instead:

You need to consider both charges and bond types. To retrieve all representations of a specific sulfone, you require these settings:

Type of Bond Match: Tautomers

Type of Charge Match: Ion Charges

Note: You can specify that all other settings are OFF (unchecked), but they are not required to be OFF.

Sulfoxides

MDL depicts sulfoxides with undisplayed charges in which there is a double bond on the sulfur atom. In your database, these compounds might be displayed with charges instead:

You need to consider both charges and bond types. To retrieve all representations of a specific sulfoxide, you require these settings:

Type of Bond Match: Tautomers

Type of Charge Match: Ion Charges

Note: You can specify that all other settings are OFF (unchecked), but they are not required to be OFF.

Thiocarboxylic Acid Salts

MDL depicts thiocarboxylic acid salts with undisplayed charges in which there is a bond from the ion to the counterion. In your database, these compounds might be displayed with charges instead:

You need to consider charges, bond types, and metal bonds. To retrieve all representations of a specific salt, you require these settings:

Type of Bond Match: Bond Type

Type of Charge Match: Both Off

Metal bonds must match

Note: You can specify that all other settings are OFF (unchecked), but they are not required to be OFF.

Organometallic Complexes

MDL depicts π ligands in organometallic complexes with radicals or with covalent bonds. You need to consider charges, bond types, metal bonds, and radicals. To retrieve all representations of a specific organometallic complex, you require these settings:

Type of Bond Match: Tautomers

Type of Charge Match: Both Off

Metal bonds must match

Radicals must match

Note 1: You can specify that all other settings are OFF (unchecked), but they are not required to be OFF.

Note 2: You can also retrieve specific organometallic complexes with an exact formula query in an FMLA search.

Source-Based and Structure-Based Polymers

To retrieve polymer structures in which the source-based representation of a polymer must match the corresponding structure-based representation, specify the following flexmatch parameters in the Flexmatch switches box in the Current Mol dialog:

FRA/HYD/MAS/MET/RAD/SAL/STE/VAL/BON/TAU/ION/CHA/MIX/POL/TYP

Note: This combination of Flexmatch parameters gives the same results as a POLY/Both search with the following settings in the Polymer dialog:

 Find the monomer or SRU representation of this polymer

 Attached data must match

 Polymer end groups must match

To retrieve polymer structures in which the source-based representation of a polymer must match the corresponding structure-based representation, and in which polymer end groups and attached data must match exactly, add the DAT and END flexmatch parameters to the previous query:

FRA/HYD/MAS/MET/RAD/SAL/STE/VAL/BON/TAU/ION/CHA/MIX/DAT/END/POL/TYP

Note: This combination of Flexmatch parameters gives the same results as a POLY/Both search with the following settings in the Polymer dialog:

 Find the monomer or SRU representation of this polymer

 Attached data must match

 Polymer end groups must match

45.3 Specifying Stereochemistry

You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

A FLEX search with the most restrictions (equivalent to an exact match search, MEXACT) produces the following results:

Cis or Trans Configurations

Your structure query must contain the exact configuration that you want to retrieve. For example, a FLEX search with the most restrictions (equivalent to an exact match search, MEXACT) produces the following results:

Chiral Flags on Molecules

In a remote database, you can create a query with a chiral flag on a molecule with at least one asymmetric center to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

45.4 Specifying Mixtures and Attached Data

You can use mixture brackets, component brackets, and attached data in MEXACT search queries. For example, the following structure represents a mixture of two components: aspirin (80% by weight) and a binder of unknown structure called Binder 46 (20% by weight):

In a FLEX search that uses the most restricted flexmatch parameters, the mixture brackets, component brackets, and attached data must match exactly. For example:

For more information and examples of non-polymer structures that use mixtures and attached data, see Drawing Mixtures: MDL Requirements for Database Searching and Registration. For more information and examples of polymer structures that use mixtures and attached data, see Drawing Polymers: MDL Requirements for Database Searching and Registration.

45.5 Guidelines for Revising the Query

If your FLEX search retrieved no records or too few records, you might want to:

*	Conduct a FLEX search with looser flexmatch parameters.

*	Add or delete the stereochemistry in your query. If you omit the stereochemistry in your query, the records retrieved will contain no stereochemistry. The records match your search query exactly, except where you specify a looser fit with flexmatch parameters.

*	Conduct a FLEX search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Conduct a different search on the same set of records with the same query. For example, you might conduct one of the following searches: Molecule Similarity (MSim), Tautomer (TAUT), and Isomer (ISOMER). For more information on these searches, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click the search of your choice. You will see the full definition of the search and how to do it.

If your FLEX search retrieved too many records, you might want to:

*	Conduct a FLEX search with stricter flexmatch parameters.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

45.6 Searching Example 1: Structural Representations in the Database

The following searching example shows you how to retrieve all molecules that match your structure query. The molecules might be represented in a variety of ways in the database.

45.6.1 Problem

You want to retrieve all isotopes of the following structure:

45.6.2 Approach

Draw the structure. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE.

Then conduct a FLEX search in the remote molecule database of your choice, such as the ISISMX demo database. During the search, you are prompted to enter the flexmatch parameters. You require this setting:

Isotopes must match

Note: You can specify that all other settings are OFF (unchecked), but they are not required to be OFF.

45.6.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for FLEX, how to/examples.

45.6.4 Results

You retrieve molecules that have different isotopic labels. One of the molecules that you might retrieve from the remote molecule database of your choice is as follows:

45.7 Searching Example 2: All Salt Forms of a Charged Molecule

The following searching example shows you how to retrieve all salt forms of your charged molecule query.

Note: Salts might be represented differently in your database than in this example.

45.7.1 Problem

You want to retrieve all salts of the following charged molecule:

45.7.2 Approach

Draw the charged molecule. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE.

Then conduct a FLEX search in the remote molecule database of your choice, such as the ISISMX demo database. During the search, you are prompted to enter the flexmatch parameters. You require these settings:

Fragments must match

Salts must match

Note: You can specify that all other settings are OFF (unchecked), but they are not required to be OFF.

45.7.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for FLEX, how to/examples.

45.7.4 Results

You retrieve all salts of your charged molecule query. Some of the molecules that you might retrieve from the remote molecule database of your choice are as follows:

45.8 Searching Example 3: All Sodium Salts in the Database

The following searching example shows you how to retrieve all molecule records that contain structures with sodium salts.

Note: Salts might be represented differently in your database than in this example.

45.8.1 Problem

You want to retrieve all molecule records that contain structures with sodium salts.

45.8.2 Approach

Draw the sodium counterion. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE.

Then conduct a FLEX search in the remote molecule database of your choice, such as the ISISMX demo database. During the search, you are prompted to enter the flexmatch parameters. To retrieve records that contain the parent structures as well as your counterion, you require these settings:

Fragments must match

Salts must match

Note: You can specify that all other settings are OFF (unchecked), but they are not required to be OFF.

45.8.3 Query

Note: Obtain the sodium atom from the PTable instead of the list of atoms that you see with the ISIS atom query feature List.

45.8.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for FLEX, how to/examples.

45.8.5 Results

You retrieve molecules that are sodium salts. One of the molecules that you might retrieve from the remote molecule database of your choice is as follows:


Remote TAUT: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote TAUT Search	46.1

*	Guidelines for Revising the Query	46.2

*	Searching Example 1: Tautomers in the Database	46.3

We recommend that you print this 3-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote TAUT search, click here.

46.1 Definition of a Remote TAUT Search

A remote Tautomer (TAUT) search finds molecule records in your remote database that are tautomers of your query. For example:

A tautomer is a group of atoms with any of the following patterns:

Where	Q = O, N, S, Se, or Te

X = C, O, N, S, Se, or Te

Y = C, I, P, As, Sb, Cl, or Br

Tautomer groups must contain the same number of hydrogens in the tautomeric region, with a tolerance limit. The tolerance limit is the sum of the absolute values of charges plus the sum of the number of radicals plus the number of metal bonds. Diradicals count as two radicals.

You can have multiple tautomeric groups in a single molecule. For example:

In addition, any bonds in the tautomeric region can be aromatic. For example:

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

46.2 Guidelines for Revising the Query

If your TAUT search retrieved no records or too few records, you might want to:

*	Conduct a TAUT search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Conduct a different search on the same set of records with the same query. For example, you might conduct one of the following searches: Molecule Similarity (MSim), Isomer (ISOMER), and Flexmatch (FLEX). For more information on these searches, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click the search of your choice. You will see the full definition of the search and how to do it.

If your TAUT search retrieved too many records, you might want to:

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

46.3 Searching Example 1: Tautomers in the Database

The following searching example shows you how to retrieve all molecules that are tautomers of your structure query.

46.3.1 Problem

You want to retrieve molecules that are tautomers of the following structure:

46.3.2 Approach

Draw the structure. (You do not need to add any stereochemistry.) Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE. Then conduct a TAUT search in the remote molecule database of your choice, such as the ISISMX demo database.

46.3.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for TAUT, how to/examples.

46.3.4 Results

Some of the molecules that you might retrieve from the remote molecule database of your choice are as follows:


Remote ISOMER: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote ISOMER Search	47.1

*	Guidelines for Revising the Query	47.2

*	Searching Example 1: Isomers in the Database	47.3

We recommend that you print this 3-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote ISOMER search, click here.

47.1 Definition of a Remote ISOMER Search

A remote Isomer (ISOMER) search finds molecule records in your remote database that are geometric isomers and stereoisomers of your structure query. For example:

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

47.2 Guidelines for Revising the Query

If your ISOMER search retrieved no records or too few records, you might want to:

*	Conduct an ISOMER search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Conduct a different search on the same set of records with the same query. For example, you might conduct one of the following searches: Molecule Similarity (MSim), Tautomer (TAUT), and Flexmatch (FLEX). For more information on these searches, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click the search of your choice. You will see the full definition of the search and how to do it.

If your ISOMER search retrieved too many records, you might want to:

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

47.3 Searching Example 1: Isomers in the Database

The following searching example shows you how to retrieve all molecules that are isomers of your structure query.

47.3.1 Problem

You want to retrieve molecules that are isomers of the following structure:

47.3.2 Approach

Draw the structure. (You do not need to add any stereochemistry.) Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE. Then conduct an ISOMER search in the remote molecule database of your choice, such as the ISISMX demo database.

47.3.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ISOMER, how to/examples.

47.3.4 Results

Some of the molecules that you might retrieve from the remote molecule database of your choice are as follows:


Remote PARENT: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote PARENT Search	48.1

*	Specifying Stereochemistry	48.2

*	Guidelines for Revising the Query	48.3

*	Searching Example 1: Parent Structures of Salts in the Database	48.4

We recommend that you print this 4-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote PARENT search, click here.

48.1 Definition of a Remote PARENT Search

A remote Parent (PARENT) search finds molecule records in your remote database that are parent molecules of your salt query. For example:

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

48.2 Specifying Stereochemistry

You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

A PARENT search produces the following results:

Cis or Trans Configurations

Your structure query must contain the exact configuration that you want to retrieve. For example, an PARENT search produces the following results:

Chiral Flags on Molecules

In a remote database, you can create a query with a chiral flag on a molecule with at least one asymmetric center to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

48.3 Guidelines for Revising the Query

If your PARENT search retrieved no records or too few records, you might want to:

*	Conduct a PARENT search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Conduct a different search on the same set of records with the same query. For example, you might conduct one of the following searches: Molecule Similarity (MSim), Isomer (ISOMER), Tautomer (TAUT), and Flexmatch (FLEX). For more information on these searches, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click the search of your choice. You will see the full definition of the search and how to do it.

If your PARENT search retrieved too many records, you might want to:

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

48.4 Searching Example 1: Parent Structures of Salts in the Database

The following searching example shows you how to retrieve the parent structures of your salt query.

Note: Salts might be represented differently in your database than in this example.

48.4.1 Problem

You want to retrieve the parent structures of the following salt:

48.4.2 Approach

Draw the charged molecule. Enter the query into the Structure box or table cell on the form in ISIS/Base that connects to the database field MOLSTRUCTURE. Then conduct a PARENT search in the remote molecule database of your choice, such as the ISISMX demo database.

48.4.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for PARENT, how to/examples.

48.4.4 Results

You retrieve all parent structures of your salt query. One of the molecules that you might retrieve from the remote molecule database of your choice is as follows:


Remote MSim: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote MSim Search	63.1

*	Guidelines for Revising the Query	63.2

*	Searching Example 1: Structurally Similar Reaction Components	63.3

We recommend that you print this 3-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote MSim search, click here.

