MolEdit 1.0.b ************* Editor for Mopac-Files ====================== Peter Gedeck Inst. f. Phys.Chem.I University of Erlangen Egerlandstraße 3 8520 Erlangen Tel: ++9131-857335 Fax: ++9131-858307 E-mail: gedeck@pctc.chemie.uni-erlangen.de WWW: http://pctc.chemie.uni-erlangen.de/~gedeck/gedeck.html Index ===== 1. Introduction 2. Installation 3. General Information 3.1 Conventions 3.2 Short description of the menu 4. The Editor 4.1 Editor control-keys 4.2 A typical edit-session 5. The conversion utilities 5.1 The GIP-format (geometry-interchange-program) 5.2 Formating input-files 5.3 Conversion between different formats 5.4 Converting using the Babel program 6. The molecule viewer 6.1 The menu 6.2 Changing the molecules viewpoint 6.3 Determination of geometrical parameters 6.4 Options which control graphical output 6.5 Creation of HPGL-files 7. The configuration-file 8. Plans 9. Copyright 10. History 11. Credits Appendix 1: DPMI (DOS-Protected-Mode-Interface) Appendix 2: Babel (Version 1.06) 1. Introduction =============== MolEdit is an editor specially designed to prepare input-files for quantum-chemical programs. During the construction of an input-file it is always possible to check the correctness of the defined structure. In case of errors MolEdit provides informative error messages for the implemented input formats. In addition the combination of the editor with a molecule-viewer allows to examine the defined geometrical structure. This is especially valuable for the creation of z-matrices. The molecule-viewer allows to rotate and to translate the molecule. The structure can be displayed in five different ways: o Wire-frame o Ball-and-Stick o Dot-clouds o Grid o Spheres The combination of an editor with a molecule-viewer will make it very easy for beginning students to learn to write z-matrices. Other features included in MolEdit are: o Formatting input-files o Converting between different formats (Mopac <=> GIP) o Deleting Dummy-Atoms o Inserting and deleting of atoms (while keeping the references correct). o Creation of HPGL-files In the current version MolEdit fully supports several file formats. These are: o The Mopac file format, which is used by the semiempirical program packages Ampac, Mopac and Vamp. o The GIP (geometry-interchange-program) format o The Xmol format Other file formats, among those the Gaussian-file formats are accessible through the conversion utility Babel. MolEdit provides a interface that simplifies the usage of Babel. MolEdit is also able to load, edit and save UNIX-Files. The is useful, if UNIX-filesystems are mounted via NFS. MolEdit is a DOS-application written for the IBM-PC-AT and needs a VGA or EGA-card, either monochrome or color. A coprocessor is recommended but not necessary. In case the real-mode-version of the program is used, either the use of expanded-memory or of a disk-cache is recommended. The program was tested with monochrome-VGA-cards and should adjust itself to this mode. 2. Installation =============== MolEdit is available by ftp from ftp://pctc.chemie.uni-erlangen.de/pub/moled/. In this directory you will find 5 files, the installation program and 4 self-extracting files: o Install.exe - Installation program o MolEdRM.exe - Real-mode version, for IBM-PC's without a coprocessor o MolEdRM7.exe - Real-mode version, for IBm-PC's with a coprocessor o MolEdPM.exe - Protected-mode version, for IBM-PC's without a coprocessor o MolEdPM7.exe - Protected-mode version, for IBm-PC's with a coprocessor Protected-mode versions can use all memory available on your PC, including normal and extended memory. Retrieve all files and copy them to a floppy-disk or to a directory on your hard-disk, after the installation these files are not needed anymore. The call the programm install and follow the instructions. The install programm will created several files in the installation directory: o MolEdit.exe - the main-program o egavga.bgi - The BGI-graphic-driver o *.chr - BGI-font-files o MolEdit.doc - The document in ascii-format (not for the newest version) o MolEdit.htm - The document in HTML-format o changes.mol - Summary of changes in each version o Real-mode packages contain: o MolEdit.ovr - Overlay-file for MolEdit.exe o Protected-mode packages contain: o rtm.exe - Various files used to run protected-mode programs. o rtmres.exe - See appendix I for details. o dpmi16bi.ovl o dpmiinst.exe o dpmiload.exe If you