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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.
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