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------------------------------------------------------------------------------- Preliminary Manual for MolSys v0.74 ------------------------------------------------------------------------------- © September 1992 Helion Graphics. Written by Robert Mellish & Howard Jones. MolSys v0.74 is shareware and may not be distributed for profit or without this text file. All source code, text files and file formats remain copyright Helion Graphics. The programmers make no claim for accuracy or fitness of purpose for MolSys or any of its related files and documentation. About MolSys ------------------------------------------------------------------ MolSys is a molecular modelling package for the Atari ST. It requires an ST-mono monitor but should run irrespective of memory size. It was developed from MolView v2.5, MolBuild v0.7 and MolScript v0.1. These programs were inspired by a PC program written by Alan Mynett and published in the October 1987 edition of Personal Computer World. MolSys is powerful, but quick and easy to learn and use, and is capable of directly printing output or producing files which may be imported into DTP packages for inclusion in documents. MolSys was written using the Lattice C V5 development package from HiSoft. Limitations of This Version --------------------------------------------------- MolSys v0.74 contains only a limited animation function, and is also limited to a maximum of 100 atoms and 16 molecule fragments in memory at one time. To register for the latest version of MolSys, see the section at the end of this file. Please register if you like MolSys, and especially if you intend to use it for any serious work. Registering will encourage me to produce future versions with more features. Changes From Previous Versions ------------------------------------------------ If you have used MolSys before, it will be necessary to re-install MolSys as the format of the MOLSYS.INF file has changed. More importantly, the format of MLS (molecule fragment) files has also changed, and so it is necessary to convert any you have made with previous versions of MolSys into the new format. This can be done with the supplied program MS_5_6.TTP. See its accompaning text file for instructions. Installing MolSys ------------------------------------------------------------- Configuration of MolSys is done via the MOLSYS.INF file. This file is best edited by using the supplied installation program, MSI. The supplied INF file should allow you to run MolSys without need for further installation. Just double click on MOLSYS.PRG to begin. If you later want to adapt the installation, follow the instructions below. You should first copy the MOLSYS.PRG, MOLSYS.RSC, MOLSYS.INF, SYSTEM.FNT, SYSTEM.FN8, MSI.PRG and MSI.RSC into the same folder, and then double click on MSI.PRG. After the credit dialogue, you are presented with a menu which allows you to access a series of dialogue boxes containing options and default values which you may change. The first dialogue is the main options. The first editable field is the file path of the resource file. Normally, this will just be '\', which will cause the program to search in the current directory. Note that if the resource file cannot be found, the program will abort. The second field is the file path and name of the 16x8 screen font to be used by MolSys. (Usually 'SYSTEM.FNT'). This path and name will also be used when MolSys loads the replacement 8x8 screen font, but with the extender '.FN8' substituted (i.e. 'SYSTEM.FN8'). These are optional, and the replacement fonts will not be used if the 'disabled' button is highlighted. These fonts are Harlekin format screen fonts. The third field is the default path of the molecule fragment files. The forth field is maximum number of atoms which may be added to the molecule. In this version of MolSys, this number cannot be set greater than 100. If you register, you will receive a version where the maximum number of atoms is limited only by available memory. On a 'clean' 520ST this value can be up to about 3000, which should be adequate for most purposes. By decreasing this number, it is possible to make more memory available for animation, ramdisks, print spoolers, desk accessories etc. The second dialogue is the default values dialogue. This allows the setting of the default translation distance, rotation angle, zoom level, size of spheres in reduced size mode and size of sticks in stickmode 3 (thick). It also allows you to set the units displayed in measuring operations to Angstroms (Å) or nanometers (nm). This option is currently not supported and nanometers are always used. The third dialogue allows the setting of the type of shading used to display the various atom types. Clicking on an atom displays the type of shading used. Click on a shading type to change the display of the selected atom type to that shade. Clicking on 'Save and Exit' saves the MOLSYS.INF file and exits the program. Clicking on just 'Exit' exits without saving the file. Running MolSys ---------------------------------------------------------------- The file MOLSYS.INF should be in the current directory when MOLSYS.PRG is run, i.e. in the same directory as MOLSYS.PRG. On running, the program will attempt to load MOLSYS.INF and the resource file. If these files cannot be found the program will abort. It will then attempt to load the fonts, and