haven't already got the PC-version of the conversion program Babel (see Appendix 2) you find version 1.06 in the same directory. This program was written by Pat Walters and Matt Stahl from the University of Arizona. The newest versions of Babel can always be found at their ftp-site ftp://xxx/xxx. 3. General information ====================== MolEdit is written as an event-driven program. Input can be provided either using the keyboard or the mouse. After you started the program the screen consists of three different parts. The first line is the menu-line, the status line displays several hot-keys. 3.1 Conventions +++++++++++++++ The main menu can be selected by entering the red-highlighted letter combined with the Alt-key, e.g. pressing Alt-F selects the File-menu. As a result a sub-menu appears. To select one of the menupoints, press the red-highlighted letter without the Alt-key, e.g. to select File|Display press Alt-f and then d. If an option is disabled in a specific context, it will be written in grey. Some menu-options can be chosen by pressing hot-keys. E.g. F3 will open a file-open dialog and is therefore equivalent to the File|Open menu point. 3.2 Short description of the menu +++++++++++++++++++++++++++++++++ This is the structure of the Expert-Menu, the Beginner-Menu has a restricted functionality and might be especially usefull for educational purposes. File New : Start editing a new file Open ... (F3) : Read a file and open an editor window Save (F2) : Save file in active editor window Save as ... : Save file in active editor window using a different name Save all : Save files in all editor windows Print : Send file to printer Change dir ... : Change the current directory DOS-Shell : Open a DOS-Shell. To return to the program enter exit Info : Information about the program (version and copyright) Exit (Alt-X) : Exit program Edit (Tools for copying and pasting in an editor-window or between different Editors) Undo : Undo the last editing command Cut (Shift-Del) : After selecting text cut it and copy it into the clipboard. Copy (Ctrl-Ins) : Copy highlighted text into the clipboard. Paste (Shift-Ins) : Copy text from the clipboard Clear (Ctrl-Del) : Delete highlighted text Insert lines (Alt-I) : Add lines, adjust atom references as needed. Delete lines (Alt-D) : Delete lines, adjust atom references as needed. Filetype (Dos-Unix) : MolEdit not only allows to edit files saved in DOS format, but also UNIX-Ascii files. The filetype dialog allows to select either DOS or UNIX format Molecule Fileformat : Change format of file. After loading a file MolEdit tries to detect the correct format. Information : Displays information about the molecule (e.g. sum formula, symmetry, mass) Check (F4) : Check the active file View (F9) : View the active file Conversion Format : Format the active file Create Z-Matrix : Automatic construction of a Z-Matrix. This will only work, if the geometry of the molecule can be read correctly. Delete Dummies : Delete dummy-atoms. Here as well, the definition must be correct, in order for this option to work. After the dummy-atoms are deleted a new Z-Matrix is constructed automatically. Convert (Babel) : Convert active file using the Babel program Convert -> Mopac : Convert active file to Mopac-format -> GIP : Convert active file to GIP-format Options Beginner/Expert-Menu : Toggle between the two Menu-types Conversion : Enables you to choose, whether the new created file should be displayed in a new fileeditor window or in the current. Graphic-Display : See chapter 6.4 select the rules of bond determination. Bond Options : If the distance between two atoms is less than a certain fraction of the sum of the van-der- Waals-radii of these atoms, than a bond will be drawn between them. Another option makes it possible to make long-range interactions visible by a dotted line. If for an atom the van-der-Waals-radius is not known, a radius of 2 is assumed. Configuration : Change the configuration of the program (Chapter 7) 25/50 lines : Switch between 25 and 50 display lines Color/BW-Mode : Switch between Color and BW-Mode Change colors : Change colors used by the application Printer-options : Configure MolEdit to work with your printer. Plotter-options : Configure MolEdit for the creation of HPGL-files. Window (Window-handling tools) Tile : Two differnt ways of getting the windows in some Cascade : order. Size/Move (Ctrl-F5) : Move and resize the active window Zoom (F5) : Zoom window Next (F6) : Switch to the next window Prev (Shift-F6) : Switch to the previous window Close (Alt-F3) : Close active window and save file if necessary Help (Display this manual) To switch between various windows you can either use the menu-options Window|Next (F5) and Window|Prev (Shift-F6) or select the menu by pressing the Alt-key together with the window number, e.g. Alt-1 to select window 1. 