home *** CD-ROM | disk | FTP | other *** search
- ******************************************************************
- Molecule 3D is a Public Domain Share-ware release from West
- Germany. You are welcome to copy this program and distribute it
- as long as it is not sold and this documentation remains with it.
- The author is: Rainer Paape
- Paschenburgstr. 67
- 2800 Bremen 1
- West Germany
- (The newest update may be purchased from him)
- The documentation was imported and translated by:
-
- Robert Zimmerer
- 131 W 2nd Street
- Port Angeles, WA 98362
- (206) 452-7529
-
- If you are interested in more software from germany and for
- details about this and other progrrams, feel free to call or write
- me. *See adendum for more info.
- ******************************************************************
-
-
- Molecule 3D Info
-
- You must have the following files in a folder named MOLEKUEL on
- your disk in order for the program to work:
-
- - MOLEKUEL.PRG (contains the program)
-
- - MOLEKUEL.DAT (contains the program logo)
-
- - RADIEN.DAT (contains Atom-, Ion- and v.d. Waals-Radii)
-
- - FARBEN.DAT (contains graphics for color coordination)
-
- - RGB.DAT (contains data for color coordination)
-
- The following files are also useful:
-
- - DEMO.KOO (Demo-file for coordinates)
-
- - DEMO.BIN (include file of bonds for DEMO.KOO)
-
- - DEMOx.PI2 (Demo graphics for high resolution)
-
- - DEMOx.PI1 (Demo graphics for medium resolution)
-
- - TEST.KOO (Demo-file for positions of axi in space)
-
- - TEST.BIN (include file of bonds for TEST.KOO)
-
- - Molecule.DOC (This file in 1st-Word format)
-
- - Molecule.TXT (This file in ASCII)
-
-
- General notes:
-
- Two sets of information are necessary for molecule representation.
-
- - Atom symbols and X,Y and Z-coordinates
-
- - Binding list of the atoms
-
-
- Up to 216 atomic coordinates and 216 bonds can be defined. The
- maximum number of pictures in a sequence depends on the amount of
- free memory. The program determines the maximum number of
- pictures allowed, each requiring about 19 Kbytes of RAM. Around
- 40 pictures can be made using a 1040ST (or 520ST with 1Megabyte of
- RAM) having with TOS in ROM. After about 30 pictures the going
- gets pretty slow.
-
- The program operates in high and medium resolution!
-
-
- Starting the program:
-
- Once you are in the Molcule folder, double-klick on
- "MOLEKUEL.PRG" to start the program. If the necessary files are
- not in order an error message will appear and you will be returned
- to the desktop.
- If all goes well, you will be given a menu. The bottom of
- the screen displays memory and data information as well as the
- free space on the disk in the drive. The drive shown is the
- default drive, from which the program was initiated. If you want
- to change drive specifications (to a second disk drive, a RAM disk
- or Hard disk), click on the right or left arrow until you are at
- the drive.
- To check how much free space you have on the selected drive,
- click on the "Freier Speicher" box (to the left of the drive
- selection box)
-
- 1 Data ( Daten )
-
- 1.1 Editing the coordinates ( Koordinaten editieren )
-
- In order to edit the coordinate values of the molecule, pull
- down the menu item labeled "Daten" and click on the
- "KOORDINATEN EDITIEREN" entery. This takes you to an editor
- displaying the data entries in a ledger format.
- Once in the editor, you may edit any column by clicking on
- the entry. The <Return> key will take you to the next line of the
- column and write the new information to that line of the column.
- When you are finished entering data in the column, press the <Esc>
- key. (Be sure to press <Return> to write the information before
- pressing <Esc>)
- To move through the list, click on the arrow symbols at the
- top of the screen. The single arrows move the list one entry in
- either direction, the double arrows move it 15.
- The column labeled "Art" is for the atomic symbol, and the
- coordinates of the molecule go in the X, Y and Z columns. In the
- line marked "Molekül" you may enter the name of the molecule.
- Clicking on the box marked "Menue" returns you to the main
- menue.
-
- 1.2 Editing bonds( Bindungen editieren )
-
- Here you may enter/change the bonds list. Entering and
- editing the data follows the same rules in with the coordinate
- editing section.
- After entering the atom pairs, the type of bond will be shown
- (eg. C-C). The bond lengths are also calculated and displayed.