then allocate memory for screen buffers and variables. If the program runs out of memory on loading, try decreasing the maximum number of atoms set. Overview of Terms Used in MolSys ---------------------------------------------- In MolSys, a molecule consists of a number of sites and atoms. Atoms are shown by their chemical symbol (e.g. C,H,O,Cl etc.) and sites are shown by a number between 0 and 3. Sites are the only place where atoms may be placed. The type of site shows the type of atoms which may be placed there, 0 means all atoms, and 1,2 or 3 means only singly, doubly or triply bonded atoms. One of these sites or atoms will be the current (or marked) site or atom. In build mode, this site or atom will have a diamond-shaped marker placed around it. If stick mode is on, bonds between sites and atoms are shown by lines. A collection of sites and atoms bonded together forms a molecule fragment. The fragments currently in memory can be shown on the fragment selector (see below), where the visibility of fragments can be turned on or off. One of these fragments will be the current fragment, and its title will appear at the top of the display. Note that the current fragment does not necessarily have to contain the current atom. The current fragment is the one on which normally all manipulations are made. Throughout MolSys, all distances are expressed in nanometres (1E-9 metres), and all angles in degrees. Selecting Functions in MolSys ------------------------------------------------ When a function icon is selected (or the corresponding keyboard shortcut is pressed), the icon may invert, which means that further input is required. For functions such as the freehand rotate and move controls, the mouse cursor will change to an open hand, and the mouse moved to manipulate the molecule. For functions such as rotate bond and measure bond angle, the cursor will change to a cross and one or more atoms may be required to be selected. For all these functions, pressing the right mouse button will exit or cancel the function. Dialogues in MolSys ----------------------------------------------------------- Certain dialogue boxes in MolSys show a small diamond in the upper right hand corner. Clicking on this allows you to drag the dialogue around the screen to see the screen beneath. The position you leave the dialogue in when you exit it will be the position it will subsequently reappear in when you next invoke the function. Using MolSys ------------------------------------------------------------------ Once loaded, the program will show a bank of icons down the left side, and a large blank area on the right. At the top of this area is the title bar. Click on this bar to produce a dialogue allowing you to change the title of the current molecule fragment. This title will change if the current fragment is changed. In the middle of the blank area will be a small zero. This is the place in which the first atom will appear, see the build section below. Four functions are available under the File menu option. These are: New: Clears all the current molecules. Load: Loads a molecule fragment. Save: Saves the current molecule fragment. Quit: Quits the program. All of these functions except quit are available using the File icon bank, see below. At the top of the icon bank are three large icons, with the leftmost high- lighted. Clicking on one of these selects one the three icon banks which allow control of the program. These are: Move/Display: These icons allow the molecule to be translated, rotated and displayed with various options. Build: Controls the building of molecules, deletion of atoms, measurement of distances and angles and changing of these values. Note that when build mode is active, the current atom is shown with a diamond shaped marker. File: Controls the loading, saving and animation of molecules, saving and printing of screenshots, allows access to the molecule selector and controls miscellaneous functions such as New and Help. For each of the three banks, the function of the icons, from left to right are given below. The Move/Display Icons -------------------------------------------------------- Global: Toggles global mode on and off. With global mode on, translations and rotations effect all the visible molecule fragments. With global off, transformations only effect the current molecule. The default setting is off. Translation: The 6 filled arrow icons move the molecule in the direction shown by the arrow by a set distance. Zoom out/in: Zooms the display in and out. Double click on either to set the zoom level to normal. Rotation: The 6 open arrows rotate the molecule around the current centre of rotation by a set angle. Double clicking on these icons causes the molecule to rotate around the marked atom. Set distance: Sets the distance the molecule is moved by the translation controls. The default value is 0.01 nm. Set angle: Sets the angle that is used for rotation with the rotation controls. The default value is 10°. Freehand move: Moves the molecule with the mouse. Click and hold the left button and move the mouse to drag the model in the X-Y plane. Press the right button to exit freehand move. Freehand rotate: Rotates the molecule with the mouse. Click and hold the left button and move the mouse left/right to rotate the model around the Y axis, move up/down to rotate around the X axis. Press the right button to exit. Translate to atom: Click