4. The Editor ============= 4.1 Editor control-keys +++++++++++++++++++++++ The Ctrl-key-combination are more or less wordstar-compatible. The only difference is the way to highlight, cut, copy and paste text. ^K^B begin of highlighted text. ^K^K copy text into the clipboard. ^K^C insert text from the clipboard. Instead of using ^K-commands it is also possible to mark text by pressing the Shift-Key and moving the cursor. ^A or Ctrl-Left Word left ^C or PgDn Page down ^D or Right Cursor right ^E or Arrow up One line up ^F or Ctrl-Right Word right ^G or Del Delete char at cursor position ^H or Backspace Delete char before cursor position ^L Repeat search ^M or Enter New line ^O Toggle indent-mode ^R or PgUp Page up ^S or Left Cursor left ^T Delete to end of word ^U Undo ^V or Ins Toggle insert/overwrite ^X or Arrow down One line down ^Y Delete line ^Q^A Search and replace ^Q^C or Ctrl-PgDn Goto end-of-file ^Q^D or End Goto end-of-line ^Q^F Search ^Q^H Delete to start of line ^Q^R or Ctrl-PgUp Goto begin-of-file ^Q^S or Home Goto begin-of-line ^Q^Y Delete to end-of-line ^K^B Start block (move cursor to mark text) ^K^C Insert content of clipboard ^K^H Hide block ^K^K Copy block to clipboard ^K^Y Delete highlighted text and copy it to the clipboard 4.2 A typical edit-session ++++++++++++++++++++++++++ To create a new file select the File|New menuoption and start editing. If you want to change an old file, press F3 or select the File|Open menuoption to get a file-selection dialog. If you want to create a new molecule using an old input-file, change the name of the file by selecting File|Save As. If you display the molecule the first time after modifying it, a File|Save As dialog will be displayed. MolEdit tries to detect the format of the input-file automatically. If this is impossible, mopac-format is assumed. To change the format of the file select the appropriate type with the File|Fileformat menu-option. Then edit the file. If you want to use parts of another file then open a second window, highlight the text, copy it into the clipboard, change to the first window and insert the text from the clipboard wherever you want it. This will not keep the atom-references in the correct order! To check the input-file, press the F4 function key. If you want to view what you have written so far, press F5. The program then saves the active file and starts to interpret the information in the file depending on the file-type you have choosen. In case the interpreter detects an error in your input-file it will give you a message giving some hints about the error and the position of the error. If the interpretation was successful the molecule will be displayed. About the usage of the molecule viewer see below. Stop the molecule viewer using Alt-X or press the Exit-button using the mouse. 5. The conversion utilies ========================= At the moment two different file-formats are supported by MolEdit. o mopac-input-file (look at the mopac manuals) o GIP-format (part of the mopac-tool DRAW) 5.1 The GIP-format (geometry-interchange-program) +++++++++++++++++++++++++++++++++++++++++++++++++ The GIP-format is similar to the mopac-input-file format, except two differences. There is one more line at the beginning of the file (GIP/DRAW DO NOT EDIT THIS LINE! ...) and the geometry is defined differently from the usual z-matrix format. A atom-definition line is like: an x obl y oang z odihed rbl rang rdihed an: Atom information x,y,z: x,y,z-coordinates of the molecule obl,oang,odihed: Identifier if the bond-length, angle and dihedral angle should be optimized rbl,rang,rdihed: Reference-atoms for bond-length, angle and dihedral angle. This is the z-matrix By converting the Z-matrix into the GIP-format it is possible to change the reference atoms, without having to recalculate bond-length, angles and dihedrals. Using the Conversion|Create Z-Matrix menu-option, a new Z-matrix can be created automatically for the new geometry. 