63.1 Definition of a Remote MSim Search

A remote Molecule Similarity (MSim) search finds reaction records in your remote database that are structurally similar to your structure query. You can define the degree of similarity in your query to be an arbitrary value between 0 and 100 (these are not actual units). The higher the value, the more similarity. For example:

The degree of structural similarity depends on the number of searchable keys that a stored reaction component has in common with the query compared to the total number of searchable keys (MDL sets approximately 960 searchable keys in the database). A searchable key defines a specific structural feature, such as a ring structure or the arrangement of a heteroatom in a molecule.

You can also specify that the retrieved reaction components contain:

*	The same structural complexity as your query. (Your query is not a substructure or a superstructure.) Click Normal.

*	More structural complexity than your query. (Your query is a substructure.) Click Subsimilar.

*	Less structural complexity than your query. (Your query is a superstructure.) Click Supersimilar.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

Note: If your query retrieves data that you perceive to be in the wrong place on the form, see your ISIS Administrator. (This might be the result of specifying the same name for multiple database fields on your form or in the Hview.)

63.2 Guidelines for Revising the Query

If your MSim search retrieved no records or too few records, you might want to:

*	Conduct an MSim search with lower similarity values for structure and/or reacting centers.

*	Conduct an MSim search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

If your MSim search retrieved too many records, you might want to:

*	Conduct an MSim search with higher similarity values for structure and/or reacting centers.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

63.3 Searching Example 1: Structurally Similar Reaction Components

The following searching example shows you how to retrieve all records with reaction components that are structurally similar to your structure query.

63.3.1 Problem

You want to retrieve reactants that are structurally similar to Meperidine:

63.3.2 Approach

Draw the structure (without a reaction arrow). Enter the query into the a box or table cell on the form in ISIS/Base that will hold your reactant (without a reaction arrow). For example, enter a molecule that is a reactant into the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE. Then conduct an MSim search in the remote reaction database of your choice, such as the ISISRX demo database.

During the search, you are prompted to enter a structural similarity value between 0 and 100 (these are not actual units). The higher the value, the more similarity. Enter a value of 50 for your first search. If you retrieve too many molecules, redo the search with a higher structural similarity value. Or, if you retrieve too few molecules, redo the search with a lower structural similarity value.

63.3.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for MSim, how to/examples.

63.3.4 Results

Some of the reactants that might be retrieved from the remote reaction database of your choice is as follows:


Remote FLEX: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote FLEX Search	64.1

*	Specifying Flexmatch Parameters	64.2

*	Specifying Stereochemistry	64.3

*	Guidelines for Revising the Query	64.4

*	Searching Example 1: Structural Representations in the Database	64.5

*	Searching Example 2: All Salt Forms of a Structure	64.6

*	Searching Example 3: All Sodium Salts in the Database	64.7

We recommend that you print this 12-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote FLEX search, click here.

64.1 Definition of a Remote FLEX Search

A remote Flexible Match (Flexmatch or FLEX) search finds reaction records with reaction components in your remote database that are an exact match of your query, except in the ways that you can specify with any of the flexmatch parameters. For example, you can specify in your reactant query that all bond types in the records retrieved do not have to match or that the radical value on each atom does not have to match.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

Note: If your query retrieves data that you perceive to be in the wrong place on the form, see your ISIS Administrator. (This might be the result of specifying the same name for multiple database fields on your form or in the Hview.)

64.2 Specifying Flexmatch Parameters

Flexmatch parameters define the features of retrieved molecules that must match your query molecule. If you change the default values of these parameters, you loosen the definition of an exact match. For the set of default parameters, see Section 64.2.1. (If you turn off all flexmatch parameters, you retrieve the loosest fit that is possible for an exact match.) The flexmatch parameters are as follows:

Bond Type (BON)

You can specify that all bond types must match. By default, this parameter is ON (checked).

Tautomer (TAU)

You can specify that tautomer groups must contain the same number of hydrogens in the tautomeric region, within a tolerance limit. By default, this parameter is OFF (unchecked).

The tolerance limit is the sum of the absolute values of charges plus the sum of the number of radicals plus the number of metal bonds. Diradicals count as two radicals. (If you specify this feature with the hydrogen count on, the tolerance limit is zero.)

A tautomer is a group of atoms with any of the following patterns:

Where	Q = O, N, S, Se, or Te

X = C, O, N, S, Se, or Te

Y = C, I, P, As, Sb, Cl, or Br

You can have multiple tautomeric groups in a single molecule. For example:

In addition, any bonds in the tautomeric region can be aromatic. For example:

Atom charges (CHA)

You can specify that the charge on each atom must match those in your query. This automatically ensures that the sum of the charges on each fragment must match. By default, this parameter is ON (checked).

Ion charges (ION)

You can specify that the total charge for each fragment in the query must match. By default, this parameter is OFF (unchecked).

Fragments must match (FRA)

You can specify that all fragments must match your query, and that no additional fragments are allowed. By default, this parameter is ON (checked).

For example, a single query that contains solely fragments A and B retrieves molecules that contain solely fragments A and B. However, the same query does not retrieve molecules that contain solely fragment A, solely fragment B, or fragments A, B, and C (where C is any fragment that is not in the query).

Note: Salt queries that contain fragment B as the counterion retrieve solely Fragment A, where A is the parent of the salt.

Hydrogen count must match (HYD)

You can specify that hydrogen count must match for each fragment in your query. By default, this parameter is ON (checked).

If you do not specify that hydrogen count must match on each fragment in your query, the hydrogen count within a tolerance limit for each of the fragments must match. The tolerance limit is the sum of the absolute values of charges plus the sum of the number of radicals plus the number of metal bonds. Diradicals count as two radicals.

If you specify this feature with Tautomer selected, the hydrogen count must match exactly in both the tautomeric regions and in the individual atoms of non-tautomeric regions.

If you do not specify hydrogen count in your query with Tautomer selected, the hydrogen count must match within the tolerance limit in both the tautomeric regions and in the individual atoms of non-tautomeric regions.

Isotopes must match (MAS)

You can specify that the isotopic labels on each atom must match those in your query. (Isotopic labels include H, D, and T.) By default, this parameter is ON (checked).

If you do not specify this feature, you retrieve molecules in the database that have different isotopic labels, and H, D, and T are equivalent to each other.

Metal bonds must match (MET)

You can specify that the connectivity of all metals must match your query. A metal is any atom other than H, D, T, He, B through Ne, Si through Ar, As through Kr, Te, I, Xe, At, and Rn. By default, this parameter is ON (checked).

If you do not specify this feature, you retrieve all the different representations. For example, to retrieve all representations of ferrocene even though the pi-metal bonds are represented in different ways in your database, turn this feature OFF.

If you do not specify this feature and you also do not specify Salts must match, any counterions that are attached to the metal are removed.

Radicals must match (RAD)

You can specify that the radical value on each atom must match those in your query. By default, this parameter is ON (checked).

Salts must match (SAL)

You can specify that the counterions in the structures retrieved must match the counterion in your query. A counterion is any fragment or single atom in the SALTS.DAT file (or equivalent). This file is customizable. For more information, see your ISIS Administrator. By default, this parameter is ON (checked).

If you do not specify this feature, you retrieve molecules with different counterions than those in your salt query.

If you do not specify this feature and also specify Fragments must match, you retrieve solely the parent structures of salts. For a searching example, see Section 64.6.

Stereoconfiguration must match (STE)

You can specify that the configuration of stereo centers (in geometric and optical stereoisomers) must match. You can only use this feature if you also select Bond Type.

If your query contains unspecified stereo centers, you retrieve solely those structures with unspecified stereo centers. An unspecified stereo center is the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si, that is connected to one of the following: No stereo bonds, an EITHER query bond that specifies either the Up or Down stereoconfiguration, or a DOUBLE EITHER bond that specifies either the cis or trans stereoconfiguration. By default, this parameter is ON (checked).

Valence must match (VAL)

You can specify that the valence on each atom must match those in your query. By default, this parameter is ON (checked).

Notes: (1) If no valence is specified, an implicit valence is calculated from the structure. A query with an unspecified valence (with a calculated implicit valence) might retrieve a structure that contains the matching explicit valence. Or, a query with a specified valence might retrieve a structure that does not contain an explicit valences (that contains a calculated implicit valence). (2) Some valences are illegal. For transition metals, a valence is illegal if it is smaller than the number of bonds to the atom. For other real atom types, an illegal valence is ignored in a FLEX search and the query retrieves any valence.

64.2.1 The Default Flexmatch Parameters

When you begin an ISIS/Base session, you see the following default flexmatch parameters that retrieve the most restricted exact match of your FLEX query from the database:

Type of Bond Match: Bond Order

Type of Charge Match: Atom Charges

Fragments must match

Hydrogen count must match

Isotopes must match

Metal bonds must match

Radicals must match

Salts must match

Stereoconfiguration must match

Valence must match

To retrieve the least restricted exact match of your FLEX query from the database, you require the following flexmatch parameters:

Type of Bond Match: Both Off

Type of Charge Match: Both Off

Fragments must match

Hydrogen count must match

Isotopes must match

Metal bonds must match

Radicals must match

Salts must match

Stereoconfiguration must match

Valence must match

64.2.2 Examples of the Interactivity of Flexmatch Parameters

The flexmatch parameters are typically interactive. To obtain the correct results, you need to know which flexmatch parameters require other flexmatch parameters to function correctly. With the correct interactive settings, you can retrieve closely related structures that are represented in a variety of ways in your database. For example:

Sulfones

MDL depicts sulfones with undisplayed charges in which two of the four bonds on the sulfur atom are double bonds. In your database, these compounds might be displayed with charges instead:

You need to consider both charges and bond types. To retrieve all representations of a specific sulfone, you require these settings:

Type of Bond Match: Tautomers

Type of Charge Match: Ion Charges

Note: You can specify that all other settings are OFF (unchecked), but they are not required to be OFF.

Sulfoxides

MDL depicts sulfoxides with undisplayed charges in which there is a double bond on the sulfur atom. In your database, these compounds might be displayed with charges instead:

You need to consider both charges and bond types. To retrieve all representations of a specific sulfoxide, you require these settings:

Type of Bond Match: Tautomers

Type of Charge Match: Ion Charges

Note: You can specify that all other settings are OFF (unchecked), but they are not required to be OFF.

Thiocarboxylic Acid Salts

MDL depicts thiocarboxylic acid salts with undisplayed charges in which there is a bond from the ion to the counterion. In your database, these compounds might be displayed with charges instead:

You need to consider charges, bond types, and metal bonds. To retrieve all representations of a specific salt, you require these settings:

Type of Bond Match: Bond Type

Type of Charge Match: Both Off

Metal bonds must match

Note: You can specify that all other settings are OFF (unchecked), but they are not required to be OFF.

Organometallic Complexes

MDL depicts π ligands in organometallic complexes with radicals or with covalent bonds. You need to consider charges, bond types, metal bonds, and radicals. To retrieve all representations of a specific organometallic complex, you require these settings:

Type of Bond Match: Tautomers

Type of Charge Match: Both Off

Metal bonds must match

Radicals must match

Note 1: You can specify that all other settings are OFF (unchecked), but they are not required to be OFF.

Note 2: You can also retrieve specific organometallic complexes with an exact formula query in an FMLA search.

64.3 Specifying Stereochemistry

You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

An FLEX search with the most restrictions (equivalent to an exact match search, MEXACT) produces the following results:

Cis or Trans Configurations

Your structure query must contain the exact configuration that you want to retrieve. For example, a FLEX search with the most restrictions (equivalent to an exact match search, MEXACT) produces the following results:

Chiral Flags on Reaction Components

In a remote database, you can create a query with a chiral flag on a reaction component with at least one asymmetric center or on a reaction component that is asymmetric to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

64.4 Guidelines for Revising the Query

If your FLEX search retrieved no records or too few records, you might want to:

*	Conduct a FLEX search with looser flexmatch parameters.

*	Add or delete the stereochemistry in your query. If you omit the stereochemistry in your query, the records retrieved will contain no stereochemistry. The records match your search query exactly, except where you specify a looser fit with flexmatch parameters.

*	Conduct a FLEX search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Conduct a different search on the same set of records with the same query. For example, you might conduct one of the following searches: Molecule Similarity (MSim), Tautomer (TAUT), and Isomer (ISOMER). For more information on these searches, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click the search of your choice. You will see the full definition of the search and how to do it.