on an atom with the left button to centre the atom on the screen - this also makes it the centre of rotation. Press the right button to cancel. Centre molecule: Centres the molecule on the screen. Rotation centre is now the average position of all the atoms. Note that if global mode is off, only the current fragment is centred. Ball: Toggle space filling ball display. Note that ball display drastically slows down the program, and should not be used when rotating or moving the molecule. Stick: Toggle stick display. With stick display on, bonds are shown as lines between atoms, drawn with the current stick mode. Note that if Ball mode is also active, only the portion of the bond outside the ball is drawn. Label: Toggle label display. Prints the chemical symbol on each atom when on, and also prints the site type on each site. Hide hydrogens: Toggle the display of hydrogen atoms. With this mode on, hydrogen atoms and bonds to hydrogen are not shown. Ball size: Toggles between the full and the reduced size of space filling spheres. Double clicking on this icon calls up a dialogue which allows you to change the percentage size of the spheres and the thickness of the bonds in stickmode 3 (thick) which is displayed when reduced size is selected. Use the arrows to change the values up or down. Stick modes: Four stick display modes at the bottom of the icon bank. The first is thin mode, with all bonds drawn as single width lines. The second mode is depth cueing, and shows bonds between atoms close to the viewer as thicker lines, which helps when rotating the molecule. The third mode is thick mode, which shows thick bonds scaled according to perspective. The fourth is typed mode, which shows single bonds as thin lines, and double and triple bonds as thicker lines. Fragment Names: With this mode on, all visible fragments will have their names superimposed on them, allowing easy identification. The Build Icons --------------------------------------------------------------- Add atom: Eighteen types of atom are shown, which when clicked will be added at the current site, shown with the diamond-shaped marker. This marker (only shown in build mode) may be repositioned by clicking near to an atom on the display screen. For each icon, the type of atoms is shown (carbon, hydrogen, oxygen, nitrogen, fluorine, chlorine, bromine, phosphorous, sulphur) together with its bonds. Single bonds are shown with a hyphen (-), or a greater-than (>) or less- than (<) sign in the case of two single bonds, or a greater- than-or-equal-to (≥) in the case of three single bonds. Double bonds are shown as equal signs (=) or much-less-than («) signs for two double bonds, and triple bonds as equivalence signs (≡). See section 'Building molecules', below. Add group: Nine common functional groups are shown (benzene, OH, CN, CH3, CH2, CO, NH2, PO2HO and COOH) which will be added to the current site if clicked upon. Note that these groups may not be used to start a molecule, i.e. they cannot be added to a site type of zero. Make: Joins two molecule fragments together. The marked atom must be a site, and after selecting this icon, click on another site of the same type in a different molecule fragment. This second fragment will be joined to the first fragment at the marked atom. If you click on a site in the same fragment, a ring will be formed. This is done by directly linking the atoms connected to the marked site and the selected sites. Break: Breaks a molecule into two fragments. Clicking on an atom bonded to the marked atom splits the molecule into two fragments across the bond. Note that in v0.74 you cannot break a ring structure. Make current: Clicking on this icon makes the molecule fragment containing the current atom to be the current fragment. The title bar at the top of the display will change to reflect this, and a box will flash to show the current fragment. Delete: Deletes the currently marked atom. Note that only atoms which are only attached to one other atom may be deleted (i.e. all other attached sites must be empty). So to delete a CH3 group, the hydrogens must be deleted before the carbon atom can be deleted. Also, to delete a ring structure, the whole ring must be deleted at once with a multiple delete command. Multiple Delete: Clicking on an atom bonded to the marked atom deletes all the atoms connected to that side of the marker. The atoms which will be deleted are shown crossed out and confirmation is asked for before the atoms are deleted. Group: Seperate fragments may be grouped together by using this function. Click on any other fragment, and this will become grouped together with the current fragment. Then any function such as rotation, saving etc. will act upon the whole group of fragments. Ungroup: This allows you to seperate grouped but unbonded fragments from the currently selected group. Click on a fragment to seperate it from the current group. Auto distance: Bond lenths in MolSys are calculated from the covalent radii of the atoms, which does not always give the correct value. With auto distance on, bond distances when adding atoms are automatically calculated. With it off, when atoms are added a dialogue appears which shows the computers choice for the bond distance (in nm), which may be changed to a different value. Press OK to add the atom, or Cancel to abort the add. Note that auto distance defaults to on. Geometry: Clicking on this item produces a