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A glimpse into another universe: ---------------- M O L E C 3 D ---------------- An interactive 3D solid modelling program for molecules. Running on all AMIGA models. 1 MByte memory required. Written by Dr.Stefan Abrecht, Baumgartenweg 14 CH-4142 Münchenstein Switzerland Checked by Beat Steiger Basel, Switzerland 1. INTRODUCTION Molec3D is a program for the graphic, three dimensional repre- sentation of molecules, based on 3D coordinates data from geometry optimization programs, X-ray measurements, or any other source. The program can handle up to 500 atoms at a time, is written 100% in assembler and runs on Amiga's with at least 1 MByte memory. It automatically adjusts the vertical display resolution to american (NTSC) or european (PAL) machines. The program consits of two modes: In wire frame mode the molecule can be real time positioned in space. The color picture mode then produces a variety of 3D-color representations out of this. The generation of these ray-tracing-like pictures is very fast: 10-15 seconds are typical for molecules consisting of about 100 atoms (on a normal AMIGA with a 8 MHz/68000 processor and without math coprocessor). 1.1 The menu system To avoid descriptions for menu selections like "go to the PROJECT menu, choose the SAVE item and select its PROTOCOL subitem", this is written throughout this text as e.g. PROJECT->SAVE ->PROTOCOL. There are keyboard shortcuts available for frequently used menu items (shown on the right edge of the menu items), which allow convenient work with the program. Settings are switched on and off by selecting an re-selecting a menu item (toggle). When molecules containing more than about 150 atoms are displayed, the response on menu selections becomes slow. If this is the case, keep the right mouse button pressed for a while, until the menu appears. Keyboard shortcuts are not recommended in this special case. 1.2. AMIGA's with 512 KBytes memory It is definitely not recommended to run the program on 512 K memory under Kickstart 1.3. Altough the wire frame mode will work in most cases, the system could crash when it is attempted to switch to the color picture mode (especially if a second disk drive is mounted under these tight memory conditions). 2. WIRE FRAME MODE In wire frame mode a molecule is positioned in 3D space for sub- sequent generation of a color picture. Distances and angles be- tween atoms may be determined and are automatically protocolled. Settings are defined and files can be speech-synthesized. To display a molecule, its coordinate file (see chapter 4) has to be loaded by PROJECT->LOAD. Examples of such files are available in the "DEMOS" directory of the program disk. A file requester (see chapter 5) with following content will appear: DIR DEMOS DIR fileconversion DIR Manual DIR tables Molec3D Only the DEMOS-directory contains coordinate files. Click at this directory to see its files, select one of these, and the corres- ponding molecule will be displayed. Rotation and translation of a molecule are controlled by the keys of the numeric keypad. The ENTER key toggles their functionality between rotation and translation. In step-mode (toggled by the ZERO-key) only one motion frame is displayed at a time. Just try now to move the molecule you just loaded! For maximum animation speed and accuracy, a transformation method is applied, in which the original coordinates rotate along with the molecule. This may cause two axes to coincide or other incon- veniences. Use therefore the JUSTIFY-function (see below) for exact positioning of the molecule in space. 2.1. Center and reset molecules FUNCTIONS->CENTER moves the molecule to the center of the screen (actually its pivot point is centered). FUNCTIONS->RESET resets the molecule to its position immediately after loading. This is helpful, if a molecule is accidentially moved out of view. 2.2. The Justify-function An atom, line or plane can be adjusted parallel to the viewing axis by marking 1-3 atoms followed by FUNCTIONS ->JUSTIFY. This is a very powerful function for positioning molecules in space. An atom is marked by moving the mouse pointer on it and pressing the SPACE bar. A "#" mark will be attached to it. Marks are re- moved by FUNCTIONS->MARKS OFF. One mark defines