Almathera Ten Pack 4: Demo 1/almathera_demo1.bin/commercial/mog/mog.doc

Text File | 1995-03-16 | 24KB | 505 lines

                       MM    MM        GGG
                       M M  M M       G   G
                       M  MM  M       G
                       M      M  ooo  G  GG
                       M      M o   o G   G
                       M      M o   o G   G
                       M      M  ooo   GGG

                       ====================


            Molecular Graphics for the Commodore Amiga

                      SciTech Software ©1991


Copyright Information
=====================

This demonstration version of MoG is copyright of SciTech Software 1991.
However, it is freely distributable providing all files are distributed
and the files remain unaltered.

The full version of MoG supports conversion to and from PDB and CSSR
structure formats (used for proteins and small organic molecules
respectively) including selection of protein backbone atoms. In
addition, `space-filling' images may be produced in quick preview,
shaded or ray-traced modes.

MoG is available from:

            SciTech Software,
            23, Stag Leys,
            Ashtead,
            Surrey.
            KT21 2TD.

            Tel.: [phone]

MoG is available in 3 versions with substantial academic discounts being
available for all versions.

            -----------------------------------------
            | Version | Full Price | Academic Price |
            +---------------------------------------+
            | Basic   | £100.00    | £ 60.00        |
            | CoPro   | £150.00    | £ 90.00        |
            | Library | £250.00    | £150.00        |
            -----------------------------------------

To claim the academic discount you should place your order on headed
notepaper or include a photocopy of student identification. School pupils
should get a teacher to supply a sheet of headed notepaper and sign the
order.

The Basic version will run on all Amigas with at least 1MByte of memory.
The CoPro version requires a 68020 or 68030 processor and a 68881 or
68882 maths co-processor and is recommended for users who will work with
proteins rather than small molecules. The Library version comes with
a linkable library, and a certain amount of source code and additional
documentation allowing the user to link in his/her own code via the
`Project/User' menu item.

Introduction
============

MoG is a full-featured molecular graphics program for the Commodore Amiga
(Amiga is a trademark of Commodore-Amiga, Inc.). The program is fully
compatible with AmigaDOS V2.0, the enhanced chip set and the Amiga A3000.
The first version of MoG was written in 1986 when the graphics
capabilities of the Amiga made it unique amongst personal computers. At
this time, molecular graphics programs were rare on anything less that
Evans and Sutherland vector graphics workstations and Silicon Graphics
workstations costing tens or hundreds of times the price of the Amiga.
The current version of MoG was written during 1991.


Running MoG
-----------
If the disk on which you are running MoG is not called `MoGDemo', you
should first double-click on the MoGAssigns icon.

From the Workbench, MoG is run by double-clicking on its icon. A high
resolution interlaced custom screen will be opened in which you will be
able to display stick representations of molecules and manipulate them
in real time. From a CLI, MoG is started by typing:

         MoG

This demonstration version of MoG will load one of two structures
depending on your response to the requester displayed when the
program starts:

         -----------------------------------------------------
         | ORGANIC  |  A small organic molecule.             |
         | PROTEIN  |  An alpha-helix region from a protein. |
         -----------------------------------------------------

Some of the menu items are disabled in the demonstration version. These
are:

   -------------------------------------------------------------------
   | Project/Open         |  Reads a structure file                  |
   | Project/Add Fragment |  Adds a fragment allowing you to build   |
   |                      |  molecules on screen.                    |
   | Project/Save,Save As |  Save a modified structure to disk       |
   | Project/Set Convert  |  Set the command for creating MoG format |
   |                      |  structure files                         |
   | Project/Convert      |  Convert a file to MoG format            |
   | Space Fill/Run CPK   |  Create a space-filled image.            |
   -------------------------------------------------------------------


Tutorial
========

This tutorial will let you experiment with the features of MoG. The
tutorial appears in 2 parts depending which structure is loaded on
startup.

ORGANIC
-------
This is the structure of a `small molecule' as opposed to a protein.
Typically small molecules are shown with hydrogens while proteins are
shown without hydrogens (see below).