If your FLEX search retrieved too many records, you might want to:

*	Conduct a FLEX search with stricter flexmatch parameters.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

64.5 Searching Example 1: Structural Representations in the Database

The following searching example shows you how to retrieve all reaction components that match your structure query. The reactants might be represented in a variety of ways in the database.

64.5.1 Problem

You want to retrieve all isotopes of the following reactant:

64.5.2 Approach

Draw the structure (without a reaction arrow). Enter the query into the a box or table cell on the form in ISIS/Base that will hold your reactant (without a reaction arrow). For example, enter a molecule that is a reactant into the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE.

Then conduct a FLEX search in the remote reaction database of your choice, such as the ISISRX demo database. During the search, you are prompted to enter the flexmatch parameters. You require this setting:

Isotopes must match

Note: You can specify that all other settings are OFF (unchecked), but they are not required to be OFF.

64.5.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for FLEX, how to/examples.

64.5.4 Results

You retrieve reactants that have different isotopic labels. One of the reactants that you might retrieve from the remote reaction database of your choice is as follows:

64.6 Searching Example 2: All Salt Forms of a Charged Molecule

The following searching example shows you how to retrieve all salt forms of your charged reaction component query.

Note: Salts might be represented differently in your database than in this example.

64.6.1 Problem

You want to retrieve all salts of the following charged reactant:

64.6.2 Approach

Draw the charged reactant (without a reaction arrow). Enter the query into the a box or table cell on the form in ISIS/Base that will hold your reactant (without a reaction arrow). For example, enter a molecule that is a reactant into the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE.

Then conduct a FLEX search in the remote reaction database of your choice, such as the ISISRX demo database. During the search, you are prompted to enter the flexmatch parameters. You require these settings:

Fragments must match

Salts must match

Note: You can specify that all other settings are OFF (unchecked), but they are not required to be OFF.

64.6.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for FLEX, how to/examples.

64.6.4 Results

You retrieve all salts of your charged molecule query. Some of the reactants that you might retrieve from the remote reaction database of your choice are as follows:

64.7 Searching Example 3: All Sodium Salts in the Database

The following searching example shows you how to retrieve all records that contain reaction components with sodium salts.

Note: Salts might be represented differently in your database than in this example.

64.7.1 Problem

You want to retrieve all records that contain reactants with sodium salts.

64.7.2 Approach

Draw the sodium counterion. Enter the query into the a box or table cell on the form in ISIS/Base that will hold your reactant (without a reaction arrow). For example, enter a molecule that is a reactant into the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE.

Then conduct a FLEX search in the remote reaction database of your choice, such as the ISISRX demo database. During the search, you are prompted to enter the flexmatch parameters. To retrieve records that contain the parent structures as well as your counterion, you require these settings:

Fragments must match

Salts must match

Note: You can specify that all other settings are OFF (unchecked), but they are not required to be OFF.

64.7.3 Query

Note: Obtain the sodium atom from the PTable instead of the list of atoms that you see with the ISIS atom query feature List.

64.7.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for FLEX, how to/examples.

64.7.5 Results

You retrieve records from the database that are sodium salts of reactants. Some of the reactants that you might retrieve from the remote reaction database of your choice are as follows:


Remote TAUT: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote TAUT Search	65.1

*	Guidelines for Revising the Query	65.2

*	Searching Example 1: Tautomers in the Database	65.3

We recommend that you print this 3-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote TAUT search, click here.

65.1 Definition of a Remote TAUT Search

A remote Tautomer (TAUT) search finds reaction records with reaction components in your remote database that are tautomers of your query. For example:

A tautomer is a group of atoms with any of the following patterns:

Where	Q = O, N, S, Se, or Te

X = C, O, N, S, Se, or Te

Y = C, I, P, As, Sb, Cl, or Br

Tautomer groups must contain the same number of hydrogens in the tautomeric region, with a tolerance limit. The tolerance limit is the sum of the absolute values of charges plus the sum of the number of radicals plus the number of metal bonds. Diradicals count as two radicals.

You can have multiple tautomeric groups in a single molecule. For example:

In addition, any bonds in the tautomeric region can be aromatic. For example:

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

Note: If your query retrieves data that you perceive to be in the wrong place on the form, see your ISIS Administrator. (This might be the result of specifying the same name for multiple database fields on your form or in the Hview.)

65.2 Guidelines for Revising the Query

If your TAUT search retrieved no records or too few records, you might want to:

*	Conduct a TAUT search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Conduct a different search on the same set of records with the same query. For example, you might conduct one of the following searches: Molecule Similarity (MSim), Isomer (ISOMER), and Flexmatch (FLEX). For more information on these searches, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click the search of your choice. You will see the full definition of the search and how to do it.

If your TAUT search retrieved too many records, you might want to:

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

65.3 Searching Example 1: Tautomers in the Database

The following searching example shows you how to retrieve all reactants that are tautomers of your structure query.

65.3.1 Problem

You want to retrieve reactants that are tautomers of the following structure:

65.3.2 Approach

Draw the structure (without a reaction arrow). Enter the query into the a box or table cell on the form in ISIS/Base that will hold your reactant (without a reaction arrow). For example, enter a molecule that is a reactant into the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE. Then conduct a TAUT search in the remote reaction database of your choice, such as the ISISRX demo database.

65.3.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for TAUT, how to/examples.

65.3.4 Results

Some of the reactants that you might retrieve from the remote reaction database of your choice are as follows:


Remote ISOMER: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote ISOMER Search	66.1

*	Guidelines for Revising the Query	66.2

*	Searching Example 1: Isomers in the Database	66.3

We recommend that you print this 3-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote ISOMER search, click here.

66.1 Definition of a Remote ISOMER Search

A remote Isomer (ISOMER) search finds reaction records with reaction components in your remote database that are geometric isomers and stereoisomers of your structure query. For example:

You can retrieve isomers that contain:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

You might not retrieve isomers that contain:

*	Allenes and other cumulenes.

*	Metal complexes.

*	Complex structural stereochemistry, such as hindered biphenyls and other rotationally challenged single bonds and spiral polyphenanthrenes.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

Note: If your query retrieves data that you perceive to be in the wrong place on the form, see your ISIS Administrator. (This might be the result of specifying the same name for multiple database fields on your form or in the Hview.)

66.2 Guidelines for Revising the Query

If your ISOMER search retrieved no records or too few records, you might want to:

*	Conduct an ISOMER search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Conduct a different search on the same set of records with the same query. For example, you might conduct one of the following searches: Molecule Similarity (MSim), Tautomer (TAUT), and Flexmatch (FLEX). For more information on these searches, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click the search of your choice. You will see the full definition of the search and how to do it.

If your ISOMER search retrieved too many records, you might want to:

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

66.3 Searching Example 1: Isomers in the Database

The following searching example shows you how to retrieve all reactants that are isomers of your structure query.

66.3.1 Problem

You want to retrieve reactants that are isomers of the following structure:

66.3.2 Approach

Draw the structure (without a reaction arrow). Enter the query into the a box or table cell on the form in ISIS/Base that will hold your reactant (without a reaction arrow). For example, enter a molecule that is a reactant into the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE. Then conduct an ISOMER search in the remote reaction database of your choice, such as the ISISRX demo database.

66.3.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ISOMER, how to/examples.

66.3.4 Results

Some of the reactants that you might retrieve from the remote reaction database of your choice are as follows:


Remote PARENT: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote PARENT Search	67.1

*	Specifying Stereochemistry	67.2

*	Guidelines for Revising the Query	67.3

*	Searching Example 1: Parent Structures of Salts in the Database	67.4

We recommend that you print this 4-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote PARENT search, click here.

67.1 Definition of a Remote PARENT Search

A remote Parent (PARENT) search finds molecule records in your remote database that are parent molecules of your salt query. For example:

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

Note: If your query retrieves data that you perceive to be in the wrong place on the form, see your ISIS Administrator. (This might be the result of specifying the same name for multiple database fields on your form or in the Hview.)

67.2 Specifying Stereochemistry

You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve molecules with matching stereochemistry. For example:

A PARENT search produces the following results:

Cis or Trans Configurations

Your structure query must contain the exact configuration that you want to retrieve. For example, an PARENT search produces the following results:

Chiral Flags on Reaction Components

In a remote database, you can create a query with a chiral flag on a reaction component with at least one asymmetric center or on a reaction component that is asymmetric to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

67.3 Guidelines for Revising the Query

If your PARENT search retrieved no records or too few records, you might want to:

*	Conduct a PARENT search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Conduct a different search on the same set of records with the same query. For example, you might conduct one of the following searches: Molecule Similarity (MSim), Isomer (ISOMER), Tautomer (TAUT), and Flexmatch (FLEX). For more information on these searches, choose The ISIS/Base Chemical Searches -- and How To Do Them from the Searching with ISIS/Base screen, and then click the search of your choice. You will see the full definition of the search and how to do it.

If your PARENT search retrieved too many records, you might want to:

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

67.4 Searching Example 1: Parent Structures of Salts in the Database

The following searching example shows you how to retrieve the parent structures of your salt query.

Note: Salts might be represented differently in your database than in this example.

67.4.1 Problem

You want to retrieve the starting compounds that are the parent structures of the following salt:

67.4.2 Approach

Draw the charged molecule (without a reaction arrow). Enter the query into the a box or table cell on the form in ISIS/Base that will hold your reactant (without a reaction arrow). For example, enter a molecule that is a reactant into the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE. Then conduct a PARENT search in the remote reaction database of your choice, such as the ISISRX demo database.

67.4.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for PARENT, how to/examples.

67.4.4 Results

You retrieve all reactants that are parent structures of your salt query. One of the reactants that you might retrieve from the remote reaction database of your choice is as follows:


Remote RGROUP: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a remote Rgroup Search	68.1

*	Definition of Aromaticity	68.2

*	Specifying Query Features on Atoms and Bonds in Structures	68.3

*	Specifying Stereochemistry	68.4

*	Guidelines for Revising the Query	68.5

*	Searching Example 1: Basic Rgroup Search	68.6

*	Searching Example 2: Nesting Rgroups	68.7

*	Searching Example 3: Specifying Zero Occurrence for an Rgroup	68.8

*	Searching Example 4: Applying Conditional Logic	68.9

We recommend that you print this 25-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote RGROUP search, click here.

68.1 Definition of a Remote RGROUP Search

A remote Rgroup (RGROUP) search finds reaction records that contain your query as a substructure wholly within a larger structure with additional restrictions. For example, you can:

*	Specify the structural fragments (such as functional groups or atoms) of your choice at specific sites within a reaction component.

*	Exclude structural fragments of your choice at specific sites within a reaction component.

*	Specify that the presence of one structural fragment requires the presence of another (Rgroup conditions).

You can also increase the power of an RGROUP search by the addition of specific restrictions (called query features) on atoms and/or bonds. There are a number of query features available for use.

An example of an Rgroup query is as follows:

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

Note: If your query retrieves data that you perceive to be in the wrong place on the form, see your ISIS Administrator. (This might be the result of specifying the same name for multiple database fields on your form or in the Hview.)

68.1.1 The Root Structure

The root structure contains the portion of the structure that does not vary among the structures retrieved. For example, if you want to find 2, 5-Dihydroxypyridine in which the substituent at position 2 can be COOH, CN, or Ph, and the substituent at position 5 can be OH or CH3, the root structure is 2, 5-Dihydroxypyridine with Rgroups (such as R1 and R2):

Rgroups

On the root structure, Rgroups (R1 through R32) are placeholders that designate where the lists of functional groups and atoms that can attach to the root structure. In the example above, the Rgroup R1 designates that the members of the list R1 (the Rgroup substituents) are allowed at position 5 on the root structure. The Rgroup R2 designates that the members of the list R2 (the Rgroup substituents) are allowed at position 2 on the root structure.

Multiple Rgroups at One Position

You can specify multiple Rgroups at a single site on the root structure. For example:

One Rgroup at Multiple Positions

You can specify a single Rgroup (such as R1) at multiple positions on the root structure. For example:

Note: See Section 68.1.3 to restrict the number of Rgroups that must be occupied in the records retrieved. A reaction component might not have to satisfy all the Rgroup sites on the root structure to be retrieved. For example, the Rgroup condition R1 > 0 specifies that any reaction component in which at least one of the R1 sites is filled by an R1 member will be retrieved. In addition, the Rgroup condition RestH determines whether the unsatisfied sites must be filled with hydrogen atoms or if other reaction component fragments are allowed to be attached if they are not on the list.

Multiple Root Structures in a Single Rgroup Query

If you choose to specify multiple root structures in a single Rgroup query, you must group the root structures before you do a search. To group multiple root structures, select them, and then choose Object > Group.