- This allows you to check the accuracy of your entries and find
- bonds that are to short or long. The program also checks if the
- atoms are available. If, for example, 37 atomic coordinates were
- defined and a bond between atoms 34 and 38 were entered, a bond
- between "34 + 0" would be displayed. It is therefore important to
- enter or load the atomic coordinates.
-
- 1.3 Saving coordinates/bonds ( Koordinaten/Bindungen speichern )
-
-
- When you are finished entering the data you should always
- save it right away. Click on the boxes marked "KOORDINATEN
- SPEICHERN" and "BINDUNGEN SPEICHERN" to save coordinates and
- bonds respectively. The extensions should be ".KOO" for
- coordinate data and ".BIN" for bonding data. (from the german
- KOOrdinaten and BINdungen)
-
- 1.4 Loading coordinates/bonds ( Koordinaten/Bindungen laden )
-
-
-
- In order to load a Coordinate or Bonds file, click on the
- entries "KOORDINATEN LADEN" for coordinate data and "BINDUNGEN
- LADEN" for bonds in the "Daten" drop down menu.
-
- 1.5 Deleting Coordinate/Bonding ( Koordinaten/Bindungen löschen )
-
- When you click on the entries "KoordinatenLöschen" or
- "BindungenLöschen", all the data is erased from memory.
-
- 1.6 Merging Coordinates/Bonds ( Koordinaten/Bindungen mischen )
-
- This menu entry allows for the union of two or more data
- groups. For example, if you wanted to compare two molecules
- together on the same screen you would: first load in the
- coordinate data of the first molecule followed by its bonding
- data. Next merge the coordinate data of the second molecule with
- the menu entry "Koordinaten mischen". Follow this by merging the
- bonding data of the second molecule with the menu entry "Bindungen
- mischen".
- You may merge as many molecules as you want, so long as there
- is enough space in the memory. (see above for maximum values)
- It is very important that you are careful to follow this
- procedure exactly, always alternate between loading coordinates
- and bonds!
-
- 1.7 Editing Radii( Radien editieren )
-
- To get into the radius editor, click on the menu entry maked
- "Radien Editieren". (See above for editor controls)
- The elemental symbol "CA" stands for carbon in aromatic
- orbits, and "CM" stands for carbon in methylene groups.
- This distinction is only meaningful in the van der Waals-
- radius. All the radii are given in units of the coordinate system
- (Angstoms).
-
- 1.8 Saving Radii ( Radien speichern )
-
- To save radius data, the diskette in the default drive must
- contain the folder "MOLEKUEL" since the data is always saved to
- the file "RADIEN.DAT" in the folder "MOLEKUEL". If the folder is
- not found, error # -34 (pathname not found) occurs.
- This data is automatically loaded at the beginning by the
- program since all th necessary information for the diagram of the
- radii is contained in it. Great care should be taken to ensure
- that this data is not lost!
-
- 2. Importing data ( Inport )
-
- Since the atomic coordinates come originally from a mini
- computer, you should try to port coordinate data from a mini
- computer through the RS-232 port if the opportunity shoild present
- itself. This will save you the time consuming and "typo"-full
- task of entering all the data by hand. Data entry routines will
- be released for normal calculations.
-
- 2.1 Loading MNDO-Data ( MNDO-Daten laden )
-
- If you want to load atomic coordinate data from an MNDO list
- (MNDO-Rechnung), the data must have the following structure:
-
- Row 1 Column 1-80: Molcule's name (comments)
-
- Row 2-n Symbol and coordinates of the atom, with the
- following requirements:
-
- Columns 16-17: atomic symbol or number upto 20
- Columns 21-30: X-coordinates
- Columns 31-40: Y-coordinates
- Columns 41-50: Z-coordinates
-
- Row n+1 Columns 1-2: /*
-
- Row n+2 Columns 1-2: //
-
- The format of rows 2 to n are in the form of the output from the
- "MOPAC" program in version 2.00. Rows 1, n+1 and n+2 must be
- filled out by hand prior to loading.
-
- 2.2 Loading "Ab-Initio-Daten" ( Ab-Initio-Daten laden )
-
- This feature hasn't been implemented yet!
-
- 2.3 Loading "Gauss80-Daten" ( Gauss80-Daten laden )
-
- This feature hasn't been implemented either!