Once the structure has loaded and is displayed, you can rotate,
translate or scale it using the gadgets on the right hand side of the
screen. The top pair of gadgets rotates the structure about the X-axis
(which runs horizontally across the screen); the next pair of gadgets
rotates about the Y-axis (which runs vertically down the screen); the
next pair of gadgets rotates about the Z-axis (which goes into the
screen); the next pair of gadgets translates the structure along the
X-axis; the next pair translates along the Y-axis; the next pair
translates along the Z-axis; the last pair magnifies or reduces the
structure. Parts of the structure which are farther away are indicated
by being in a darker colour than parts in the foreground. As you
translate the structure along the Z-axis, you will see parts of the
structure get lighter or darker.

If you click on one of the gadgets and move the mouse away from the
gadget while holding the left mouse button down, the structure will
continue to rotate when you release the mouse button. To stop the
rotation click again on one of the gadgets. (Under AmigaDOS V2.0, you
should click in the logo at the bottom right of the screen rather than
on one of the gadgets.)

Select the `Colour/Set Colours' menu item. A requester will appear
where you can set colouring based on:
   atom type
   amino acid (or `residue') type
   residue number range (zone)
   bond (link) between specific atom pairs
Colouring based on amino acid type or residue range is used with
proteins rather than small molecules. Enter H* as the atom type and 3
as the colour number then click on the `Do It!' gadget. All bonds to
hydrogens will now be coloured in red. Repeat the process to set atom
type N* to colour 2. This will colour bonds to nitrogen in blue.
Select the `EXIT' gadget to remove the requester.

The `Colour/Set Palette' menu item will let you alter the colour
palette. When you are using depth cueing (parts of the molecule farther
away are shown in a darker colour) the second 6 colours are the darker
versions of the first 6 colours. If you alter the foreground colours,
you should also alter the background colours to maintain the depth
cueing effect. There is, however, an easy way to do this. Once you are
happy with your foreground colours, simply switch off depth cueing
using the `Display/Depth Cue' menu item and switch it on again by
selecting the menu item a second time. This will automatically set the
background colours to darker versions of the foreground colours.
The rest of this tutorial assumes that you still have the default
colours, so select the `CANCEL' gadget in the palette requester, or
reload the default palette by selecting the `Colour/Load Palette' menu
item and loading the file tutorial.pal.

The lines which you see on the screen represent bonds between atoms;
the atoms themselves are represented by the joints between lines. Try
clicking the left mouse button on one of the atoms. A label will
appear near the atom identifying it. The first three letters will
always be ATM. These are normally used to identify amino acid types in
proteins (see below). This is followed by the number 1 which is used
to identify the amino acid number in proteins. Finally, after a dash,
is the atom label.

Select the `Display/Labels/Show Coordinates' menu item. Now, when you
click on an atom, a requester will appear showing the X,Y,Z coordinates
of the atom as well as the atom name, residue name and residue number.
Click on one of the `OK' gadgets to proceed. When you have finished
experimenting with this feature, select the menu item again to switch
off the show coordinates feature. Selecting the `Display/Labels/Off'
menu item will remove all the labels from the display.

You can gain other information about the geometry of the structure.
Select the `Calculate/Distance' menu item. The cursor will change to
an arrow with a 2 next to it. This indicates that you must click on
two atoms. Select 2 atoms and a requester will appear indicating the
distance between the two atoms. Click on one of the `OK' gadgets in the
requester to proceed. In the same way, you can measure angles and
torsion (twist) angles. In these cases, you will have to select 3 or 4
atoms respectively.