68.1.2 Rgroup Substituents

Rgroup substituents are the members of the list of Rgroups. You define the Rgroup substituents that you will allow to be found at specified positions in the molecules retrieved. Rgroup substituents can be any structural fragment, including functional groups and single atoms.

In the example below, the Rgroup substituents COOH, CN, or Ph are allowed at position 5 (R1) on the root structure and the Rgroup substituents OH or CH3 are allowed at position 2 (R2) on the root structure:

Attachment Points

An attachment point (marked with an arrow and an asterisk) designates the atom on the Rgroup substituent that is attached to the root structure:

You must designate an attachment point on an Rgroup substituent for each bond that is attached to the substituent.

If an Rgroup is attached to two bonds on the root structure, you must designate two attachment points:

In this example, one bond on the root structure is marked with a single quote that corresponds to the attachment point with a single quote on the Rgroup substituent. The other bond on the root structure is marked with a double quote that corresponds to the attachment point with a double quote on the Rgroup substituent.

Rule: To obtain the correct search results, be certain to assign the attachment point with a single quote on the Rgroup substituent to the corresponding atom on the root structure that contains the lower atom number of the two attachment sites. In the above example, you cannot see the atom numbers on the root structure, which are assigned automatically to the root structure during the drawing process.

Nested Rgroups

A nested Rgroup is an Rgroup that is a placeholder within another Rgroup rather than within the root structure. (You cannot nest an Rgroup any lower than this level.) In the following example, Rgroup R2 is nested within the Rgroup R1:

Nested Rgroups are equivalent to the following structures:

Note: You cannot specify more than one nested occurrence of a single Rgroup substituent (such as R2) within another (unnested) Rgroup substituent (such as R1). For example, you cannot specify that the nested Rgroup R2 be retrieved at both positions 1 and 2 within the R1 Rgroup substituent benzene. Instead, create a query in which a set of nested Rgroups (such as R2 and R3) contains identical substituents. Then specify the occurrence of each nested Rgroup only one time. For example, specify that the nested Rgroup R2 be retrieved at position 1 and that the nested Rgroup R3 be retrieved at position 2 within the R1 Rgroup substituent benzene.

68.1.3 Rgroup Conditions

You can apply restrictions to each Rgroup in your query after you assemble all the Rgroups. The set of restrictions is called the Rgroup conditions.

If you do not apply Rgroup conditions, ISIS assigns the default conditions: Occurrence > 0 and RestH off for each Rgroup.

Occurrence

With the Rgroup condition Occurrence, you can specify the number of Rgroup sites that must be occupied in the records retrieved. For example, the occurrence designation R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved. Type one of the following values in the Occurrence range text box:

Value	Explanation

0	All members of the Rgroup are excluded from the Rgroup site (such as R1). To allow any other Rgroup substituent at the Rgroup site, set RestH to off.

> 0	At least one Rgroup must be satisfied. If RestH is off, any other substituent can attach to unsatisfied sites. If RestH is on, unsatisfied sites must be filled solely by hydrogens.

n	Exactly n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

< n	Less than n number of sites (including zero) must be satisfied. RestH controls substitution at unsatisfied sites.

m - n	Any number of sites falling within the range of m to n number of sites must be satisfied. RestH controls substitution at unsatisfied sites.

m,n,...	Any combination of the above expressions, separated by commas. For example: 1, 3-5, 9, >12.

For example, the Rgroup condition R1 > 0 specifies that an Rgroup substituent from the R1 list occupies at least one R1 site on the root structure in the records retrieved.

In another example, the Rgroup condition R1 > 0 and R2 > 0 specifies that an Rgroup substituent from the R1 list AND an Rgroup substituent from the R2 list must occupy at least one site on the root structure in the records retrieved.

Finally, the Rgroup conditions R1 = 1, 3-5, 9, >12 specify that either 1, 3, 4, 5, 9, or more than 12 sites must be satisfied:

RestH

With the Rgroup condition RestH, you can specify whether you will allow non-hydrogen substituents other than your defined Rgroup substituents to be attached to an Rgroup site.

An unsatisfied Rgroup site is an Rgroup site on the root structure that does not have an Rgroup member attached: If RestH is off, any functional group or atom may be attached at unsatisfied Rgroup sites on the root structure. If RestH is on, solely hydrogens are allowed to be attached at unsatisfied Rgroup sites on the root structure.

If/Then

With the Rgroup condition If/then, you can specify whether the presence of one Rgroup is dependent on the presence of another Rgroup.

For example, If R1 then R2 specifies that if the conditions for R1 are satisfied, then the conditions for R2 must also be satisfied. (If the conditions for R1 are not satisfied, then the conditions for R2 are ignored.) The If/then condition implies that a molecule may be retrieved even though R1 is not satisfied.

In the following query, R1 contains a nitro group and a sulfonic acid group. R2 contains a chlorine atom. The condition If R1 then R2 specifies that if a nitro group or a sulfonic acid group is attached at R1 on the root structure, then a chlorine must also be attached at R2. However, if the R1 site on the root structure does not have either the nitro or the sulfonic acid group (R1 is unsatisfied), then R2 can have any substituent (R2 is ignored):

68.2 Definition of Aromaticity

For remote databases: ISIS interprets the following ring systems as aromatic:

*	Five-membered rings such as the structures shown below:

For example:

*	Six-membered rings that can be drawn as alternating double and single bonds:

*	Perimeter bonds in azulenes:

Note: The bonds of six-membered aromatic ring systems and the perimeter bonds of azulenes are stored as aromatic bonds in the database. The bonds of five-membered aromatic rings, however, are stored as single and double bonds and interpreted as aromatic during a search. The differences between five-membered rings and other types of aromatic rings can cause different search results for five- and six-membered rings/azulenes when you use the following bonds in queries: Single, Double, and Single/Double query bonds. For more information on the Single/Double query bond, see Section 68.3.7.

68.3 Specifying Query Features on Atoms and Bonds in Structures

A query feature on an atom and/or a bond in a reaction component is a restriction that specifies the retrieval of certain types of reaction records from an ISIS/Base database.

If you do not use query features, the records retrieved contain solely your exact substructure query embedded wholly within them. For example:

68.3.1 Allowing or Excluding Specific Atoms

Use atom query features to allow or exclude the atoms of your choice.

Atom Query Feature: Any Atom (A)

Specifies any atom except hydrogen, and requires that there be a substituent at A:

Notes: To retrieve all molecules that have a chiral flag (the absolute stereoconfigurations), create the following query: A[chiral]. To retrieve all molecules that contain a valence of 14, create the following query: A[XIV].

Atom Query Feature: Heteroatoms (Q)

Specifies any atom except hydrogen or carbon:

Atom Query Feature: List

Specifies any atom on a list of your choice. In the following example, only the atoms C, N, and O are allowed at the position specified within the list brackets:

Atom Query Feature: Not List

Specifies any atom except those on a list of your choice and hydrogen atoms. In the following example, only the atoms C, N, O, and H ARE NOT allowed at the position specified within the list brackets:

Note: If you specify Not[C], you retrieve both no carbons and no hydrogens.

68.3.2 Prohibiting Hydrogens on an Atom

Use an atom query feature to specify the prohibition of the attachment of hydrogens, whether they are implicit (implied but not present) or explicit (present).

Atom Query Feature:H0

Prohibits the attachment of hydrogens. For example:

68.3.3 Allowing an Unsaturated Atom

Use an atom query feature to specify that an atom is attached to at least one multiple bond (double, triple, or aromatic).

Atom Query Feature: Unsaturated Atom (u)

Specifies that the atom of your choice is attached to at least one multiple bond (double, triple, or aromatic). For example, the following query specifies both an unsaturated atom (u) and single or double bonds (the double dashed lines).

68.3.4 Allowing a Specific Number of Attachments (Substituents)

Use explicit hydrogens (those hydrogens that are present on the structure, and not implied) to block non-hydrogen attachments on atoms or use atom query features to specify the number of non-hydrogen attachments on atoms. A non-hydrogen attachment is also called a substituent.

Explicit Hydrogens

To block non-hydrogen attachments on atoms, draw hydrogens explicitly. For example:

Atom Query Feature: Substitution Count of Zero, s0

Specifies that the records retrieved have no non-hydrogen attachments at the specified position. All open valences at that position have solely implicit hydrogen atoms. This query feature implies the retrieval of a single atom with attached hydrogens (if any).

Atom Query Feature: Substitution Count of One, s1

Specifies that the records retrieved have solely one non-hydrogen attachment of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Two, s2

Specifies that the records retrieved have solely two non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Three, s3

Specifies that the records retrieved have solely three non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Four, s4

Specifies that the records retrieved have solely four non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of Five, s5

Specifies that the records retrieved have solely five non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count of at Least Six, s6

Specifies that the records retrieved have at least six non-hydrogen attachments of any bond type at the specified position. For example:

Atom Query Feature: Substitution Count as Drawn, s*

Specifies that the records retrieved have solely those non-hydrogen attachments that you see at the specified position. For example:

68.3.5 Allowing a Specific Number of Ring Bond Attachments

Use atom query features to specify the number of ring bond attachments.

Atom Query Feature: Ring Bond Count of Zero, r0

Specifies that the records retrieved have no ring bond attachments at the specified position. All atoms with this mark are not part of a ring. For example:

Atom Query Feature: Ring Bond Count of Two, r2

Specifies that the records retrieved have solely two ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of Three, r3

Specifies that the records retrieved have solely three ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count of at Least Four, r4

Specifies that the records retrieved have at least four ring bond attachments at the specified position. For example:

Atom Query Feature: Ring Bond Count as Drawn, r*

Specifies that the records retrieved have solely those ring bond attachments that you see at the specified position. For example:

68.3.6 Allowing Additional Atoms and/or Bonds in a Chain or a Ring

Use a query feature that is for either atoms or bonds to specify the addition of atoms and/or bonds in a chain or a ring.

Atom or Bond Query Feature: Link Node

Use a link node to specify the addition of variable numbers repeating units (atoms and/or bonds) to a ring or chain. A repeating unit must be attached to two adjacent bonds. For example, you can specify between one and three repeating carbon atoms in an existing 5-membered ring with the link node [L1-3]:

Or, you can specify between one and three repeating carbon atoms in an existing 3-carbon chain with the link node [L1-3]:

68.3.7 Allowing a Specific Bond Type

Use bond query features to specify a specific bond type.

Bond Query Feature: Any Bond

Specifies any bond type, single, double, triple, or aromatic, at that position:

Bond Query Feature: Aromatic Bond

Specifies solely an aromatic bond at that position:

Note: An aromatic query bond hits any bond in all types of aromatic rings: 6-membered ring bonds, 5-membered ring bonds, and azulene perimeter bonds. For more information on the structures that ISIS interprets as aromatic, see Section 68.2.

Bond Query Feature: Single/Double Bond

Specifies either a single or a double bond at that position:

Note: A Single/Double query bond does not hit bonds in 6-membered aromatic rings, or perimeter bonds of azulenes, because bonds in these structures are stored in the database as aromatic bonds. However, a Single/Double query bond does hit bonds in 5-membered rings that ISIS interprets as aromatic. For more information on the structures that ISIS interprets as aromatic, see Section 68.2.

Bond Query Feature: Single/Aromatic Bond

Specifies either a single or an aromatic bond at that position:

Bond Query Feature: Double/Aromatic Bond

Specifies either a double or an aromatic bond at that position:

68.3.8 Allowing Solely Chain Bonds

Use a bond query feature to specify that the bond is part of a chain.

Bond Query Feature: Ch

Specifies the bond is part of an acyclic structure. For example:

68.3.9 Allowing Solely Ring Bonds

Use a bond query feature to specify that the bond is part of a ring.

Bond Query Feature: Rn

Specifies that the bond is part of a cyclic structure. For example:

(The dashed lines indicate the ISIS bond query S/A, which specifies that the retrieved molecules contain either single or aromatic bonds at the specified positions.)

68.4 Specifying Stereochemistry

For remote databases: You can specify stereochemistry in the following ways:

Up and Down Bonds

An Up bond ( [image]) or a Down bond ( [image]) on the asymmetric tetrahedral center of atoms C, N, O, P, S, or Si allows you to retrieve reactions with matching stereochemistry on the reaction components. For example:

An RGROUP search produces the following results for each reaction component:

An Either bond ( [image]) that is attached to any of these atoms allows you to retrieve records from the database that contain Up and Down bonds (unspecified) at the specified position.