5.2 Formating input-files +++++++++++++++++++++++++ After selecting the Conversion|Format menu-option it is possible to format the input-files. 5.3 Conversion between different format +++++++++++++++++++++++++++++++++++++++ At the moment the following conversions are possible: o Conversion to GIP o Conversion to Mopac 6. The molecule viewer ====================== The screen consists of 2 parts, on the right side a menu and on the left side the display of the molecule. The various options of the menu can be selected either using the mouse or the Alt-key together with the high- lighted letter. 6.1 The menu ++++++++++++ Displaytype : Radiobuttons - only one is selectable Wire frame : Draw molecule as a wire frame Ball and Stick : Draw molecule in the ball and stick model Dot cloud : Draw molecule as a wire frame and display the surface by dots Net : Show the surface using a grid Spheres : Show the surface using spheres Displayoption : Checkbox - multiple selection possible Show dummys Show labels : Display element names Show numbers : Display number of atom Principal Axis : Transformation into the principal coordinate system Center Molecule (Enter) : Translate molecule so that center of gravity is the Origin of the coordinate system Reset VP (Ctrl-Enter) : After rotating and zooming the viewpoint, this resets the viewpoint to the default values Redraw : Interpret Displaytype and Displayoptions and redraw molecule Plot it : Create a HPGL-file of the current drawing. Exit : Stop molecule viewer 6.2 Changing the molecules viewpoint ++++++++++++++++++++++++++++++++++++ Translation and rotations of the molecule is controled by the number-block of the keyboard. To translate the molecule use the numbers to translate the viewport. To zoom in press the grey-plus + key, to zoom out press the grey-minus - key. To rotate the molecule you have to press the a number, the grey-plus or the grey-minus key together with the Shift-key. To set the origin of the molecular coordinate system to the center of the viewport select the Center-button. 6.3 Determination of geometrical parameters +++++++++++++++++++++++++++++++++++++++++++ To determine geometrical parameters, select the Query-Option (Alt-Q). This will start the query-mode and gives you the opportunity to enter commands. At the moment the following commands are implemented: exit - stop query-mode quit - stop query-mode help - information about implemented commands pos n1 - position of atom n1 bl n1 n2 - determine bondlength between atoms n1 and n2 ang n1 n2 n3 - determine angle between atoms n1, n2 and n3 dihed n1 n2 n3 n4 - determine dihedral between atoms n1, n2, n3 and n4 oop n1 n2 n3 n4 - determine oop-bend. The atoms n1, n2 and n3 define a plane. The angle of the bond n2-n4 to this plane is determined. 6.4 Control of graphic output +++++++++++++++++++++++++++++ Beside the already described options, other parameters are provided to control the display of the molecule. Theses can be set using the dialog under the menu option Options|Graphic-Display. Displaytype and Displayoption is described above. In addition the following parameters control the output: Resolution The quality of the drawing is controlled by this value. A small value (e.g. 10) results in faster drawing, but in poor quality. Whereas a larger value produces better output. Density of dots This controls the density of dots in the display type Dot cloud Perspective A large value (e.g. 100000) results in no perspective drawing, whereas a smaller value (e.g. 2000) produces a perspective output. 6.5 Creation of HPGL-files ++++++++++++++++++++++++++ !! This options is not enough tested yet, so there might be problems. With the Plot It button, a HPGL-file (Hewlett-Packard Graphic Language) of the current drawing is created. After pressing the button MolEdit switches back to text mode and displays the dialog. Here you can define the name of the HPGL-file to be created. If the file already exists MolEdit will ask you, if it can be overwritten. The created HPGL-file is also controlled by the Plot-Faktor value. This can only be changed in the Options|Configuration dialog. It controlls the precision of the created drawings. A value of 1000 gives relatively good pictures but might lead to problems for large molecules. 