The Modify menu allows you to make changes to the structure. First
identify the green bond between atom 1-C18 and atom 1-C20. Identify
atom 1-C17 attached to atom 1-C18 and atom 1-C23 attached to atom
1-C20. Select the `Modify/Torsion' menu item and click on the atoms in
the order:

   1-C17, 1-C18, 1-C20, 1-C23

A label will appear in the top left corner of the screen indicating the
torsion angle which these 4 atoms define. The structure will also change
colour. Assuming you have not altered the palette, part of the structure
will be blue and the rest green. The Z-translate gadgets now have a new
function. They now cause the part of the structure attached to the
third and fourth atoms you clicked (1-C20 and 1-C23) to rotate about the
bond between the second and third atoms. As this part of the structure
rotates, the torsion angle indicated in the top left corner of the
screen will alter. All the other gadgets work as before letting you
change your view of the structure. Selecting the `Modify/Torsion' menu
item again will retain the new torsion angle you have set and restore
the original colouring.

The `Modify/Break Bond' menu item will remove a bond between 2 atoms.
Try breaking the bond between atoms 1-C18 and 1-C20. Now select the
`Modify/Move Group' menu item and click on atom 1-C20. The two groups
of atoms which were formed by breaking the bond will now be coloured
blue and green and the group on which you clicked will now be moved by
the gadgets, the rest of the structure remaining stationary. Rotations
will occur about the atom on which you clicked to define the group to
move. Selecting the `Modify/Move Group' menu item again will cause the
gadgets once again to move the whole structure and will restore the
colouring. You can now remake the bond between atoms 1-C18 and 1-C20
using the `Modify/Make Bond' menu item.

The full version of MoG lets you save your modified structure to disk.
Since a library of fragments is supplied, you can build molecules on
the screen using the `Project/Add Fragment' menu item.


PROTEIN
-------
This is an alpha-helix region from a protein. Proteins are made up of
amino acids each of which consists of a `backbone' (or `mainchain')
with a sidechain. There are 20 amino acids each of which has the same
backbone, but varying sidechains.

For example:

   Alanine:    H        Serine:      O-H
               |                     |
             H-C-H                 H-C-H     Sidechain
               |                     |       ----------
           H-N-C-C=O             H-N-C-C=O   Backbone
             | | |                 | | |
             | H |                 | H |
             ^   ^                 ^   ^

A protein is formed by linking amino acids via a nitrogen (N) to
carbon (C) bond in the backbone.

Because proteins can consist of hundreds of these amino acids, the
hydrogens are generally excluded from graphical representations.
In each amino acid, the central backbone carbon to which the sidechain
is attached is known as the alpha-carbon (or CA). Moving along the
sidechain, each non-hydrogen atom is named using the Greek alphabet
abbreviated with the English equivalent:

                     ---------------
                     | alpha   | A |
                     | beta    | B |
                     | gamma   | G |
                     | delta   | D |
                     | epsilon | E |
                     | zeta    | Z |
                     | eta     | H |
                     ---------------

Once the structure has loaded and is displayed, you can rotate,
translate or scale it using the gadgets on the right hand side of the
screen. The top pair of gadgets rotates the structure about the X-axis
(which runs horizontally across the screen); the next pair of gadgets
rotates about the Y-axis (which runs vertically down the screen); the
next pair of gadgets rotates about the Z-axis (which goes into the
screen); the next pair of gadgets translates the structure along the
X-axis; the next pair translates along the Y-axis; the next pair
translates along the Z-axis; the last pair magnifies or reduces the
structure. Parts of the structure which are farther away are indicated
by being in a darker colour than parts in the foreground. As you
translate the structure along the Z-axis, you will see parts of the
structure get lighter or darker.

If you click on one of the gadgets and move the mouse away from the
gadget while holding the left mouse button down, the structure will
continue to rotate when you release the mouse button. To stop the
rotation, click again on one of the gadgets. (Under AmigaDOS V2.0, you
should click in the logo at the bottom right of the screen rather than
on one of the gadgets.)

Select the `Colour/Read Colour File' menu item and select the file
backbone.col from the MoGDemo: directory. The colours of the structure
will change such that the sidechains are in green, with the backbone
mainly in blue with its oxygens in red. As you rotate the structure,
you will be able to see how the backbone runs through the helix with
the sidechains sticking out from the bulk of the helix. Note also how
the backbone oxygens (shown in red) all point along the helix in the
same direction.