Stereo Boxes on Cis or Trans Configurations

Stereo boxes on asymmetric double bonds that are attached to atoms C, N, O, P, S, or Si allow you to retrieve reactions with matching cis or trans stereochemistry on the reaction components. (Without the stereo boxes, you retrieve both the cis and trans configuration.) For example:

The cis configuration is not retrieved:

An RGROUP search produces the following results for each reaction component:

Chiral Flags on Reaction Components

In a remote database, you can create a query with a chiral flag on a reaction component with at least one asymmetric center or on a reaction component that is asymmetric to retrieve solely the absolute stereoconfiguration. The chiral flag eliminates the relative stereoconfigurations. (In a local database, the chiral flag is ignored.) For example, in a remote database:

You can use queries with:

*	Geometric stereochemistry for the following atoms that are separated by a double bond: C, O, S (sulfoxide), Si, and trivalent N and P.

*	Tetrahedral stereochemistry for the following atoms: C, N, O, S (sulfate and sulfoxide), P, Si, and pentavalent N and P (3 or 4 attachments with 1 double bond).

Other types of stereochemistry are ignored. For example: Allenes and other cumulenes, metal complexes, and rotationally hindered single bonds (such as sterically hindered biphenyls) and spiral polyphenanthrenes.

68.5 Guidelines for Revising the Query

If your RGROUP search retrieved no records or too few records, you might want to:

*	Conduct an RGROUP search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the structural constraints in your query more general, and then search the same set of records. For example, you can remove any explicit bonds or atoms that are not required, change bond types to increase bond variation, use the atom query features List, Q, or A to increase atom variation, remove substituent limits, or remove stereochemical requirements.

*	Make the Rgroup conditions in your query more general, and then search the same set of records. For example, you can decrease the number of Rgroup sites that must be satisfied or allow unsatisfied Rgroup sites to be filled with non-Rgroup substituents (instead of with hydrogens solely).

If your RGROUP search retrieved too many records, you might want to:

*	Refine the structural constraints of your query, and then search the same set of records. For example, you can limit substitution at specific positions, change bond types to force the retrieval of solely rings or solely chains, increase the number of functional groups, restrict atom or bond variation with explicit atoms or bonds, or add an additional substructure to the query so that it is a multiple-fragment query.

*	Make the Rgroup conditions in your query more specific, and then search the same set of records. For example, you can increase the number of Rgroup sites that must be satisfied or restrict unsatisfied Rgroup sites to be filled solely with hydrogens.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

68.6 Searching Example 1: Basic RGROUP Search

The major advantage of an RGROUP search over a substructure (SSS) search is the ability to conduct a single search with a query that contains multiple structural variations. In an SSS search, you would have to conduct separate searches (with a different query for each search) to obtain the same results.

68.6.1 Problem

You want to find all reactants that are nitrogen-containing heteroaryl phenyl ethers.

68.6.2 Approach

Draw phenol as the root structure. Attach the Rgroup R1 to the oxygen, and then define the Rgroup substituents of R1 as all possible nitrogen-containing heteroaryl groups. To create the ether link, define a carbon atom on each heteroaryl group as the attachment point. Define the Rgroup conditions.

Enter the query into the a box or table cell on the form in ISIS/Base that will hold your reactant (without a reaction arrow). For example, enter a molecule that is a reactant into the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE.

Conduct an RGROUP search in the remote reaction database of your choice, such as the ISISRX demo database.

68.6.5 Query

The single N atom in each ring guarantees that the heteroaryl group contains at least one nitrogen. The three rings with the nitrogen at different positions are sufficient to define all possible nitrogen-containing heteroaryls.

The atom query feature A specifies any atom except hydrogen in the rings.

The Rgroup query features are as follows: The Rgroup R1 contains three Rgroup substituents. Each Rgroup substituent is a unique ring structure with an attachment point that is a carbon atom. This carbon atom replaces the R1 label on the root structure to form ether in the records retrieved.

68.6.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for RGROUP, how to/examples.

68.6.5 Results

Some of the reactants that you might retrieve from the remote reaction database of your choice are as follows:

68.7 Searching Example 2: Nesting Rgroups

This example shows you how to nest an Rgroup with an Rgroup substituent. You can only nest to one level.

68.7.1 Problem

You want to retrieve all reactants that are either 1-, 2-, and 3-carbon straight-chain alkyl esters or carboxylic acid anhydrides of benzoic, benzenesulfonic, and benzenephosphonic acids.

68.7.2 Approach

Draw benzene as the root structure. Attach the Rgroup R1 to the ring by a single bond, and then define the Rgroup substituents of R1 as the carboxylic, sulfonic, and phosphonic acid groups. Attach the nested Rgroup R2 to the single-bonded oxygen, and then define the Rgroup substituents of R2 as the 1-, 2-, and 3-carbon chains (to form esters) and as a carbonyl (to form the anhydride). Define the Rgroup conditions.

Enter the query into the a box or table cell on the form in ISIS/Base that will hold your reactant (without a reaction arrow). For example, enter a molecule that is a reactant into the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE.

Conduct an RGROUP search in the remote reaction database of your choice, such as the ISISRX demo database.

68.7.3 Query

The atom query feature s* on each atom specifies that solely those non-hydrogen attachments that you see are allowed at the specified positions.

The Rgroup query features are as follows: The Rgroup R1 contains three Rgroup substituents. Each Rgroup substituent in R1 is a unique structure with a nested Rgroup (R2) and contains a unique attachment point. The Rgroup R2 contains four Rgroup substituents. Each Rgroup substituent in R2 is a unique structure and contains a unique attachment point.

The four members of R2 may attach to the three R1 acids and form various combinations of alkyl esters and carboxylic acid anhydrides. For example, the members of R2 that attach to the R1 substituent carboxylic acid form the following functional groups:

68.7.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for RGROUP, how to/examples.

68.7.5 Results

Some of the reactants that you might retrieve from the remote reaction database of your choice are as follows:

68.8 Searching Example 3: Specifying Zero Occurrence for an Rgroup

This example shows you how to exclude all the members of the Rgroup from the Rgroup R1 on the root structure. You exclude Rgroup members with the Rgroup condition that specifies a zero occurrence.

68.8.1 Problem

You want to retrieve all reactants that are alkyl diamines of up to ten atoms in length, that are substituted solely at one nitrogen, and that contain heteroaryl groups. You also want to exclude any aniline derivatives that involve the substituted nitrogen.

68.8.2 Approach

Draw the minimum structure for an alkyl diamine that can expand up to ten atoms in length as the root structure. On one nitrogen, prohibit substitution. On the other nitrogen, attach two Rgroups, R1 and R2. Define R1 as a phenyl group and R2 as a heteroaryl group. When R1 attaches to the root structure, an aniline derivative forms. Exclude the formation of aniline derivatives with the Rgroup condition zero occurrence, or R1 = 0. Ensure heteroaryl substitution with the Rgroup condition R2 > 0. In addition, ensure that unsatisfied sites must be filled solely by hydrogens with the Rgroup condition RestH on (since nitrogen has a valence of three or five).

Enter the query into the a box or table cell on the form in ISIS/Base that will hold your reactant (without a reaction arrow). For example, enter a molecule that is a reactant into the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE.

Conduct an RGROUP search in the remote reaction database of your choice, such as the ISISRX demo database.

68.8.3 Query

There are two atom query features: A on the Rgroup substituent in R2 specifies any atom except hydrogen. The s* specifies that solely those non-hydrogen attachments that you see are allowed at the specified position.

The bond query feature Ch allows solely an acyclic attachment (alkyl chain bonds) on the root structure.

The atom and/or bond query feature link node [L1-8] allows the 2-membered chain to expand to a 10-membered chain.

The Rgroup query features are as follows: The Rgroups R1 and R2 each contain one Rgroup substituent. Each Rgroup substituent is a unique structure and contains a unique attachment point. There is a restriction that R1 is not among the structures attached to the root structure in the molecules retrieved: Rgroup condition, R1: 0. Because benzene rings are eliminated by the zero occurrence of the R1 group, heteroaryl substitution is required.

68.8.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for RGROUP, how to/examples.

68.8.5 Results

Some of the reactants that you might retrieve from the remote reaction database of your choice are as follows:

68.9 Searching Example 4: Applying Conditional Logic

This example shows you how to use conditional, if/then logic to retrieve the correct set of reaction components and to eliminate unwanted reaction components in a single search.

68.9.1 Problem

You want to retrieve all reactants that are (2, 3, 5, 6)-nitro-, sulfonic acid-, and carboxylic acid-substituted phenols, but you do not want to retrieve nitro-cresols or nitro-4-ethylphenols.

68.9.2 Approach

Draw phenol as the root structure. To define the (2, 3, 5, 6)-nitro-, sulfonic acid-, and carboxylic acid-substituted phenols, attach R3 to positions 2, 3, 5, and 6 on the ring and specify the Rgroup condition R3 > 0.

Nitro-cresols and nitro-4-ethylphenols have nitro groups at positions 2, 3, 5, or 6 and a methyl or an ethyl group at position 4. For example:

To define the nitro-cresols or nitro-4-ethylphenols, attach R1 to position 4 and attach R2 to positions 2, 3, 5, and 6 on the ring. Then specify the Rgroup conditions R1 > 0, If R1 then R2, R2 = 0, and R3 > 0. The statement If R1 then R2 specifies that if R1 is satisfied (a methyl or an ethyl is at position 4), then R2 must also be satisfied (no nitro groups are allowed at positions 2, 3, 5, or 6).

Enter the query into the a box or table cell on the form in ISIS/Base that will hold your reactant (without a reaction arrow). For example, enter a molecule that is a reactant into the Reactant Structure box that connects to the database field RXN>reactant_link>MOL>MOLSTRUCTURE.

Conduct an RGROUP search in the remote reaction database of your choice, such as the ISISRX demo database.

68.9.3 Query

The atom query feature s* specifies that solely those non-hydrogen attachments that you see are allowed at the specified position. This feature prohibits any non-hydrogen substitutions on the methyl and ethyl groups.

The Rgroup query features are as follows: The Rgroups R1, R2, and R3 contain two, one, and three Rgroup substituents, respectively. Each Rgroup substituent is a unique structure and contains a unique attachment point. The Rgroup conditions are R1 > 0, If R1 then R2, R2 = 0, and R3 > 0.

68.9.4 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for RGROUP, how to/examples.

68.9.5 Results

Some of the reactants that you might retrieve from the remote reaction database of your choice are as follows:


Remote ID: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote ID Search	56.1

*	Guidelines for Revising the Query	56.2

*	Searching Example 1: A Record With a Text and Numeric ID Number	56.3

*	Searching Example 2: Records With Text and Numeric ID Numbers	56.4

*	Searching Example 3: A Record With Solely a Numeric ID Number	56.5

*	Searching Example 4: Records With Solely Numeric ID Numbers	56.6

We recommend that you print this 5-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote ID search, click here.

56.1 Definition of a Remote ID Search

A remote ID search finds the records in your remote database that contain the corporate identification numbers that you specify in your query. To do this type of search, you need:

*	An ID field in your database. This is a field in the database that contains corporate identification numbers for the records in your database.

*	A box or table in a form that is linked to the ID field. A form is the set of boxes and/or tables that you use to hold your query and to view the results of a search. (You can enter a maximum of 25 ID numbers into individual table cells on a form.)

If you do not have these items, see your ISIS Administrator.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

56.1.1 Specifying ID Queries

An ID query is a phrase in a box or column on the form that specifies the retrieval of specific ID numbers. For example, to find structures with an ID that is equal to the ID number CL011250, enter the ID query LIKE "CL011250".

Each phrase in an ID query contains:

*	A search operator that specifies the type of search. For example, use the search operator = (an equal sign) with numeric ID numbers or the search operator LIKE in place of = with ID numbers that contain text.

*	The text or numeric target value that you want to find (such as the ID number CL011250). A target value can contain wildcards. A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. For example, you can specify the query LIKE "%CL%" (instead of the query LIKE "CL011250"). The wildcard _ is a placeholder for solely one unspecified character. For example, you can specify the query LIKE "_L011250" (instead of the query LIKE "CL011250"). Target values that contain text or wildcards require double quotation marks.

The Search Operators

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Use LIKE with text enclosed in double quotation marks. Enter your query as follows: Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. (To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice.)

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks (such as BETWEEN "XR11" "XZ15").

Use EXISTS to retrieve all records in the database that contain data in a specific database field.

Note: You can only use this search operator for database fields that do not give you an error message.

56.2 Guidelines for Revising the Query

If your ID search retrieved no records, you might want to check that your search domain is set to the entire database.

