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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.: (0372) 275775 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.