Select the `Colour/Set Colours' menu item. A requester will appear
where you can set colouring based on:
   atom type
   amino acid (or `residue') type
   residue number range (zone)
   bond (link) between specific atom pairs
Enter ARG as the residue type and 6 as the colour number then click on
the `Do It!' gadget. Two of the amino acids (both arginines) will
change to a cyan colour. Repeat the process to set residue type PHE to
colour 5. Select the `EXIT' gadget to remove the requester. As you
rotate the structure, you will see that the backbone atoms of these
amino acids have changed colour as well. Reload the backbone.col file
using the `Colours/Read Colour File' menu item to restore the special
colouring of the backbone.

The `Colour/Set Palette' menu item will let you alter the colour
palette. When you are using depth cueing (parts of the molecule farther
away are shown in a darker colour) the second 6 colours are the darker
versions of the first 6 colours. If you alter the foreground colours,
you should also alter the background colours to maintain the depth
cueing effect. There is, however, an easy way to do this. Once you are
happy with your foreground colours, simply switch off depth cueing
using the `Display/Depth Cue' menu item and switch it on again by
selecting the menu item a second time. This will automatically set the
background colours to darker versions of the foreground colours.
The rest of this tutorial assumes that you still have the default
colours, so select the `CANCEL' gadget in the palette requester, or
reload the default palette by selecting the `Colour/Load Palette' menu
item and loading the file tutorial.pal.

The lines which you see on the screen represent bonds between atoms;
the atoms themselves are represented by the joints between lines. Try
clicking the left mouse button on one of the atoms. A label will
appear near the atom identifying it. The first three letters tell you
the amino acid type:

            -------------------------
            | ALA | Alanine         |
            | ARG | Arginine        |
            | ASN | Asparagine      |
            | ASP | Aspartate       |
            | CYS | Cysteine        |
            | GLN | Glutamine       |
            | GLU | Glutamate       |
            | GLY | Glycine         |
            | HIS | Histidine       |
            | ILE | Isoleucine      |
            | LEU | Leucine         |
            | LYS | Lysine          |
            | MET | Methionine      |
            | PHE | Phenylalanine   |
            | PRO | Proline         |
            | SER | Serine          |
            | THR | Threonine       |
            | TRP | Tryptophan      |
            | TYR | Tyrosine        |
            | VAL | Valine          |
            -------------------------

This is followed by the amino acid number (the example has amino acid
numbers 7--19) and the atom name. The backbone atoms coloured in blue
will have the atom names N, CA and C while the backbone oxygens (in
red) will have the atom name O.

Select the `Display/Labels/Show Coordinates' menu item. Now, when you
click on an atom, a requester will appear showing the X,Y,Z coordinates
of the atom as well as the atom name, residue name and residue number.
Click on one of the `OK' gadgets to proceed. When you have finished
experimenting with this feature, select the menu item again to switch
off the show coordinates feature. Selecting the `Display/Labels/Off'
menu item will remove all the labels from the display.

You can gain other information about the geometry of the structure.
Select the `Calculate/Distance' menu item. The cursor will change to
an arrow with a 2 next to it. This indicates that you must click on
two atoms. Select 2 atoms and a requester will appear indicating the
distance between the two atoms. Click on one of the `OK' gadgets in the
requester to proceed. In the same way, you can measure angles and
torsion (twist) angles. In these cases, you will have to select 3 or 4
atoms respectively.

The Modify menu allows you to make changes to the structure. Select the
`Modify/Torsion' menu item and click on 4 sequentially joined atoms
(i.e. the first atom should be joined to the second, the second to the
third and the third to the fourth). A label will appear in the top
left corner of the screen indicating the torsion angle which the 4
atoms define. The structure will also change colour. Assuming you have
not altered the palette, part of the structure will be blue and the
rest green. The Z-translate gadgets now have a new function. They now
cause the part of the structure attached to the fourth atom you
clicked to rotate about the bond between the second and third atoms.
As this part of the structure rotates, the torsion angle indicated in
the top left corner of the screen will alter. All the other gadgets
work as before letting you change your view of the structure.
Selecting the `Modify/Torsion' menu item again will retain the new
torsion angle you have set and restore the original colouring.