56.3 Searching Example 1: A Record With a Text and Numeric ID Number

This searching example shows you how to find a specific record whose ID number has both text and numbers. Any ID query that contains text (or wildcards) requires the search operator LIKE and the ID number to be enclosed in double quotation marks.

56.3.1 Problem

You want to retrieve the record with the ID number MUSE000000001.

56.3.2 Approach

Enter the ID query LIKE "MUSE000000001" into the ID box or table cell on the form that connects to the ID database field. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains text and numbers. Enter the search operator LIKE. Enter a space, and then enter the target value MUSE000000001 in double quotation marks. (You can enter the text in either upper- or lower-case characters.)

Conduct an ID search in the remote molecule demo database ISISMX.

56.3.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

56.3.4 Results

You retrieve solely the record with the ID number MUSE000000001.

56.4 Searching Example 2: Records With a Text and Numeric ID Number

This searching example shows you how to find a specific set of records whose ID numbers have both text and numbers. Any ID query that contains text (or wildcards) requires the search operator LIKE and all ID numbers to be enclosed in double quotation marks.

56.4.1 Problem

You want to retrieve the set of records with ID numbers that are between (and including) MUSE000000001 and MUSE000000009.

56.4.2 Approach

Enter the ID query BETWEEN "MUSE000000001" "MUSE000000009" into the ID box or table cell on the form that connects to the ID database field. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains text and numbers. Enter the search operator BETWEEN. Enter a space. Enter the target value MUSE000000001 in double quotation marks. (You can enter the text in either upper- or lower-case characters.) Enter a space, and then enter the target value MUSE000000009 in double quotation marks.

Conduct an ID search in the remote molecule demo database ISISMX.

56.4.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

56.4.4 Results

You retrieve solely the specific set of records with ID numbers that fall between (and that include) MUSE000000001 and MUSE000000009.

56.5 Searching Example 3: A Record With Solely a Numeric ID Number

This searching example shows you how to find a specific record whose ID number has solely numbers. Any ID query that contains solely numbers uses the search operator = (the equal sign).

56.5.1 Problem

You want to retrieve the record with the ID number 95.

56.5.2 Approach

Enter the ID query = 95 into the ID box or table cell on the form that connects to the ID database field. You can omit the single space between the equal sign and the number. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains solely a number. Enter the search operator = (an equal sign). Enter a space, and then enter the target value 95.

Conduct an ID search in the remote molecule demo database ISISMX.

56.5.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

56.5.4 Results

You retrieve solely the record with the ID number 95.

56.6 Searching Example 4: Records Solely Numeric ID Numbers

This searching example shows you how to find a specific set of records whose ID numbers have solely numbers. Any ID query that contains solely numbers uses the search operator = (the equal sign).

56.6.1 Problem

You want to retrieve the set of records with ID numbers that are between (and including) 95 and 100.

56.6.2 Approach

Enter the ID query BETWEEN 95 100 into the ID box or table cell on the form that connects to the ID database field. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains solely numbers. Enter the search operator BETWEEN. Enter a space. Enter the target value 95. Enter a space, and then enter the target value 100.

Conduct an ID search in the remote molecule demo database ISISMX.

56.6.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

56.6.4 Results

You retrieve solely the specific set of records with ID numbers that fall between (and that include) 95 and 100.


Remote FMLA: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote FMLA Search	57.1

*	Guidelines for Revising the Query	57.2

*	Searching Example 1: Records That Match Your Exact Formula Query	57.3

*	Searching Example 2: Records That Match Your Subformula Query	57.4

We recommend that you print this 4-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote FMLA search, click here.

57.1 Definition of a Remote FMLA Search

A remote formula (FMLA) search finds molecule records that contain the formula that you specify in your query. Your formula query can be:

*	An exact formula and no other atoms, such as C17 H19 N O3

*	A subformula and any additional atoms, such as C5 H10

*	A subformula and any additional atoms except a specific atom, such as C5 H10 N0, where N0 represents zero nitrogens.

Note1: If you enter a single atom within your query but you do not include spaces, you must also enter a value of 1 for the single atom. For example:  and [image] are equivalent.

Note2: To specify more than one formula in a single query, or to combine a formula search with a search for other data, use Search By Form (SBF).

Use an exact formula query to find records that contain the exact formula in your query. Your exact formula query must include all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required. For example: To find phenol, enter C6 H6 O. To find phenolphthalein sodium, enter C20 H12 Na2 O4. (If you enter a single atom within your query but you do not include spaces, you must also enter a value of 1. For example: C6H5N102.)

Use a subformula query to find records that contain solely specific atoms. Your subformula query can include a range of atom counts and typically excludes the hydrogens. You can use a single space to separate atoms, and capital letters are not required. For example, to find molecules that are sodium salts, enter Na. To find molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms, enter: C12 Br(1-2) S2. To find molecules that contain six carbons, six hydrogens, and any number of other atom types, enter: C6 H6. (If you enter a single atom within your query but you do not include spaces, you must also enter a value of 1. For example: C12Br1S2.)

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

57.1.1 Specifying Multiple Formula Queries

To specify multiple formulas in a single query, you must conduct a different type of search. For more information, choose Help > Search, and search for either SBF, how to/examples or QB, how to/examples.

57.2 Guidelines for Revising the Query

If your FMLA search retrieved no records or too few records, you might want to:

*	Conduct a FMLA search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the formula more general, and then search the same set of records.

If your FMLA search retrieved too many records, you might want to:

*	Make the formula more restrictive, and then search the same set of records.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

57.3 Searching Example 1: Records That Match Your Exact Formula Query

This searching example shows you how to find molecules that match your exact formula query exactly. Always enter all atoms with a numeric value, such as C6 H11 N1 O2.

57.3.1 Problem

You want to retrieve all molecules with the formula C6 H6 O.

57.3.2 Approach

Conduct a FMLA search in the remote molecule database of your choice, such as the ISISMX demo database. In the Formula text box, enter the exact formula query:

C6 H6 O1

All atoms must contain a numeric value. You can enter the text in either upper- or lower-case characters and either use single spaces between any characters or omit any spaces.

57.3.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for FMLA, how to/examples.

57.3.4 Results

You retrieve solely those records with the exact formula C6 H6 O. For example:

57.4 Searching Example 2: Records That Match Your Subformula Query

This searching example shows you how to find molecules that match your subformula query.  Always enter all atoms with a numeric value, such as C6 H11 N1 O2.

57.4.1 Problem

You want to retrieve all molecules that contain solely twelve carbon atoms and either one or two bromine atoms.

57.4.2 Approach

Conduct a FMLA search in the remote molecule database of your choice, such as the ISISMX demo database. In the Formula text box, enter the subformula query:

C12 Br(1-2)

All atoms must contain a numeric value. You can enter the text in either upper- or lower-case characters and either use single spaces between any characters or omit any spaces.

57.4.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for FMLA, how to/examples.

57.4.4 Results

You retrieve solely those records with the subformula C12 Br(1-2). For example:


Local FMLA: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Local FMLA Search	58.1

*	Guidelines for Revising the Query	58.2

*	Searching Example 1: Records That Match Your Exact Formula Query	58.3

*	Searching Example 2: Records That Match Your Subformula Query	58.4

We recommend that you print this 4-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a local FMLA search, click here.

58.1 Definition of a Local FMLA Search

A Formula (FMLA) search finds molecule records that contain the formula that you specify in your query. Your formula query can be:

*	An exact formula and no other atoms, such as C17 H19 N O3, or

*	A subformula and any additional atoms, such as C5 H10, or

*	A subformula and any additional atoms except a specific atom, such as C5 H10 N0, where N0 represents zero nitrogens.

Note1: If you enter a single atom within your query but you do not include spaces, you must also enter a value of 1 for the single atom. For example:  and [image] are equivalent.

Note2: To specify more than one formula in a single query, or to combine a formula search with a search for other data, use Search By Form (SBF).

Use an exact formula query to find records that contain the exact formula in your query. Your exact formula query must include all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required. For example: To find phenol, enter C6 H6 O. To find phenolphthalein sodium, enter C20 H12 Na2 O4. (If you enter a single atom within your query but you do not include spaces, you must also enter a value of 1. For example: C6H5N102.)

Use a subformula query to find records that contain solely specific atoms. Your subformula query can include a range of atom counts and typically excludes the hydrogens. You can use a single space to separate atoms, and capital letters are not required. For example, to find molecules that are sodium salts, enter Na. To find molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms, enter: C12 Br(1-2) S2. To find molecules that contain six carbons, six hydrogens, and any number of other atom types, enter: C6 H6. (If you enter a single atom within your query but you do not include spaces, you must also enter a value of 1. For example: C12Br1S2.)

A local search is a search over a database that typically exists on your hard disk. To do a local search on your hard disk, you do not need to input network information.

Note: To do a local search that is accessed from a shared network, you need to input network information.

58.1.1 Specifying Multiple Formula Queries

To specify multiple formulas in a single query, you must conduct a different type of search. For more information, choose Help > Search, and search for either SBF, how to/examples or QB, how to/examples.

58.2 Guidelines for Revising the Query

If your FMLA search retrieved no records or too few records, you might want to:

*	Conduct a FMLA search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the formula more general, and then search the same set of records.

If your FMLA search retrieved too many records, you might want to:

*	Make the formula more restrictive, and then search the same set of records.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

58.3 Searching Example 1: Records That Match Your Exact Formula Query

This searching example shows you how to find molecules that match your exact formula query exactly. Always enter all atoms with a numeric value, such as C6 H11 N1 O2.

58.3.1 Problem

You want to retrieve all molecules with the formula C6 H6 O.

58.3.2 Approach

Conduct a FMLA search in the local molecule database of your choice, such as the LOCALMX demo database. In the Formula text box, enter the exact formula query:

C6 H6 O1

All atoms must contain a numeric value. You can enter the text in either upper- or lower-case characters and either use single spaces between any characters or omit any spaces.

58.3.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for FMLA, how to/examples.

58.3.4 Results

You retrieve solely those records with the exact formula C6 H6 O. For example:

58.4 Searching Example 2: Records That Match Your Subformula Query

This searching example shows you how to find molecules that match your subformula query. Always enter all atoms with a numeric value, such as C6 H11 N1 O2.

58.4.1 Problem

You want to retrieve all molecules that contain solely twelve carbon atoms and either one or two bromine atoms.

58.4.2 Approach

Conduct a FMLA search in the local molecule database of your choice, such as the LOCALMX demo database. In the Formula text box, enter the subformula query:

C12 Br(1-2)

All atoms must contain a numeric value. You can enter the text in either upper- or lower-case characters and either use single spaces between any characters or omit any spaces.

58.4.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for FMLA, how to/examples.

58.4.4 Results

You retrieve solely those records with the subformula C12 Br(1-2). For example:


Remote FMLA: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote FMLA Search	69.1

*	Guidelines for Revising the Query	69.2

*	Searching Example 1: Records That Match Your Exact Formula Query	69.3

*	Searching Example 2: Records That Match Your Subformula Query	69.4

We recommend that you print this 4-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote FMLA search, click here.

69.1 Definition of a Remote FMLA Search

A remote Formula (FMLA) search finds reaction records in your remote database that contain the formula for any reaction component that you specify in your query. Your formula query can be:

*	An exact formula and no other atoms, such as C17 H19 N O3

*	A subformula and any additional atoms, such as C5 H10

*	A subformula and any additional atoms except a specific atom, such as C5 H10 N0, where N0 represents zero nitrogens.

Note1: If you enter a single atom within your query but you do not include spaces, you must also enter a value of 1 for the single atom. For example:  and [image] are equivalent.

Note2: To specify more than one formula in a single query, or to combine a formula search with a search for other data, use Search By Form (SBF).

Use an exact formula query to find records that contain the exact formula in your query. Your exact formula query must include all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required. For example: To find phenol, enter C6 H6 O. To find phenolphthalein sodium, enter C20 H12 Na2 O4. (If you enter a single atom within your query but you do not include spaces, you must also enter a value of 1. For example: C6H5N102.)

Use a subformula query to find records that contain solely specific atoms. Your subformula query can include a range of atom counts and typically excludes the hydrogens. You can use a single space to separate atoms, and capital letters are not required. For example, to find molecules that are sodium salts, enter Na. To find molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms, enter: C12 Br(1-2) S2. To find molecules that contain six carbons, six hydrogens, and any number of other atom types, enter: C6 H6. (If you enter a single atom within your query but you do not include spaces, you must also enter a value of 1. For example: C12Br1S2.)