sub-menu with eight options: Rotate bond: Rotates part of a molecule along a bond. Click on an atom which is bonded to the marked atom. (Right button to cancel.) A dialogue appears which allows you to type in the angle to rotate the part of the molecule which is bonded to the marked atom. Click on plus or minus to set the direction, and then click on OK or Cancel. Alternatively, you may click on Freehand, which allows you to move the mouse up and down to rotate along the bond. Press the left button to stop rotating and the right to exit. Note that this will temporarily change the display mode to stick mode 2. Note however that for large molecules, the freehand function is not recommended. Also, you may click on Minimize Energy, which attempts to rotated around the bond to minimize their van der Waals energy (see below). In the dialogue you can set the total angle to rotate by and the number of steps for which the energy will be calculated. The total angle will normally be 360°, but other angles may be specified if necessary. The Global button selects whether the energy calculations will be carried out for the current fragment or all the fragments in memory. After calculation, a graph is displayed of energy against rotation angle. The minimum energy position found is shown with a dotted vertical line, and this will be the position the molecule is rotated into. The calculation of the minimum energy position may take a very long time even with small molecules, so the number of steps should be chosen to be low. Set bond angle: Sets the angle between two bonds of the marked atom. Click on two atoms which are bonded to the marked atom. (Note that the atoms bonded to the second atom selected will be the ones which are moved.) A dialogue appears with the angle between the bonds at the marked atom. Change this value and click on OK to set, or Cancel to abort the function. Note that you cannot set any angles in a ring structure. Set bond length: Sets the length of a bond. Click on an atom bonded to the marked atom. A dialogue appears which shows the current length of this bond. Change this value and click on OK to set, or Cancel to abort the function. Note that you cannot set any lengths in a ring structure. Torsion angle: The torsion angle of a row of atoms A-B-C-D is the apparent angle between bonds A-B and C-D when looking down the axis B-C. Click on three atoms bonded in a chain with the first connected to the marked atom. The marked atom corresponds to A, the first selected to B and so on. A dialogue appears with the torsion angle. Clicking on 'Align' will set the torsion angle to zero (i.e. align atoms A and D) if this does not involve rotating a bond in a ring structure. Bond angle: Click on two atoms, not necessarily bonded to the marked atom. A dialogue appears with the angle between these two atoms at the marked atom. Length: Click on an atom. A dialogue appears with the distance (in nanometers) from this atom to the marked atom. Set in-plane bond angle: This requires you to choose 3 further atoms, all bonded to the currently marked atom. Thus the marked atom must have at least 3 bonds when using this function. First click on 2 more atoms bonded to the marked atom. These (along with the marked atom) define a plane in which the angle is measured. Then click on the atom for which the angle is to be set. The projection of this atom's bond onto the defined plane forms an angle with respect to a 'normal' in the plane. This angle can be set in the resulting dialogue. Set out-of-plane bond angle: The marked atom must have at least 3 bonds to use this function. First select two bonded atoms, which defines a plane with the marked atom. Then select a bonded atom for which the angle is to be set. This atom's bond defines an angle with respect to the plane. This angle can be set in the resulting dialogue. The File Icons ---------------------------------------------------------------- Load: Loads a .MLS file from disk. The loaded file becomes a new fragment, and is placed in the same position as when it was saved. Save: Saves the current fragment as a .MLS file to disk. Molecule fragment selector: Shows a dialogue which lists all the molecule fragments currently built. The current fragment may be changed by the buttons on the left, and the fragments visible may be changed by selecting the buttons on the right. Clicking on a fragment title allows you to change it's name. Clicking on create will create a new fragment at the centre of the display (a site type 0) and makes this the current site and fragment. Clicking on delete deletes the whole of the current fragment. Note that if there is only one fragment left, this cannot be deleted. Copy makes a copy of the current fragment 0.25 nm to the left (-x direction) of the original. Load and Save perform the same operation as those icons on the File bank, see above. Click on OK to exit this dialogue. Calculate van der Waals energy: The energy of a molecule may be calculated from the energies of interactions between its atoms. The interactions between non-bonded atoms are called van der Waals forces, and the energy-seperation relationship caused by these forces is called the Lennard-Jones 6-12 potential. The form of this potential gives a prefered seperation distance between atoms, which is called the van der Waals radius of the atom. This function calculates the energy of the current fragment by summing the energies