the line beween the marked atom and the pivot point of the molecule. Two marks define the line between them- selves. Three marks define a plane. FUNCTIONS->JUSTIFY moves the marked atoms to the desired position in space. This is either done animated or in one jump; select the desired mode with SETTINGS->SET_JUSTIFY->ANIMATED. By default, the marked atom(s) will be moved to the center of the screen. If this is not desired, toggle SETTINGS->SET_JUSTIFY->CENTERED. As a rule, JUSTIFY rotates the molecule along its actual pivot point in such a way, that the marked atoms are positioned in front of the molecule relative to the viewer (plane,atom). In the case of a line, the first marked atom will be moved in front of the second one. 2.3. Labels, distances/angles and protocol Atoms can be labelled to find out which is which. Simply click at one with the mouse pointer, and its label will be displayed, e.g. "C21". Such labels also remain attached to their atoms when the molecule is animated. All labels are switched off by FUNCTIONS-> LABELS OFF. Distances and angles between any atoms in the molecule are de- termined by labelling - not marking! - two (distance) or three atoms (angle), followed by FUNCTIONS->DISTANCE or FUNCTIONS-> ANGLE, respectively. The corresponding value will be displayed in a requester. The latest 20 displayed values are stored in a ring buffer in memory (protocol). This protocol can be saved as ASCII-file by PROJECT->SAVE-> PROTOCOL. 2.4. Speak, IFF, interlace and multitasking For proof reading your coordinate files, the PROJECT->SPEAK func- tion will read them aloud for you. Its advantage over the AMIGA- DOS command "say" is, that the reading can be stopped/continued after every line. Moreover, the line currently being read is displayed on screen. The contents of the current wire frame screen can be saved as IFF file by PROJECT->SAVE->SCREEN and is thus available for all stan- dard paint programs. The resolution of the wire frame screen is doubled vertically by SETTINGS->WIRE_FRAME->INTERLACE. The disadvantage of this mode is a slight flickering and the increased memory consumption of the graphics display. Therefore it is not recommended to use this mode if you are short in memory, otherwise the color display (see be- low) is no more possible. Multitasking is fully supported. However, in wire frame mode double buffering does not allow to return to the workbench in the usual manner, namely by pressing left-AMIGA-N. Instead, PROJECT-> CLI/WB will do this. Once in the workbench screen, click into the desired window. When you are done with the workbench screen, press left-AMIGA-M to return to MOLEC3D. Don't forget to click inside the screen to re-activate the program again! 3. COLOR PICTURE MODE Color picture mode generates 3D color (or black & white) repre- sentations of a molecule in a variety of display options. The high resolution picture may be saved in compressed IFF-format (com- patible with all standard paint programs). The color picture screen displays objects in 16 colors in the highest possible resolution (hires/interlace). Altough in inter- lace mode, the display is virtually flicker-free due to the chosen geometries and colors of the objects (except in black&white repre- sentation, see below). The possibility to save the screen as IFF-file is a direct com- munication link to other programs. E.g. for printing, additional painting or page flipping, specialized programs in these fields will do an excellent job. There are two ways to enter the color picture mode from the wire frame screen: press the "."-key of the numeric keypad, or use FUNCTIONS->COLORPIC alternatively. Actually, all settings for the color picture mode are defined in the SETTINGS menu of the wire frame mode, since menus are avail- able only in this mode. Pressing a mouse buttton in color picture mode will produce a requester with following options: save screen as IFF-file (Save Pic), cancel the requester (Cancel) and go to wire frame mode (Quit Pic). The latter also can be accomplished by pressing "." on the numeric keypad. For the color representation there are 7 individual atom colors available (each of these consiting of two different shades plus white). They are assigned to their atoms by the color assign table of SETTINGS->COLOR_TABLE-> ASSIGN. For