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

Note: If your query retrieves data that you perceive to be in the wrong place on the form, see your ISIS Administrator. (This might be the result of specifying the same name for multiple database fields on your form or in the Hview.)

69.1.1 Specifying Multiple Formula Queries

To specify multiple formulas in a single query, you must conduct a different type of search. For more information, choose Help > Search, and search for either SBF, how to/examples or QB, how to/examples.

69.2 Guidelines for Revising the Query

If your FMLA search retrieved no records or too few records, you might want to:

*	Conduct a FMLA search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the formula more general, and then search the same set of records.

If your FMLA search retrieved too many records, you might want to:

*	Make the formula more restrictive, and then search the same set of records.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

69.3 Searching Example 1: Records That Match Your Exact Formula Query

This searching example shows you how to find reactants that match your exact formula query exactly. Always enter all atoms with a numeric value, such as C6 H11 N1 O2.

69.3.1 Problem

You want to retrieve all reactants with the formula C6 H6 O.

69.3.2 Approach

Conduct a FMLA search in the remote reaction database of your choice, such as the ISISRX demo database. In the Formula text box, enter the exact formula query:

C6 H6 O1

All atoms must contain a numeric value. You can enter the text in either upper- or lower-case characters and either use single spaces between any characters or omit any spaces.

69.3.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for FMLA, how to/examples.

69.3.4 Results

You retrieve solely those records with the exact formula C6 H6 O. Examples of reactant records that you might retrieve from your database are as follows:

69.4 Searching Example 2: Records That Match Your Subformula Query

This searching example shows you how to find reactants that match your subformula query. Always enter all atoms with a numeric value, such as C6 H11 N1 O2.

69.4.1 Problem

You want to retrieve all molecules that contain solely twelve carbon atoms and either one or two bromine atoms.

69.4.2 Approach

Conduct a FMLA search in the remote reaction database of your choice, such as the ISISRX demo database. In the Formula text box, enter the subformula query:

C12 Br(1-2)

All atoms must contain a numeric value. You can enter the text in either upper- or lower-case characters and either use single spaces between any characters or omit any spaces.

69.4.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for FMLA, how to/examples.

69.4.4 Results

You retrieve solely those records with the subformula C12 Br(1-2). Examples of reactant records that you might retrieve from your database are as follows:


Local FMLA: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Local FMLA Search	70.1

*	Guidelines for Revising the Query	70.2

*	Searching Example 1: Records That Match Your Exact Formula Query	70.3

*	Searching Example 2: Records That Match Your Subformula Query	70.4

We recommend that you print this 4-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a local FMLA search, click here.

70.1 Definition of a Local FMLA Search

A local formula (FMLA) search finds reaction records with a specific reaction component that contains the formula that you specify in your query. Your formula query can be:

*	An exact formula and no other atoms, such as C17 H19 N O3, or

*	A subformula and any additional atoms, such as C5 H10, or

*	A subformula and any additional atoms except a specific atom, such as C5 H10 N0, where N0 represents zero nitrogens.

Note1: If you enter a single atom within your query but you do not include spaces, you must also enter a value of 1 for the single atom. For example:  and [image] are equivalent.

Note2: To specify more than one formula in a single query, or to combine a formula search with a search for other data, use Search By Form (SBF).

Use an exact formula query to find records that contain the exact formula in your query. Your exact formula query must include all hydrogens, standard atom symbols, and atom counts. You can use a single space to separate atoms, and capital letters are not required. For example: To find phenol, enter C6 H6 O. To find phenolphthalein sodium, enter C20 H12 Na2 O4. (If you enter a single atom within your query but you do not include spaces, you must also enter a value of 1. For example: C6H5N102.)

A subformula and any additional atoms. Use a subformula query to find records that contain solely specific atoms. Your subformula query can include a range of atom counts and typically excludes the hydrogens. You can use a single space to separate atoms, and capital letters are not required. For example, to find molecules that are sodium salts, enter Na. To find molecules that contain twelve carbon atoms, one to two bromine atoms, and two sulfur atoms, enter: C12 Br(1-2) S2. To find molecules that contain six carbons, six hydrogens, and any number of other atom types, enter: C6 H6. (If you enter a single atom within your query but you do not include spaces, you must also enter a value of 1. For example: C12Br1S2.)

A local search is a search over a database that typically exists on your hard disk. To do a local search on your hard disk, you do not need to input network information.

Note: To do a local search that is accessed from a shared network, you need to input network information.

70.1.1 Specifying Multiple Formula Queries

To specify multiple formulas in a single query, you must conduct a different type of search. For more information, choose Help > Search, and search for either SBF, how to/examples or QB, how to/examples.

70.2 Guidelines for Revising the Query

If your FMLA search retrieved no records or too few records, you might want to:

*	Conduct a FMLA search on a different set of records with the same query.

*	Check that your search domain is set to the entire database.

*	Check that you did not search at too low a level in the database hierarchy. For more information, see your ISIS Administrator.

*	Make the formula more general, and then search the same set of records.

If your FMLA search retrieved too many records, you might want to:

*	Make the formula more restrictive, and then search the same set of records.

*	Save a list of the records retrieved, refine your query, and then search the saved list.

*	Save a list of the records retrieved, conduct an additional search for compounds that you want to exclude (and save them), and then subtract the two lists.

70.3 Searching Example 1: Records That Match Your Exact Formula Query

This searching example shows you how to find reactants that match your exact formula query exactly. Always enter all atoms with a numeric value, such as C6 H11 N1 O2.

70.3.1 Problem

You want to retrieve all reactants with the formula C6 H6 O.

70.3.2 Approach

Conduct a FMLA search in the local reaction database of your choice, such as the LOCALRX demo database. In the Formula text box, enter the exact formula query:

C6 H6 O1

All atoms must contain a numeric value. You can enter the text in either upper- or lower-case characters and either use single spaces between any characters or omit any spaces.

70.3.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for FMLA, how to/examples.

70.3.4 Results

You retrieve solely those records with the exact formula C6 H6 O. Examples of reactant records that you might retrieve from your database are as follows:

70.4 Searching Example 2: Records That Match Your Subformula Query

This searching example shows you how to find reactants that match your subformula query. Always enter all atoms with a numeric value, such as C6 H11 N1 O2.

70.4.1 Problem

You want to retrieve all molecules that contain solely twelve carbon atoms and either one or two bromine atoms.

70.4.2 Approach

Conduct a FMLA search in the local reaction database of your choice, such as the LOCALRX demo database. In the Formula text box, enter the subformula query:

C12 Br(1-2)

All atoms must contain a numeric value. You can enter the text in either upper- or lower-case characters and either use single spaces between any characters or omit any spaces.

70.4.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for FMLA, how to/examples.

70.4.4 Results

You retrieve solely those records with the subformula C12 Br(1-2). Examples of reactant records that you might retrieve from your database are as follows:


Remote ID: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Remote ID Search	71.1

*	Guidelines for Revising the Query	71.2

*	Searching Example 1: A Record With a Text and Numeric ID Number	71.3

*	Searching Example 2: Records With Text and Numeric ID Numbers	71.4

*	Searching Example 3: A Record With Solely a Numeric ID Number	71.5

*	Searching Example 4: Records With Solely Numeric ID Numbers	71.6

We recommend that you print this 5-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a remote ID search, click here.

71.1 Definition of a Remote ID Search

A remote ID search finds the records in your remote database that contain the corporate identification numbers that you specify in your query. To do this type of search, you need:

*	An ID field in your database. This is a field in the database that contains corporate identification numbers for the records in your database.

*	A box or table in a form that is linked to the ID field. A form is the set of boxes and/or tables that you use to hold your query and to view the results of a search. (You can enter a maximum of 25 ID numbers into individual table cells on a form.)

If you do not have these items, see your ISIS Administrator.

A remote search is a search over a database that typically exists on a mainframe. To do a remote search, you need to input network information.

Note: If your query retrieves data that you perceive to be in the wrong place on the form, see your ISIS Administrator. (This might be the result of specifying the same name for multiple database fields on your form or in the Hview.)

71.1.1 Specifying ID Queries

An ID query is a phrase in a box or column on the form that specifies the retrieval of specific ID numbers. For example, to find structures with an ID that is equal to the ID number CL011250, enter the ID query LIKE "CL011250".

Each phrase in an ID query contains:

*	A search operator that specifies the type of search. For example, use the search operator = (an equal sign) with numeric ID numbers or the search operator LIKE in place of = with ID numbers that contain text.

*	The text or numeric target value that you want to find (such as the ID number CL011250). A target value can contain wildcards. A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. For example, you can specify the query LIKE "%CL%" (instead of the query LIKE "CL011250"). The wildcard _ is a placeholder for solely one unspecified character. For example, you can specify the query LIKE "_L011250" (instead of the query LIKE "CL011250"). Target values that contain text or wildcards require double quotation marks.

Note: You cannot use the query LIKE "_" if you search a REACCS database.

The Search Operators

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Use LIKE with text enclosed in double quotation marks. Enter your query as follows: Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. (To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice.)

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks (such as BETWEEN "XR11" "XZ15").

Use EXISTS to retrieve all records in the database that contain data in a specific database field.

Note: You can only use this search operator for database fields that do not give you an error message.

71.2 Guidelines for Revising the Query

If your ID search retrieved no records, you might want to check that your search domain is set to the entire database.

71.3 Searching Example 1: A Record With a Text and Numeric ID Number

This searching example shows you how to find a specific record whose ID number has both text and numbers. Any ID query that contains text (or wildcards) requires the search operator LIKE and the ID number to be enclosed in double quotation marks.

71.3.1 Problem

You want to retrieve the record with the ID number RXC192000092.

71.3.2 Approach

Enter the ID query LIKE "RXC192000092" into the ID box or table cell on the form that connects to the ID database field. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains text and numbers. Enter the search operator LIKE. Enter a space, and then enter the target value RXC192000092 in double quotation marks. (You can enter the text in either upper- or lower-case characters.)

Conduct an ID search in the remote reaction demo database ISISRX.

71.3.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

71.3.4 Results

You retrieve solely the record with the ID number RXC192000092.

71.4 Searching Example 2: Records With a Text and Numeric ID Number

This searching example shows you how to find a specific set of records whose ID numbers have both text and numbers. Any ID query that contains text (or wildcards) requires the search operator LIKE and all ID numbers to be enclosed in double quotation marks.

71.4.1 Problem

You want to retrieve the set of records with ID numbers that are between (and including) RXC192000092 and RXC192071525.

71.4.2 Approach

Enter the ID query BETWEEN "RXC192000092" "RXC192071525" into the ID box or table cell on the form that connects to the ID database field. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains text and numbers. Enter the search operator BETWEEN. Enter a space. Enter the target value RXC192000092 in double quotation marks. (You can enter the text in either upper- or lower-case characters.) Enter a space, and then enter the target value RXC192071525 in double quotation marks.

Conduct an ID search in the remote reaction demo database ISISRX.

71.4.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

71.4.4 Results

You retrieve solely the specific set of records with ID numbers that fall between (and that include) RXC192000092 and RXC192071525.

71.5 Searching Example 3: A Record With Solely a Numeric ID Number

This searching example shows you how to find a specific record whose ID number has solely numbers. Any ID query that contains solely numbers uses the search operator = (the equal sign).

71.5.1 Problem

You want to retrieve the record with the ID number 95.

71.5.2 Approach

Enter the ID query = 95 into the ID box or table cell on the form that connects to the ID database field. You can omit the single space between the equal sign and the number. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains solely a number. Enter the search operator = (an equal sign). Enter a space, and then enter the target value 95.

Conduct an ID search in the remote reaction demo database ISISRX.

71.5.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

71.5.4 Results

You retrieve solely the record with the ID number 95.

71.6 Searching Example 4: Records Solely Numeric ID Numbers

This searching example shows you how to find a specific set of records whose ID numbers have solely numbers. Any ID query that contains solely numbers uses the search operator = (the equal sign).

71.6.1 Problem

You want to retrieve the set of records with ID numbers that are between (and including) 95 and 100.

71.6.2 Approach

Enter the ID query BETWEEN 95 100 into the ID box or table cell on the form that connects to the ID database field. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains solely numbers. Enter the search operator BETWEEN. Enter a space. Enter the target value 95. Enter a space, and then enter the target value 100.

Conduct an ID search in the remote reaction demo database ISISRX.

71.6.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

71.6.4 Results

You retrieve solely the specific set of records with ID numbers that fall between (and that include) 95 and 100.