-
- 3 Graphics ( Grafik )
-
- 3.1 View ( Zeigen )
-
- Shows the last calculated or loaded graphic.
-
- 3.2 Inverting ( Invertieren )
-
- Shows the last calculated or last loaded graphic in
- inverted form.
-
- 3.3 Hardcopy
-
- Prints a copy of the last shown graphic. The operating
- systems printing routine is used for this. If your printer isn't
- supported, you must first load the appropriate printer driver for
- your machine. The hardcopy can be printed then through the screen
- dump command ( <Alt><Help> ).
-
- 3.4 Loading ( Laden )
-
- Loads a previously saved graphic.
-
- 3.5 Saving ( Speichern )
-
- This saves the last calculated and shown graphic as an entire
- screen. In monochrome the pictures have the extension ".PI2" and
- can be loaded into and modified by graphics programs that handle
- monochrome. When saved from a color monitor system, the color
- information isn't saved. You can use "PAINTER.ST" to modify these
- pictures.
-
- 4 Colors ( Farben )
-
- This menu selection can only be selected from medium
- resolution.
-
- 4.1 Setting RGB values ( RGB-Werte einstellen )
-
- This menu selection allows you to adjust the settings of the
- red, green and blue for the display. By wearing a pair of
- red/green glasses and loading the file called "FARBEN.DAT", you
- can get the real "3D" effect.
-
- 4.2 Loading/Saving Color settings ( RGB-Werte laden/speichern )
-
- With these menu selections (RGB-Werte laden/RGB-Werte
- Speichern), the color settings can be loaded and saved.
-
- 5 Graphics Calculations ( Menue_2 / Grafik Berechnen )
-
- Here you get a new drop down menu which allows all the
- parameters for the representation of the molecule to be laid out
- and adjusted. This menu will only be selectable after coordinates
- and bonds are available (having been entered or loaded). This
- screen contains a window (2/3 the screen) for displaying the
- molecule, and a group of parameter control boxes on the right.
-
- 5.1 Modes ( Modi )
-
- 5.1.1 Rotation around Original/Actual Axis
- ( Rotation um Ursprungs/aktuelle Achse )
-
- When rotating around the original axis, the molecule is
- turned around the X, Y or Z axis. These axii are horizontal and
- verticle from the observer's perspective. When rotating around
- the actual axis, the chosen spin is taken into consideration for
- the X and Y axii respectively. (se below for details) The default
- is rotation about the original axis.
-
- 5.1.2 Rotation around the X, Y or Z axis
- ( Rotation um die X, Y oder Z-Achse )
-
- Determines which of the three axii the rotation will be
- around. The default is the X axis.
-
- 5.1.3 Projection ( Projektion )
-
- With verticle (senkrechter) projection the molecule is
- represented without distortions. Perspective (perspektivischer)
- projection distorts objects which are closer in the view more than
- the objects which are further away. The default is "senkrechte"
- projection.
-
- 5.2 Graphics ( Grafik )
-
- 5.2.1 Radii ( Radien )
-
- Determines if and which radius should be at the end of bond
- (only in "senkrechter" projection). If the radii (Radien) is
- selected, the "BINDUNGEN ZEICHNEN" should first be deselected.
- The default setting for radii is no radius (kein Radius).
-
- 5.2.2 Atom symbols ( Atomsymbol )
-
- Determines if the atom symbol will be displayed. (this
- feature only works in "senkrechter" projection and only when the
- radii are not selected!) The default is no atom symbols (kein
- Atomsymbol).
-
- 5.2.3 Atomic number( Atomnummer )
-
- This displays the atomic number of the atom (same
- restrictions as with atomic symbols). The default is no atomic
- number (keine Atomnummer).
-
- 5.2.4 Show Axis ( Achsen zeichnen )
-
- Determines if the axii of the coordinate system will be
- displayed or not. The default is no axis (nicht einzeichnen).
-
- 5.2.5 Show bonds ( Bindungen zeichnen )
-
- Determines if the bonds will be displayed or not. The
- default is show bonds (einzeichnen).
-
- 5.3 Pictures ( Bilder )
-
- 5.3.1 Single/Animate ( Einzelbild/Bildfolge )
-
- When single picture (Einzelbild) is selected, only one
- molecule is displayed. When Animate (Bildfolge) is selected, the
- molecule is rotated around the axis selected in Mode (Modus). The
- default is single (Einzelbild).