example, blue can be as signed to all C-atoms, red to all O-atoms, green to all Cl, Br and J atoms, and so on. All unassigned atoms will be represented in grey. Just click inside a box of the color assign table and enter the required atom symbol (up to 2 letters - it doesn't matter if in upper or lower case letters or both). Individual color assign ment tables can be saved with SETTINGS-> COLORTABLE->SAVE and loaded with SETTINGS->COLOR_TABLE ->LOAD. Load the file Tables/ OrigCols to restore the default colors. There are various options for the color representation of mole- cules. Almost all of these can be active at the same time or indi- vidually switched on (checked in the menu) or off (not checked). This is done by SETTINGS->BONDMODE..... -> SPHERES: Toggles the display of spheres. All atoms are dis- played in the same relative sphere radius, i.e. van der Waals radii are not considered. -> CONNECT: Both halfs of a bond stick obtain the color of the atom they are connected to. If switched off, the whole bond will be represented in grey. -> SHADED STICK: Switches the simulated shadows on the bond sticks on/off. There are two functions for depth-cueing the display, i.e. fading the molecule with increasing distance from the viewer: -> GRADPAT: Superimposes a background color pattern onto the more distant half of the molecule, which therefore seems to disappear in the background. In SHADOWS mode (grey background) shadows are temporarely set to none. -> GRADCOL: Gradually darkens the molecule from front to end in five stages. Only five atom colors (the first five actually used in the color assign requester) are available in this mode, SPHERES and SHADED are not active, also SHADOWS, BLACK&WHITE and PATFADE are switched off automatically. If CONNECT is off, the first color used in the color assign table will be used as bond color. Finally, there are two functions dealing with overall display effects: -> SHADOWS: Generates shadows of the molecule on an imaginary surface slightly below it. This option greatly en- hances the 3D-effect the whole representation. The intensity of the shadows can be adjusted by SETTINGS ->SET_SHADOWS->... to STRONG, NORMAL, WEAK and NONE (no shadow at all but grey background, useful in connection with GRADPAT). GRADCOL will be switched off automatically. When using grey atoms, at least one color of the color table should remain unused and thus be available to the shadow algorithm, otherwise errors in the shadow generation will occur. -> BLACK&WHITE: Generates a black and white representation of the color picture. Although initially meant and very useful for black and white publication purposes, this display mode is quite intriguing by itself. GRADCOL is automatically switched off in this mode. The screen will flicker significantely, especially when working with shadows. 4. COORDINATE FILES: A coordinate file contains atomic coordinates (x,y,z), their con- nectivities, and a bond length definition (used for scaling). It may be created as ASCII-file on any text editor. All entries are separated by one or more spaces or tabs, not by semicolons. For examples, please refer to the "DEMOS" drawer of your program disk. MOLEC3D produces detailed error messages, if the file format should be incorrect (cf. chapter 7). The first part of the file contains atomic labels and coordina- tes. Labels are descriptors for atoms, e.g."C21" or "Si14". Their size is limited to four characters, starting with the element sym- bol, followed by a number (not vice versa!). Atomic coordinates are cartesian x,y,z-coordinates which must be in the range between +-(99'999 and 0.0001). C1 123.4 432.5 -15.8 Si11 233.6 -231.7 122.8 The second part of the file contains a bond length definition. In this statement, one bond out of the molecule is defined: single (=s), double(=d), triple(=t) or aromatic(=a). The program extracts from this the actual size of the molecule (scaling). The bond length definition is introduced by an asterik ("*") followed by the bond-descriptor and the two labels defining the bond. All en- tries are connected with a "-". Again, just one bond of the whole molecule needs to be defined this way. *d-C3-C7 The third and last part of the file contains the connections between the above atoms. These are defined by