Local ID: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Local ID Search	74.1

*	Guidelines for Revising the Query	74.2

*	Searching Example 1: A Record With a Text and Numeric ID Number	74.3

*	Searching Example 2: Records With Text and Numeric ID Numbers	74.4

*	Searching Example 3: A Record With Solely a Numeric ID Number	74.5

*	Searching Example 4: Records With Solely Numeric ID Numbers	74.6

We recommend that you print this 5-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a local ID search, click here.

74.1 Definition of a Local ID Search

A local ID search finds the records in your local database that contain the corporate identification numbers that you specify in your query. To do this type of search, you need:

*	An ID field in your database. This is a field in the database that contains corporate identification numbers for the records in your database.

*	A box or table in a form that is linked to the ID field. A form is the set of boxes and/or tables that you use to hold your query and to view the results of a search. (You can enter a maximum of 25 ID numbers into individual table cells on a form.)

If you do not have these items, see your ISIS Administrator.

A local search is a search over a database that typically exists on your hard disk. To do a local search on your hard disk, you do not need to input network information.

Note: To do a local search that is accessed from a shared network, you need to input network information.

74.1.1 Specifying ID Queries

An ID query is a phrase in a box or column on the form that specifies the retrieval of specific ID numbers. For example, to find structures with an ID that is equal to the ID number CL011250, enter the ID query LIKE "CL011250".

Each phrase in an ID query contains:

*	A search operator that specifies the type of search. For example, use the search operator = (an equal sign) with numeric ID numbers or the search operator LIKE in place of = with ID numbers that contain text.

*	The text or numeric target value that you want to find (such as the ID number CL011250). A target value can contain wildcards. A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. For example, you can specify the query LIKE "%CL%" (instead of the query LIKE "CL011250"). The wildcard _ is a placeholder for solely one unspecified character. For example, you can specify the query LIKE "_L011250" (instead of the query LIKE "CL011250"). Target values that contain text or wildcards require double quotation marks.

The Search Operators

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Use LIKE with text enclosed in double quotation marks. Enter your query as follows: Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. (To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice.)

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks (such as BETWEEN "XR11" "XZ15").

Use EXISTS to retrieve all records in the database that contain data in a specific database field.

Note: You can only use this search operator for database fields that do not give you an error message.

74.2 Guidelines for Revising the Query

If your ID search retrieved no records, you might want to check that your search domain is set to the entire database.

74.3 Searching Example 1: A Record With a Text and Numeric ID Number

This searching example shows you how to find a specific record whose ID number has both text and numbers. Any ID query that contains text (or wildcards) requires the search operator LIKE and the ID number to be enclosed in double quotation marks.

74.3.1 Problem

You want to retrieve the record with the ID number MUSE000000001.

74.3.2 Approach

Enter the ID query LIKE "MUSE000000001" into the ID box or table cell on the form that connects to the ID database field. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains text and numbers. Enter the search operator LIKE. Enter a space, and then enter the target value MUSE000000001 in double quotation marks. (You can enter the text in either upper- or lower-case characters.)

Conduct an ID search in the local molecule demo database LOCALMX.

74.3.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

74.3.4 Results

You retrieve solely the record with the ID number MUSE000000001.

74.4 Searching Example 2: Records With a Text and Numeric ID Number

This searching example shows you how to find a specific set of records whose ID numbers have both text and numbers. Any ID query that contains text (or wildcards) requires the search operator LIKE and all ID numbers to be enclosed in double quotation marks.

74.4.1 Problem

You want to retrieve the set of records with ID numbers that are between (and including) MUSE000000001 and MUSE000000009.

74.4.2 Approach

Enter the ID query BETWEEN "MUSE000000001" "MUSE000000009" into the ID box or table cell on the form that connects to the ID database field. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains text and numbers. Enter the search operator BETWEEN. Enter a space. Enter the target value MUSE000000001 in double quotation marks. (You can enter the text in either upper- or lower-case characters.) Enter a space, and then enter the target value MUSE000000009 in double quotation marks.

Conduct an ID search in the local molecule demo database LOCALMX.

74.4.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

74.4.4 Results

You retrieve solely the specific set of records with ID numbers that fall between (and that include) MUSE000000001 and MUSE000000009.

74.5 Searching Example 3: A Record With Solely a Numeric ID Number

This searching example shows you how to find a specific record whose ID number has solely numbers. Any ID query that contains solely numbers uses the search operator = (the equal sign).

74.5.1 Problem

You want to retrieve the record with the ID number 95.

74.5.2 Approach

Enter the ID query = 95 into the ID box or table cell on the form that connects to the ID database field. You can omit the single space between the equal sign and the number. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains solely a number. Enter the search operator = (an equal sign). Enter a space, and then enter the target value 95.

Conduct an ID search in the local molecule demo database LOCALMX.

74.5.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

74.5.4 Results

You retrieve solely the record with the ID number 95.

74.6 Searching Example 4: Records Solely Numeric ID Numbers

This searching example shows you how to find a specific set of records whose ID numbers have solely numbers. Any ID query that contains solely numbers uses the search operator = (the equal sign).

74.6.1 Problem

You want to retrieve the set of records with ID numbers that are between (and including) 95 and 100.

74.6.2 Approach

Enter the ID query BETWEEN 95 100 into the ID box or table cell on the form that connects to the ID database field. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains solely numbers. Enter the search operator BETWEEN. Enter a space. Enter the target value 95. Enter a space, and then enter the target value 100.

Conduct an ID search in the local molecule demo database LOCALMX.

74.6.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

74.6.4 Results

You retrieve solely the specific set of records with ID numbers that fall between (and that include) 95 and 100.


Local ID: Searching Concepts/Examples

Click [image] to print, or click [image] to close this Request-A-Document.

This Request-A-Document contains:

*	Definition of a Local ID Search	75.1

*	Guidelines for Revising the Query	75.2

*	Searching Example 1: A Record With a Text and Numeric ID Number	75.3

*	Searching Example 2: Records With Text and Numeric ID Numbers	75.4

*	Searching Example 3: A Record With Solely a Numeric ID Number	75.5

*	Searching Example 4: Records With Solely Numeric ID Numbers	75.6

We recommend that you print this 5-page Request-A-Document, and then browse through it. To print this document, click the Printer icon at the top of the screen.

For step-by-step instructions on conducting a local ID search, click here.

75.1 Definition of a Local ID Search

A local ID search finds the records in your local database that contain the corporate identification numbers that you specify in your query. To do this type of search, you need:

*	An ID field in your database. This is a field in the database that contains corporate identification numbers for the records in your database.

*	A box or table in a form that is linked to the ID field. A form is the set of boxes and/or tables that you use to hold your query and to view the results of a search. (You can enter a maximum of 25 ID numbers into individual table cells on a form.)

If you do not have these items, see your ISIS Administrator.

A local search is a search over a database that typically exists on your hard disk. To do a local search on your hard disk, you do not need to input network information.

Note: To do a local search that is accessed from a shared network, you need to input network information.

75.1.1 Specifying ID Queries

An ID query is a phrase in a box or column on the form that specifies the retrieval of specific ID numbers. For example, to find structures with an ID that is equal to the ID number CL011250, enter the ID query LIKE "CL011250".

Each phrase in an ID query contains:

*	A search operator that specifies the type of search. For example, use the search operator = (an equal sign) with numeric ID numbers or the search operator LIKE in place of = with ID numbers that contain text.

*	The text or numeric target value that you want to find (such as the ID number CL011250). A target value can contain wildcards. A wildcard is a placeholder within a string of text or numeric values that represents unspecified characters: The wildcard % is a placeholder for at least one unspecified character. For example, you can specify the query LIKE "%CL%" (instead of the query LIKE "CL011250"). The wildcard _ is a placeholder for solely one unspecified character. For example, you can specify the query LIKE "_L011250" (instead of the query LIKE "CL011250"). Target values that contain text or wildcards require double quotation marks.

Note: You cannot use the query LIKE "_" if you search a REACCS database.

The Search Operators

Use <, <=, >, >=, and <> with integers (such as 25 or 100) or real numbers (such as 25.0 or 12.005). With an integer, you retrieve the exact match. With a real number, you must include the exact number of decimal places in your query. If you use zero as a real number, you must enter 0.0 instead of 0. (To use a wildcard with an integer or a real number, you must use the LIKE search operator and enclose the integer or real number in double quotation marks.)

Use LIKE with text enclosed in double quotation marks. Enter your query as follows: Type LIKE. Add a space. Add a double quote. Type your target text with wildcards, such as % or _ (unless the target text is a partial formula). Add the double quote. (To retrieve data that contains a percent sign or an underscore that is not a wildcard, type the percent sign or underscore, preceded by the \ (backslash) symbol. To retrieve data that contains a backslash that is not used to change a wildcard to normal text, enter the backslash twice.)

Use BETWEEN with a range of integers, real numbers, and/or text fields. Enter a single space between the two range values. You retrieve all values that fall between (and include) your two values. Enclose all values that include text in double quotation marks (such as BETWEEN "XR11" "XZ15").

Use EXISTS to retrieve all records in the database that contain data in a specific database field.

Note: You can only use this search operator for database fields that do not give you an error message.

75.2 Guidelines for Revising the Query

If your ID search retrieved no records, you might want to check that your search domain is set to the entire database.

75.3 Searching Example 1: A Record With a Text and Numeric ID Number

This searching example shows you how to find a specific record whose ID number has both text and numbers. Any ID query that contains text (or wildcards) requires the search operator LIKE and the ID number to be enclosed in double quotation marks.

75.3.1 Problem

You want to retrieve the record with the ID number RXC192000092.

75.3.2 Approach

Enter the ID query LIKE "RXC192000092" into the ID box or table cell on the form that connects to the ID database field. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains text and numbers. Enter the search operator LIKE. Enter a space, and then enter the target value RXC192000092 in double quotation marks. (You can enter the text in either upper- or lower-case characters.)

Conduct an ID search in the local reaction demo database LOCALRX.

75.3.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

75.3.4 Results

You retrieve solely the record with the ID number RXC192000092.

75.4 Searching Example 2: Records With a Text and Numeric ID Number

This searching example shows you how to find a specific set of records whose ID numbers have both text and numbers. Any ID query that contains text (or wildcards) requires the search operator LIKE and all ID numbers to be enclosed in double quotation marks.

75.4.1 Problem

You want to retrieve the set of records with ID numbers that are between (and including) RXC192000092 and RXC192071525.

75.4.2 Approach

Enter the ID query BETWEEN "RXC192000092" "RXC192071525" into the ID box or table cell on the form that connects to the ID database field. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains text and numbers. Enter the search operator BETWEEN. Enter a space. Enter the target value RXC192000092 in double quotation marks. (You can enter the text in either upper- or lower-case characters.) Enter a space, and then enter the target value RXC192071525 in double quotation marks.

Conduct an ID search in the local reaction demo database LOCALRX.

75.4.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

75.4.4 Results

You retrieve solely the specific set of records with ID numbers that fall between (and that include) RXC192000092 and RXC192071525.

75.5 Searching Example 3: A Record With Solely a Numeric ID Number

This searching example shows you how to find a specific record whose ID number has solely numbers. Any ID query that contains solely numbers uses the search operator = (the equal sign).

75.5.1 Problem

You want to retrieve the record with the ID number 95.

75.5.2 Approach

Enter the ID query = 95 into the ID box or table cell on the form that connects to the ID database field. You can omit the single space between the equal sign and the number. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains solely a number. Enter the search operator = (an equal sign). Enter a space, and then enter the target value 95.

Conduct an ID search in the local reaction demo database LOCALRX.

75.5.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

75.5.4 Results

You retrieve solely the record with the ID number 95.

75.6 Searching Example 4: Records Solely Numeric ID Numbers

This searching example shows you how to find a specific set of records whose ID numbers have solely numbers. Any ID query that contains solely numbers uses the search operator = (the equal sign).

75.6.1 Problem

You want to retrieve the set of records with ID numbers that are between (and including) 95 and 100.

75.6.2 Approach

Enter the ID query BETWEEN 95 100 into the ID box or table cell on the form that connects to the ID database field. (If you do not have an ID box or table cell that connects to the ID database field, see your ISIS Administrator.)

This query contains solely numbers. Enter the search operator BETWEEN. Enter a space. Enter the target value 95. Enter a space, and then enter the target value 100.

Conduct an ID search in the local reaction demo database LOCALRX.

75.6.3 Search

To execute this search, follow the step-by-step instructions. Alternatively, choose Help > Search, and search for ID, how to/examples.

75.6.4 Results

You retrieve solely the specific set of records with ID numbers that fall between (and that include) 95 and 100.