7. The configuration-file ========================= After executing the program for the first time you will find two new files in the directory in which you stored the MolEdit-program. One of them, moledit.dsk, stores the so called history-lists. Whenever you want to select a file, a file-open dialog is created. On the right of the input-line you will find a green-arrow. By either clicking the green-arrow with the mouse or by pressing the down-arrow-key a history- list is opened. This offers you the opportunity to select one of the files. The change-directory dialog also provides a similar history-list. The other file, moledit.cfg, stores configuration-information. The following informations may be stored: [MolEdit-Konfiguration] BGI-Path : Path where the BGI-drivers and fonts can be found. Screen-Mode : Color-mode of the application smCO80 for color, smBW80 for black/white-mode (Menu-option General|Color/BW-mode) Screen-Lines : Number of lines in text-mode (25 or 43/50) (Menu-option General|25/50 lines) Working-Directory : Current working-directory. (Menu-option General|Change dir ...) mpp-Program : Full-path of the mpp-program Display-Type : Change this configuration with the menu-option Display-Option : Graphic|Options Display-Perspective : Controls perspective of drawing. Display-Resolution : Controls the resolution of the drawings. The larger the value, the more precise is the picture, but the time needed to draw it increases. Display-DensityOfDots : Controls the number of dots in the dot-cloud picture Printer-Port : Port to send the file to after selecting the File|Print menu-option (can also be a filename) New-Window : Create a new Window after converting files between different formats. (Menu-option Conversion|Option) Menu-Type : Select beginner or expert-menu Plot-File : Defines the filename under which HPGL-files are created. Plot-Faktor : Controls the precision of the created HPGL-file. [Printerconfiguration] Type : Use the Options|Printer-options menu to change the Port : Printer-configuration Most of the configuration parameters can be changed with menu-options. To change BGI-Path, mpp-Program or Printer-Port you have to select the Options|Configuration menu-option. This will open a dialog, that allows you to select and edit all configuration-parameters. An option can be selected by positioning the cursor on the name and pressing either the space-bar or the enter-key. Another way is by double-clicking on the option. Default-values are given in square-brackets. 8. Plans ======== o Plotting (already in testing) o User-defined file-formats o Porting to Windows 9. Copyright ============ Copyright (c) 1993-1995 by Peter Gedeck In this version the program may be freely copied, but not be distributed for commercial purposes. The author makes no warranties, either express or implied, as to the reliability of this software or its fitness of use for any particular purpose. This software is provided on an "as is" basis, and without warranty of any kind, including but not limited to any implied warranty of merchantability or fitness for a particular purpose. In no event shall the authors or the University of Erlangen-Nürnberg be liable for any direct, indirect, incidental, special, or consequential damages arising from use or distribution of this software. The University of Erlangen-Nürnberg also shall not be liable for any claim against any user of this program by any third party. I guess I have to include the following information about the programs mentioned: o Created using Borland Pascal with Objects (c) Borland International 1992 o Ampac, Version 1.0 - QCPE Program No. 506 o Babel version 1.06 Copyright (C) 1992,1993,1994 - Pat Walters, Matt Stahl. (Contact: babel@mercury.aichem.arizona.edu) o Mopac, Version 6.0 - Stewart J.J.P. o VAMP, Version 5.0 - Rauhut G., Alex A., Chandrasekhar J., Clark T., Oxford Molecular Ltd. Oxford 1993 o NOTE: MolEdit is packaged using Info-ZIP's compression utility. The individual installable parts were created using the zip-program and converted to self-extracting executables using the unzipsfx tool. Info-ZIP's software (Zip, UnZip and related utilities) is free and can be obtained as source code or executables from various bulletin board services and anonymous-ftp sites, including CompuServe's IBMPRO forum and ftp.uu.net:/pub/archiving/zip/*. 