-
- 5.3.2 Picture size ( Bildgrö₧e )
-
- When 1/1 is selected, the entire display window is used for
- the molecule diagram. When 4/4 is selected, the window is divided
- into quarters, each showing a different view of the molecule. The
- default is 1/1.
-
- 5.3.3 Color Stereo Picture ( Farbiges Stereobild )
-
- This feature may only be selected in medium resolution. Two
- pictures are drawn (detailed in 5.5.7) which differ by a specified
- angle. With the help of Red/Green glasses you can get an
- appearence of space (see 4.1). This only works in 1/1 picture
- setting.
-
- 5.4 Measure ( Ma₧stab )
-
- Determines whether the size of the diagram is automatically
- or manually set. Default is automatic.
-
- 5.5 Setting the numerical Parameters
-
- Setting the numerical parameters is done by clicking on the
- left or right arrow associated with the parameter. Clicking the
- right mouse button will increase or decrease the value by ten, the
- left button will change the value by one. Holding either button
- down will cause the value to change until the button is released.
-
- 5.5.1 Pictures ( Bilder )
-
- This is the number of pictures used in an animation sequence.
- The maximum value depends on the amount of free memory. The
- number of pictures is inversely proportional to the rotation
- angle. The default is the maximum.
-
- 5.5.2 Rotation angle( Drehwinkel )
-
- Shows the angle of rotation between pictures in an animation.
- The minimum value depends on the amount of free memory. The angle
- is closely related to the number of pictures in the animation.
- The default is the smallest angle possible for the amount of free
- memory.
-
- 5.5.3 X/Y Rotation ( Drehung um X/Y )
-
- Determines how many degrees the molecule will be rotated in
- space. The default is 0 in each case.
-
- 5.5.4 Size in Pixels( Grö₧e in Pixeln )
-
- Determines the half size of the graphic in pixels. Also
- works when the measure is automatically calculated. The default
- is 150.
-
- 5.5.5 Distance ( Abstand )
-
- Determines the distance the observer is from the object (only
- in perspective projection). The default value is 16.
-
- 5.5.6 Unity ( Einheit )
-
- Determines how many pixels a unity in the coordinate system.
- A change in this value only has an effect when the setting for the
- Measure is in manual. the default value is 40.
-
- 5.5.7 Stereo picture difference ( Stereobild Differenz )
-
- Determines how many degrees the stereo pictures are seperated
- from one another. The setting is in tenths of degrees. The
- default value is 2.5 degrees.
-
- 5.5.8 Show Picture ( Zeige Bild )
-
- Displays the pictures in the animation on the entire screen
- as long as an animation has been calculated.
-
- 5.5.9 Speed ( Geschwindigkeit )
-
- Adjusts the speed with which the molecule rotates in an
- animation.
-
- 5.5.10 Start
-
- Begins the calculation of a molecule or shows a prepared
- animation. All of the previous functions like calculating and
- drawing may be canceled by pressing the right mouse button.
-
- 5.5.10 To Menu ( Zum Menue )
-
- Returns you to the main menu.
-
-
- Subject to change w/o notice
-
- -----------------------------------------------------------------
-
- * Translater's Adendum:
-
- I must apologize for any inaccuracies in relation to
- chemical terminology. I have had the usual High School chemistry
- courses and found some of the german terms identifiable. I cannot
- be held responsible for any possible damage or defamation of
- character that might be incured upon use of this software.
-
- As stated above, this is Public Domain Share-ware from West
- Germany, and may contain references to programs and software not
- available in the USA. This translation of the documentation is
- also released into the Public Domain with the only restrictions
- being that it may not be sold. Copy it and pass it on.
-
- I have organized a disk which includes: a copy of the
- original software package, including german documentation, my most
- recent translation and a handy translation sheet to help you in
- operating the program and reading the menus.
-
- If you would like the disk & translations, send $5.50 (to
- cover disk, shipping & handling, import costs & translating) to:
-
- Robert Zimmerer
- Disk order
- 131 W 2nd Street
- Port Angeles, WA 98362
-
- For more information about other PD software from West
- Germany you may write to the above address or call at:
-
- (206) 452-7529
-