The `Modify/Break Bond' menu item will remove a bond between 2 atoms.
Try breaking a bond between two backbone atoms shown in blue. Now
select the `Modify/Move Group' menu item and click on one of the two
groups of atoms which have been formed by breaking the bond. The two
groups will now be coloured blue and green and the group on which you
clicked will now be moved by the gadgets, the rest of the structure
remaining stationary. Rotations will occur about the atom on which you
clicked to define the group to move. Selecting the `Modify/Move Group'
menu item again will cause the gadgets once again to move the whole
structure and will restore the colouring.

The full version of MoG lets you save your modified structure to disk.
Since a library of fragments is supplied, you can build molecules on
the screen using the `Project/Add Fragment' menu item.



Reference
=========

Each of the menu functions is described briefly:

Project/Open                     Read a structure file
Project/Save                     Save a structure file
Project/Save As                  Save a structure file
Project/Plot/IFF                 Save an image in IFF-ILBM format
Project/Plot/PostScript          Save an image in PostScript format
Project/Plot/HPGL                Save an image in HPGL format
Project/Paper                    Sets dimension of the plot
Project/Set Convert              Set the command for creating MoG format
                                 structure files
Project/Convert                  Convert a file to MoG format
Project/Defaults/Read            Read a `defaults' command file
Project/Defaults/Write           Write a `defaults' command file
Project/About                    Display information about the program
Project/User                     Allows interfacing to users own code
Project/Quit                     Exit from MoG
Display/Labels/Show Coordinates  Display coordinates when an atom is
                                 clicked
Display/Labels/Off               Switch off all labels
Display/Labels/All Atoms         Label all atoms
Display/Depth Cue                Toggle depth cueing
Display/Step Size                Set step sizes for rotation,
                                 translation and scaling
Display/Screen To Back           Send the MoG screen to the back
Display/Centre On Atom           Centre the display on an atom
Calculate/Distance               Calculate distance between 2 atoms
Calculate/Angle                  Calculate angle between 3 atoms
Calculate/Torsion                Calculate torsion angle between 4 atoms
Calculate/View                   Calculate a view matrix
Modify/Torsion                   Rotate part of the structure about a
                                 torsion angle
Modify/Move Group                Move a group of atoms independently
Modify/Make Bond                 Bond 2 atoms
Modify/Break Bond                Break a bond between 2 atoms
Modify/Set View                  Set the view of the structure
Modify/Kill Unlinked             Removes any unlinked atoms.
Modify/Change Label              Allows the atom label information and
                                 hence the atom characteristics to be
                                 changed
Colour/Set Colours               Set colours of residues, atoms, residue
                                 ranges or specific bonds
Colour/Read Colour File          Read a file of colouring commands
Colour/Set Palette               Set the palette
Colour/Save Palette              Save a palette file
Colour/Load Palette              Load a palette file
Space Fill/CPK Setup             Set up parameters for creating space-
                                 filled images
Space Fill/Run CPK               Generate space-filled image


Plotting
========
MoG supports PostScript, EPSF and HPGL plotting formats as well as IFF
ILBM bit-mapped graphics files. A public domain HPGL interpreter (PLT:)
is available on the Fish Disks and is supplied free with the full
version of MoG. This allows plots to be produced at the maximum
resolution of any Preferences supported printer.


Space Filling Pictures
======================
The full version of MoG also allows the generation of `space-filling'
CPK (Corey, Pauling, Kendrew) images of molecules. These may be
produced in quick preview mode or rendered using sphere shading or full
ray-tracing. Three sample ray-traced images are supplied with this
demonstration version.


Acknowledgements
================

SciTech Software acknowledges the use of Charlie Heath's file requester
and the palette requester from the copyrighted, but freely distributable
`The Amiga Programmer's Suite Book 1' by R. J. Mical which is available
on Fish Disk 107.