connecting their labels with a "-". Make sure that the labels exactly match the ones defined in the coordinates part of the file, otherwise an error message will occur. Any number of such lines may be created. C1-C2-C5-C7 O27-C16-S12-O15-C12 5. FILE REQUESTER If you already are familiar with file requesters on the Amiga, then please feel free to skip this chapter. When functions like LOAD, SAVE or SPEAK are selected, a file re- quester will appear, displaying the files and directories of a given disk. When starting MOLEC3D from CLI, the file requester will contain the contents of "df0:" as default. When started from the workbench, the contents of the actual program disk are shown. The pathname gadget contains information of where a file is to be found (drive or diskname, directory, subdirectory), without speci- fying the filename itself, e.g. "df1:demos". The contents of the pathname gadget are either updated automatically by the file view (see below) or may be edited manually, e.g. for changing the current drive. The filename gadget contains the name of the file to be selected in the current path. As above, the contents of the gadget are either updated by the file view or may be edited manually. The file view contains eight directories and/or files of a given path in alphabetical order. Directories are labelled as "DIR" and displayed first. When clicking such a directory, its name will be copied to the pathname gadget and its content is loaded from disk and displayed. A selected filename is copied into the file name gadget. If there are more than eight entries in a directory, the slider to the right of the file view can be moved to define the section of entries to be displayed. This is graphically represented by the size and position of the slider bar. If there are eight or less entries within a directory, the slider bar will fill the whole slider and cannot be moved. The more entries there are, the smal- ler the bar becomes. Update updates the contents of the current path. This is useful when a file has been deleted or created during a multitasking session with CLI. Cancel cancels the file requester without any further actions to the program. After clicking the OK box, the file requester disappears and the currently selected filename will be used by the program for further actions. This can also be accomplished by pressing RETURN inside the filename gadget. 6. CONVERSION OF ALCHEMY-FILES TO MOLEC3D-FILES Alchemy-files can be converted to the Molec3D format. This enables you to view your own molecular constructions in Molec3D pictures. All programs needed for this conversion are contained in the file conv directory of the program disk. The first thing to do is to convert the IBM-format file to AMIGA format. This can either be done by the public domain program "PcPatch" on this program disk (please refer to the PcCopy-doc for the procedure), or by any other IBM->AMIGA conversion program. The ConvertAlchem program then converts Alchemy files (AMIGA-for- mat) to Molec3D files. It must be executed from CLI and from with in the fileconv-directory ("cd Molec3D:fileconv") in the following way: ConvertAlchem <sourcefile> <destfile> where <sourcefile> is the Alchem-file including its path, <dest file> is the corresponding Molec3D file including its path. Exam- ple: ConvertAlchem df1:testos.txt ram:testosterone. If a label contains more than 4 characters, e.g. CU234, the second digit will be omittet to fit the Molec3D format; so 234 CU will become CU24. Note that the bonddescriptor line (e.g. *s-c1-c3) of the Molec3D file is generated from the first bond definition encountered in the alchemy-file. This may not be a C-C bond. In this case you will have to edit this line manually for a correct C-C bond de- finition. 