10. History =========== Version 0.1 Changes in way the program treats new files Version 0.1.b Command line to determine molecular information (bond-distances, angles, dihedrals, oop-bends) in graphic-mode EGA-graphiccards are supported, feature was not tested. Version 0.1.c Protected-Mode version. Format of the mopac and mpp input-files. Conversion mopac-format to GIP-Format and vice versa. Conversion mpp-format to mopac-format. Beginner and expert menus Version 0.1.d Menu restructured Set colors of the desktop Version 0.1.e Improved graphical representation Version 0.9 Completely changed the way different formats are treated. Removed mpp-format Automatical creation of Z-matrizes Inserting and deleting atoms Delete dummies Version 0.9.a MolEdit now allows to edit DOS and UNIX-textfiles. Version 0.9.b - Version 0.9.c Several bugfixes (see changes.mol) Version 0.9.d Boundary box Perspective output If the directory is changed using the load-file dialog, the new directory will become the working directory. Version 1.0 XMol-Fileformat Integration of the Babel conversion utility Version 1.0.a Creation of HPGL-Files (Test-Version!) Version 1.0.b Included simple HTML-viewer to view this document. 11. Credits =========== I would like to thank the following people for bug-reports and ideas. o Holger Busse o Peter Freunscht o Stephan Landgraf o Xiaoming Zhou Appendix 1: DPMI ================ (DOS-Protected-Mode-Interface) ============================== This document is taken from the documentation to Borland Pascal 7.0 ------------------------------------------------------------------- To run protected-mode applications, the programs RTM.EXE, RTMRES.EXE, DPMI16BI.OVL, DPMIINST.EXE and DPMILOAD.EXE are needed. In the next section the following topics are treated: o Execution of DOS-Protected-Mode-Programs o What to do if the DPMI-Server of Borland is not running on your system o How to use DOS-Environmentvariables to change the behaviour of the DPMI- Server o Running DPMI-Programs under Windows o How to change the memory-management of the DPMI-Loader Execution of DOS-Protected-Mode-Programs ++++++++++++++++++++++++++++++++++++++++ To run a protected-mode-program you have to make sure, that DPMI16BI.OVL (the DPMI-Server), RTM.EXE (the DPMI-Loader) and all needed DLLs (Dynamic- Link-Librarys) can be found in on of the follwing places: o in the current directory o in the same directory as the application o in the DOS-search-path Protected Mode and memory DPMI (for DOS Protected Mode Interface) enables a DOS-Program to run in protected-mode and therefore use all available memory of your computer. DPMIINST If you run the protected-mode-program for the first time on a computer with a 80286-processor. you may get the follwing message: Machine not in database (RUN DPMIINST) This means that the protected-mode-interface has to be configured to be able to run with your computer. So if you get this message, enter DPMIINST on the DOS-prompt and follow the instructions. DPMIINST will run several test, to find out the best way to activate protected-mode on your machine. Afterwards the DPMI-interface will be configured for your machine. You only have to run this program once. Some memory-management-programs, device-drivers and memory-resident- programs will make problems, so that DPMIINST can not finish all tests. If this happens, remove them, so that DPMIINST can run without problems. Afterwards you can reinstall them. You will not have to run DPMIINST neither on a machine that runs HIMEM (or equivalent), nor on computers with the 80386- or 80486-processor. DPMIMEM By Default the DPMI-interface uses all available extended-memory. To avoid this, you can define DOS-Environment-variables to declare a upper limit of memory to be used. These definition can be entered either on the DOS-prompt or in the file AUTOEXEC.BAT. The syntax is: SET DPMIMEM=MAXMEM nnnn nnnn is the memory-size in kilobyte. E.g. if your computer has 4 MB und you want DPMI to use only 2MB, use the following command: SET DPMIMEM=MAXMEM 2048 RTMRES RTMRES load the DPMI-System. If you do this, protected-mode-programs will start faster. If you enter RTMRES the program will be started. Else RTMRES opens a DOS-Shell, which you can exit with the command EXIT. RTMRES is useful, if you want to use a protected-mode-program more often. Usually the DPMI-Server will be loaded whenever you start the program, whereas RTMRES will make it memory resident. EXTENDED MEMORY The communication of a protected-mode-program with the DPMI-server works using the DPMI-Lader RTM.EXE. By default the protected-mode-program uses all the memory