of interaction of its atoms. The more atoms in a molecule, the longer this will take. About 30 seconds is necessary to calculate the energy of a 100-atom molecule. If Global mode is on, the energy of interaction between atoms in different fragments is also calculated. After calculation, the energy is displayed in kilocalories per mole. This is the standard unit for conformational energy calculations. Super view: Shows a full screen display of the molecule with the current display settings. Clicking the mouse produces a menu which allows the printing of the display or saving it as a Degas (.PI3) or GEM image (.IMG) file to disk. Animate: The animation facility in available version 0.74 is only a subset of the full implimentation which will be available in future versions. However, the current version is fully usable and is comparable with animation features of other molecular modelling packages. An animation may be output in two ways, either by saving a series of Degas pictures to disk for playback with SHOW.TTP, or (if you have enough memory) by writing the screens to memory for playback inside MolSys. In the produced dialogue, these two options may be selected by the 'Degas' and 'Memory' buttons. By the side of the Memory button, the number of available screens is shown. This value will be dependent upon the memory size of your computer, the number of atoms set in MOLSYS.INF and whether you have any desk accessories resident. The number of screens available on a 520 or 1040ST is unlikely to be enough for smooth animations, but on a 2 or 4Mb ST you may be able to have over 50 frames in an animation. The program will not let you try to run a memory animation with insurficient memory available. In this case, you must use a Degas animation instead. The three buttons 'Play','Clear' and 'Save' will be disabled when you first use the animation option, and are described below. At the top of the dialogue box, the path where degas screens will be saved is shown. Next to the 'Degas' option button, the name of the files is shown. These fields may be edited in the usual way, and the path may also be set with the 'Set Path' button. The produced files will take the name 'path\name.001','path\name.002' etc. The direction of movement of the molecule is shown. Click on an icon to set the direction. (Note that the rotate bond icon is not currently available.) The angle of rotation at each step can be edited, as can the number of steps to save to memory or disk. Clicking on 'Set to Cycle' sets the angle field such that one complete revolution will take place in the number of steps shown. 'Global' sets whether all molecule fragments are to be moved, or just the current molecule. Now clicking on 'Cancel' aborts the animation, or 'OK' starts it. If you are performing a Degas animation, a dialogue shows the free space needed on the disk the files will be written to. Click on 'Cancel' to abort, or 'OK' to continue. The screen will now draw each frame of the animation, which may take some time. At each step, the screen will be written to memory or disk. If you have selected Memory animation, a dialogue appears showing the controls of the playback. Clicking on 'OK' shows the memory-saved screens in sequence, looping round at the end. Use the [+] and [-] keys on the main keyboard or the keypad to increase or decrease the speed of playback. Pressing [SPACE] exits the animation. If you have used the Degas animation option, you may now use the SHOW.TTP program the show your saved frames. Read the SHOW.TXT file for instructions of use. If you have used the memory animation function, on re-entering the Animate dialogue, three more options are available. 'Play' replays the animation, 'Clear' erases the animation and 'Save' writes the stored animation to disk as a series of Degas files, using the same file path and name as those set for Degas animations. New: Clears all the current molecules. Help: Toggles the help messages which are shown during certain operations at the bottom of the display area. Help mode also enables the display of certain error messages. Default is on. Double clicking on this icon brings up a list of keyboard shortcuts. Click the mouse to exit. Install printer: Sets the port and resolution of the printer for printing the screen. Blank 2: In v0.74, creates a file in the current directory called MOLSYS.LOG, which is used for testing purposes. Show surface: This function allows the showing of the effective 'surface' of a molecule as a 3D dot pattern. In the resulting dialogue, the pitch of the dots can be selected, which is the seperation, in degrees, between points on the sphere of the atom. The smaller the pitch, the more dots displayed and the longer it takes to display them. The visibility of the molecule can also be selected. This shows whether the normal display of the molecule will be shown on top of the dot display. The selection of van der Waals or covalent radii chooses which of these radii to display the atoms with. After showing the display, which may take a long time if the dot density is high or the number of atoms in the molecule is large, the picture can be printed or saved as for the Super View feature. Keyboard Shorcuts ------------------------------------------------------------- Certain functions may be used via a key press irrespective of the currently selected icon bank. See above for a description of the functions. Also, some icons