7. ERROR MESSAGES Coordinate file errors: Line-format: more than 3 coords. A line of the file contains more than 3 coordinate values. Fre- quent message, if it is attempted to load a non-coordinates file. Number >99999 detected in file. A number greater than the allowed maximum value of +- 99999 was found (numbers smaller than +- 0.0001 are treated as zero). Bondlength label not found. The bondlength descriptor contains a previously undefined label. Just ONE bonddescriptor allowed. More than one bond has been defined by a bonddescriptor, but only one definition is allowed. Too many labels in bonddescriptor. Only two labels make sense in the bonddescriptor. Invalid bonddescriptor format. The bonddescriptor does not match the format "*x-label1-label2" (x=s,d,t,a). Undefined connect item: xxxx The displayed label (xxxx) out of the connections section was not defined in the coordinates section. Selection errors: More than one point selected. More than one atom was in the range of the mouse pointer, when you tried to put a mark or label on it. Rotate the molecule into a new position and try again. Exactly 2 centers required. You tried to obtain a distance value by defining more or less than the required 2 labels. Exactly 3 centers required. You tried to obtain an angle value by defining more or less than the required 3 labels. No justify point(s) selected. Attempted use of the justify function without defining any marks. More than 3 justify points selected. There is a maximum number of 3 justify points (plane) that make sense. This number was exceeded. Memory-errors: Out of memory - program will abort. Not enough memory available to read in files. Hopeless situation. Reset the computer and restart the program. The program WILL run on any Amiga with 1 MByte memory. Out of memory for color display. No color display possible. Remove all other simultaneously running programs from the system and try again. The program WILL run on any Amiga with 1 MByte memory. Out of RAM for file requester. Not enough memory to display the file requester in color pict mode (save IFF). Remove all other simultaneously running programs from the system and try again. The program WILL run on any Amiga with 1 MByte memory. Not enough memory for shadows. No shadows can be generated. Remove all other simultaneously running programs from the system and try again. This function WILL work an any AMIGA with at least 1 MByte memory. DOS-errors: File not found. Error while reading disk. Disk is full. Unable to open file. All these messages should be self-explanatory other errors: This is no ASCII-file. You tried to speak a non-ASCII file. Sorry, the Amiga doesn't speak chinese. Nothing protocolled so far. There are no protocol entries around to be saved. Out of colors for correct shadows. Due to internal routines, the program requires at least one un- assigned color out of the seven available ones, in order to cast correct shadows. Rearrange the color assignments if this is not the case. 8. Literature references of demos In some demos hydrogens are omitted, solvent molecules removed, or coordinates scaled. atrovenetin: ATROVENETIN ORANGE TRIMETHYL ETHER FERRICHLORIDE I.C.Paul, G.A.Sim, J.Chem.Soc., p.1097 (1965). avenaciolide: (-)-AVENACIOLIDE D.L.Hughes, Acta Crystallogr., Sect.B, 34, p.3674 (1978). bis-porphyrine: {N3Mn(IV)(TPP)}2O B.C.Schardt, F.J.Hollander, C.L.Hill, J.Chem. Soc.Chem.Commun, p.765 (1981). bromo-edunol: BROMO-EDUNOL J.G.Leipoldt, G.J.H Rall, D.G.Roux, J.C.Breyten bach, J.Chem.Soc.,Chem.Commun. p.349 (1977). calix(8)arene: (CALIX(8)ARENE METHYL ETHER)-HEXAKIS(TRIMETHYL ALUMINIUM) BIS(TOLUENE) A.W.Coleman, S.G.Bott, J.L.Atwood, J.Inclusion Phenomena 5, p.581 (1987). coenzymeB12: 5'-DEOXYADENOSYLCOBALAMIN (VITAMIN B12 COENZYME) P.G.Lehnhert, Proc.R.Soc.London, Ser.A, 303, p.45 (1968). cucurbituril: CUCURBITURIL CALCIUM BISULFATE SULFURIC ACID TRIDECAHYDRATE W.A.Freeman, W.L.Mock, N.Y.Shih, J.Am.Chem.Soc. 103, p.7367 (1981). cyclodextrine: ALPHA-CYCLODEXTRIN HYDRATE CLATHRATE K.K.Chacko, W.Saenger, J.Am.Chem.Soc.103, p.1708 (1981). cyclosporinA: CYCLOSPORIN A H.-R.Loosli, H.Kessler, H.Oschkinat, H.-P.Weber, T.J.Petcher, A.Widmer, Helv.Chim.Acta 68, p.682, (1985). deoxyoligonuc: DEOXY(CYTIDINE PHOSPHATE GUANOSINE PHOSPHATE THYMIDINE PHOSPHATE) R.G.Brennan, E.Westhof, M.Sundaralingam, J.Biomol.Struct.Dyn.3, p.649 (1986). furan: 3-METHYL-7-METHOXY-5-(PROP-1-ENYL)-2-(3,4-ME THYLENE-DIOXYPHENYL)-2,3-DIHYDROBENZO(B)FURAN M.N.Ponnuswamy, S.Parthasarathy, Cryst.Struct.Commun. 10, p.1203 (1981). hexakisbenzene: HEXAKIS(2-PHENYLETHYLTHIOMETHYL)-BENZENE 1,4-DIOXANE CLATHRATE K.Burns, C.J.Gilmore, P.R.Mallison, D.D. Macnicol, S.Swanson, J.Chem.Res.30, p.501 (1981). tetrakisCu: A.S.Batsanov, Yu.T.Struchkov, A.S.Grigor'Eva, E.E.Kriss, N.F.Konakhovich, Yu.A.Fialkov, Koord.Khim.7, p.784 (1981).