that was reserved by the DPMI-Kernel. Execution of a Protected-Mode-Program under Windows +++++++++++++++++++++++++++++++++++++++++++++++++++ A DOS-protected-mode-program will run in the extended 386-mode of windows. Using a PIF-file you can define how much memory a program can use. Executing a Protected-Mode-Program in ++++++++++++++++++++++++++++++++++++++++++++++ Windows-Standardmode To execute a protected-mode-program in Windows-Standardmode, you have to define the DOS-environmentvariable DPMIMEM and start RTMRES, before you start windows. Both is described above. If you have loaded DPMIMEM, you will not be able to execute windows in the extended 386-mode. You have to leave RTMRES before (typing EXIT on the DOS-prompt). How to change the memory-management of the DPMI-Loader ++++++++++++++++++++++++++++++++++++++++++++++++++++++ The DPMI-Loader tries to use as much conventional memory as possible. If you want to use other protected-mode-programs, which not use the DPMI- Loader (e.g. Paradox 4.0), you have to control the memory usage with the DOS-environment-variable RTM. Using the SET-command you can define the RTM-environment-variable from the DOS-prompt. SET RTM=[Option nnnn] The following options are available. nnnn can be a dezimal or a hexadezimal number. (hexadezimal numbers are given in the format e.g. xAB54 or xab54) Option Description ------------------------------------------------------------- EXTLEAVE nnnn Leave nnnn kilobyte extended memory. Default 640 KB. EXTMAX nnnn Not more than nnnn kilobyte extended memory will be reserved. Default is 4 gigabyte resp. under windows, half of the available memory. EXTMIN nnnn If with respect to the definitions of EXTMAX and EXTLEAVE less than nnnn kilobyte memory are available the program will be stopped giving the message "Out of Memory". The default is 0. REALLEAVE nnnn Always at least nnnn paragraphs of conventional DOS-memory are left. The default is 4096 paragraphs, which is equivalent to 64 kilobyte. REALMAX nnnn Not more than nnnn paragraphs of DOS-memory are reserved. The default is 1 MB or 65535 paragraphs. REALMIN nnnn If with respect to the definitions of REALMAX and REALLEAVE less than nnnn kilobyte memory are available the program will be stopped giving the message "Out of Memory". The default is 0. E.g. with the following command RTM will reserve at last 2 MB or extended- memory and will leave 126-kb DOS-memory free. SET RTM=EXTMAX 2048 REALLEAVE 8192 Appendix 2: Babel (Version 1.06) ================================ This document is based on the file readme.1st from the distribution of Babel version 1.06 ------------------ Contact: Pat Walters and Matt Stahl, Dolata Research Group, Department of Chemistry, University of Arizona, Tucson, AZ 85721, babel@mercury.aichem.arizona.edu. The aim of Babel is to implement a general framework for converting between file formats used for molecular modeling. Babel will read the following file types : Alchemy AMBER PREP Ball and Stick Biosym .CAR Boogie Cacao Cartesian Cambridge CADPAC CHARMm Chem3D Cartesian 1 Chem3D Cartesian 2 CSD CSSR CSD FDAT CSD GSTAT Free Form Fractional GAMESS Output Gaussian Z-Matrix Gaussian Output Hyperchem HIN Mac Molecule Macromodel Micro World Molgen MM2 Input MM2 Ouput MM3 MMADS MDL MOLfile MOLIN Mopac Cartesian Mopac Internal Mopac Output PDB Quanta ShelX Spartan Sybyl Mol Sybyl Mol2 XYZ Babel will write the following file types : Alchemy Ball and Stick Cacao Cartesian CAChe MolStruct Chem3D Cartesian 1 Chem3D Cartesian 2 ChemDraw Conn. Table CSD CSSR Gamess Input Gaussian Cartesian Gaussian Z-matrix Hyperchem HIN IDATM Mac Molecule Macromodel Micro World MM2 Input MM2 Ouput MM3 MMADS MDL Molfile Molgen Mopac Cartesian Mopac Internal PDB Report Spartan Sybyl Mol Sybyl Mol2 XYZ To use the DOS-Version of Babel install the program in a subdirectory on your hard disk as described in the file readme.1st. In case Babel won't work check if the environment variable BABEL_DIR is set correctly. Information about the usage of Babel from the command line can be found in the file readme.1st. Limitations of the MolEdit interface: +++++++++++++++++++++++++++++++++++++ Multi-structure file MolEdit does NOT support the conversion of multi structure files. MacMolecule files The special option for MacMolecule files is not implemented. Quanta files Due to the fact that Quanta files are binary I did not include this format in MolEdit.