have small letters in the bottom right, which give the keyboard shortcut for that function. Key Function [LEFT],[RIGHT], [UP],[DOWN], [INS],[CLR]: Rotate the model, as for rotate icons. Keypad[4],[5],[8],[5], [7],[9]: Rotate the model around the marked atom. [SHIFT]+[LEFT],[RIGHT], [UP],[DOWN], [INS],[CLR]: Translate the model, as for translate icons. [SPACE]: Toggle between Move/Display,Build and File icon banks. [HELP]: Shows a list of keyboard shortcuts. [S]: Toggle stick mode. [B]: Toggle ball mode. [L]: Toggle labelling. [1],[2], [3],[4]: Set stick mode to thin, depth cue, thick or typed. [H]: Toggle hide hydrogens. [Z]: Toggle ball size. [C]: Centre molecule. [T]: Translate to atom. [DELETE]: Deletes the marked atom. Keypad[+], Keypad[-]: Zoom display in or out. Keypad[*]: Set zoom to normal. [M]: Engage freehand move mode. [R]: Engage freehand rotate mode. [G]: Toggles global mode on and off. [N]: Toggles fragment names on and off. [CTRL]+[C]: Creates a new fragment in the centre of the screen, and makes this the current atom and fragment. [CTRL]+[D]: Deletes the current fragment. [CTRL]+[S]: Saves the current fragment to disk. [CTRL]+[L]: Loads a fragment from disk. [CTRL]+[X]: Copies the current fragment. [TAB]: Changes the current fragment by cycling through all the fragments. [RETURN]: Makes the fragment containg the current atom to be the current fragment. (Only available in build mode.) [ESC]: Renames the current fragment. [ENTER]: Invokes MultiSys™ fragment selector. [UNDO]: Quit MolSys. [F1],[F2],[F3]: Set display types to useful defaults. Note that a list of keyboard shortcuts can be displayed by double clicking on the 'Help' icon, or by pressing the [HELP] key. Renaming Molecules ------------------------------------------------------------ When renaming molecule fragments (by clicking on the title bar, pressing [ESC] or through the molecule selector), it is possible to include the greek letters alpha, beta, epsilon, gamma, lambda, omega, pi, sigma and tau in the name by typing '\' then 'a','b','e','g','l','o','p','s' or 't'. If you require the '\' symbol in the name of a molecule, type two backslashes '\\'. Note that some letters are only available in the supplied fonts, and will be displayed as Hebrew characters if you are using the normal screen fonts. When a new fragment is created, it is automatically named 'Untitled'. This is also the name given to a fragment created with the Break Bond function. When using the Make Bond function, the amalgamated fragment takes on the name of the fragment containing the marked atom. Turning fragment names on gives a continuous update of the names of all the visible fragments. Building Molecules ------------------------------------------------------------ The procedure for building molecules is not as flexible as some systems, but is quick and easy to learn and very quick to use, and requires no knowledge of bond lengths or angles. It is recommended that you turn on the labelling and stick modes and turn off ball display mode before you attempt to build a molecule. On entering build mode for the first time (click on the icon, or press space), a zero surrounded by a diamond can be seen in the middle of the display area. This zero is a 'Site'. Sites are the only place which atoms may be added in MolSys. The diamond is the marker of the current atom or site. If there is more than one site or atom on screen, clicking on the display area in build mode sets the marker to the nearest atom or site. (Double clicking will also make the fragment this atom is in the current fragment.) The zero means this is a special type of site, as any atom can be added there. Clicking on an atom icon (e.g. '>C=') will place that type of atom at the zero site, and add more sites to the display. In this case, it will add three: two '1's and a '2'. These numbers represent the type of bond possible between the atom the site is bonded to and any atom you may subsequently place at the site. Note that this atom must have at least one bond of the correct type, e.g. only '>C=','=O' '=N-' '≥P=' and '>S«' atoms can be added at a type 2 site, and only '≡C-' and '≡N' atoms can be added at a type 3 site. Adding further atoms may produce more sites where more atoms can be bonded. It may be necessary to scale or rotate the molecule during the course of building it. This is more conveniently done with keyboard shortcuts than by switching to the Move/Display icon bank. Groups are added a similar way, except that the may only be added to type 1 sites. Clicking on a group icon adds that group to the molecule at the current site. Note that groups or atoms may not be added to a site which is of the incorrect type, or when an atom is marked. The program will also not allow you to add more atoms than is set in the configuration file. Example of Building a Molecule ------------------------------------------------ Turn on the stick and labelling modes, and turn off ball mode. Press [1],[2] or [4] to get the sticks displayed in a useful mode. Click on New (in the File icons, or under the File menu.) Click on Build mode. Press keypad[*] and then [C]: if it was not already there, a zero surrounded by a diamond will appear in the centre of the display area. Click on '>C<': The zero will be replaced by a 'C' and four lines ending in '1's will appear. Click on each '1' in turn and add hydrogens ('-H') to the first three and a carboxyl group ('-COOH') to the fourth. Click on the title bar at the top of the display area and type '[ESC]Ethanoic Acid[RETURN]'. You have made your first molecule with MolSys! Enjoy! A More Complex Example -------------------------------------------------------- Taking the molecule built above, making sure you are in build mode, delete one of the hydrogens bonded to the main carbon by selecting it and clicking delete: the 'H' will be replaced by a '1'. Now move the molecule off to one side with the translate icons or keys, so that it no longer covers the centre of the display. Now press [CTRL]+[C]: This creates a new molecule fragment and a '0' will appear in the centre of the screen, and will become the current site. Note also that the title bar changes to 'Untitled', the title of the new fragment. Now click on '>N-' to place a nitrogen atom at the new site, and replace two of the three created sites with hydrogens by clicking on each one of them in turn and clicking '-H'. Rotate the nitrogen about a bit using the cursor keys - note that, if global mode is off, the ethanoic acid molecule will not move. Make the final '1' site the current atom by clicking on it, and then click on 'Make': The icon will highlight and the cursor will change to a cross. Click now on the '1' in the ethanoic acid molecule you moved off to the side earlier. The molecule will become bonded to the nitrogen atom at the centre of the screen. Click on the title bar and type '[ESC]Glycine[RETURN]'. You have just made a model of glycine, the simplest amino acid. Tips -------------------------------------------------------------------------- When displaying molecules, the best display mode is ball mode on, stick mode 3 (thick) and reduced size mode. (This can be set by pressing [F2].) Try adjusting the ball and stick size and thickness (double click on the size icon) to find the best ratio. Because ball mode slows down the program so much, it is best to switch it off when rotating or moving the molecule. Using stickmode 2 (depth cue) gives a better feeling of orientation when rotating. When building, it is best to turn labelling on so as to see the site types, and stickmode 4 to see the bond types. Bugs -------------------------------------------------------------------------- The one major bug in MolSys is the failure of the build function to align double-bonded atoms correctly. This may be done manually by finding the torsion angle and using the 'align' feature to rotate along the double bond until the atoms are correctly aligned. This will be done automatically in future versions. If you find any bugs in MolSys, please contact me at the address below. Features of Future Versions --------------------------------------------------- MolSys version 1.00 is currently under development. Its features will include: * Support for ST medium, ST high, TT medium, TT high and larger screen resolutions, in fact any screen of width 640 pixels or more. Colour will also be supported, with support for 1, 2, 4, 8 & 16 bit colour. * Much more GEM legal programming, hopefully compatible with MultiTOS. * Faster graphics (maybe). * GEM IMG, Metafile and PostScript graphic output formats. If you would like to see a particular feature in MolSys that it does not yet have, let me know and I will try to implement it. I am also willing to produce customized versions of the program. I would also appreciate any information on file formats used by other molecular modelling programs, including those used on other machines. I may then be able to implement these types of files in the forthcoming file converter program, MSC. Failing a human readable listing, I may be able to decypher the actual files themselves, given a few small examples. For information on the MolSys molecule file format, consult the file MLS.TXT which accompanies this distribution. Information ------------------------------------------------------------------- Future versions of MolSys will continue to be released into the Public Domain, but unlimited versions will only be available by registering. Please send me a cheque/PO/cash for £10.00 to the address below, made payable to Robert Mellish. You will receive the latest (unlimited) version of the program, notification of future upgrades and (maybe- no guarantees) a printed manual. A copy of the C source code is also available to registered users. If you have any comments, recommendations or ideas for MolSys, please write to tell me, even if you don't want to register. I would especially like ideas for new features which I may implement in future versions of the program. A version of MolSys for IBM PC compatibles, PMS, will soon be available. Write to the address below for more information. Robert Mellish, Westbury, Ranelagh Drive, Bracknell, Berkshire. RG12 3DA UK Tel:(0344) 428171 email: r.mellish@ic.ac.uk Remember, MolSys is the best molecular modelling system on the ST! ------------------------------------------------------------------------------- (If you can't afford £10, or don't think MolSys is worth it, that's OK. Send me whatever you can, or just write to me. I always like to hear from users, so drop me a line at the address above if you have any comments. I will send you the latest version (with the 100 atom limit still in) if you send me a disk and postage.) ------------------------------------------------------------------------------- Robert Mellish, Helion Graphics, 09/02/93 MolSys v0.74