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PC-SIG Diskette Library (Disk #938)
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Information about “CHEMICAL MOLECULAR MODELING”
CHEMICAL -- a molecular-modeling program for 3-D representations of
chemical elements.
Select atoms from the Periodic Table and the program retrieves the
electron orbital information. The atoms can be bonded into molecules,
and the molecules bonded with other molecules to make large chemical
structures. The chemical is displayed as it is constructed, and when
formed, can be rotated and viewed. The Hybrid and Ionize commands can
be used to alter the orbitals before bonding. Read, write and view a
chemical data file from the disk. CHEMICAL also has a help function
and a tutorial.
Included is CHEMVIEW (an EGA-only function), a companion program that
shows three-dimensional animation of the models made with CHEMICAL.
CHEM.DOC
CHEMICAL Ver 4.2 Feb 23, 1990
CHEMICAL is a molecular modeling Program to aid in the formation
of three dimensional pictures of chemicals. Atoms are selected
from a Periodic Table (using the A command) and electron
orbital information retrieved. The Atoms are then bonded
(using the B command). The chemical is displayed as it is
being constructed. The chemical can be viewed from different
directions by using the up and down cursor keys and the V
command. If desired the Hybrid and Ionize commands can be used
to alter the orbitals before bonding. Atoms can be bonded
into groups, then the groups bonded to other groups to make
large chemicals. The current version for CHEMICAL (4.1)
includes support for MicroSoft Mouse Drivers.
CHEMVIEW is a companion program that shows 3-dimensional
animation of the models generated with CHEMICAL. CHEMVIEW
requires an EGA board and monitor. CHEMVIEW is written in
Turbo PROLOG with the graphics routines written in Turbo C.
To use CHEMVIEW simply start the program and select the
file desired.
BIOCHEM is a companion program that combines files made with
CHEMICAL into larger molecules. Chemical groups can be
bonded together using Covalent, Ionic, Hydrogen, or Peptide
bonds. This program provides much more capability than Group
command that was included in older versions of CHEMICAL.
BIOCHEM works with a CGA, EGA, or VGA monitor.
CRYSTAL is companion program that places atoms on a lattice
framework to form crystal structures. The structure is
defined by a text file. A text editor is built into the
program. The text file is converted to a image that is shown
rotating in three dimensions. An EGA or VGA monitor is
required.
CHEMICAL requires 640K bytes of RAM and a CGA or EGA
display. You may need to eliminate RAM resident programs
in order to run CHEMICAL.
CHEMICAL is started by entering CHEM at the DOS prompt. The
CHEM.DOC, CHEM.TUT, and *.BGI files should all be on the
same directory. Select the graphic mode desired, then push
the Enter key. The program GRAFTABL should be run prior to
running CHEMICAL with a CGA monitor. The graphic display
format is different for the various modes for a particular
monitor. Try each mode to determine your preference.
Commands are selected by depressing the first letter of
the command or by depressing (cr) if the command has already
been selected. The following commands are available:
The commands for version 4.0 of chemical are:
A - (Atom) This command displays a periodic table.
Elements are selected by moving the cursor to the
desired Element, then depressing the CR key. The esc
key is used to exit this command.
B - (Bond) This command is used to bond two atoms. A list
of all atoms selected is displayed, along with its
electron orbital configuration. The size of the atom is
determined the first time it is bonded.
A choice of three bond types: Anti, Dative, and Shared, is
provided to determine which atom in a bond will supply the
two electrons needed for a molecular orbital. A shared bond
takes two electron from each atom. A Dative bond takes both
electons from one atom. An anti bond allows three or four
electrons to be used in the bond.
C - (Clear) This command clears the screen and the buffer for
all Atoms and Bonds selected so far. A Yes/No menu is
used to reduce the change of accidently clearing the buffer.
FA - (Animate) This command executes program CHEMVIEW which shows
molecules in 3 dimensional rotation (on EGA monitors only).
The cursor keys are used to change the direction of rotation,
the + and - keys change the size, the End key stops rotation,
the space bar returns to the CHEMVIEW window and the Ctrl
Break key returns to CHEMCIAL. CHENVIEW.EXE must be on the
default disk.
FB - (View Buffer) This command stores the buffer under the
file name TEMP.DAT, then allows the file to be viewed.
FH - Show help file
FM - Minimize Chemical File size by deleting unused
orbitals. Do not use this command until you are
completely done, since no additional bonds can be
made to a minimized file.
FR - Read a Chemical File
FS - Goto Operating System
FT - Show Tutorial File
FV - View a file from disk
FW - Write a Chemical File
H - (Hybrid) This command is used to combine electron orbitals
into hybrids. A list of possible Hybrids is displayed.
A _5 or _6 ending indicates that the bonding angles have
been adjusted to make a 5 or 6 bond flat ring.
I - (Ionize) This command is used to ionize an atom. A list of
the possible ionizations is displayed.
MA - (Move) This command is used to manually move an Atom or
Group.
MC - Change color of atom. The color for all atoms of the
type selected are changed.
MD - Deletes a selected atom from the current buffer. This
command is most useful for modifing an existing file
into a similar chemical. All atoms following the one
selected are re-numbered. This command may require
several seconds on large files.
MR - (Re-center) All atoms are re-centered on the screen.
This command is used when reading files generated by
older versions of CHEMICAL.
MS - Rotate around Sigma Bond - Atoms are free to move around
sigma bonds, and will generally do so to minimize the
energy of the system. This command will rotate an atom
and other attached atoms.
MX - Rotate atoms around X axis. Do not use any of the
rotate commands until the molecule is complete. The
angle for bonds made after rotation may not be correct.
MY - Rotate atoms around Y axis
MZ - Rotate atoms around Z axis
P - Print the screen. CGA mode should be used if you want
the atoms to be labeled.
R - (Not on Menu) Read to buffer from TEMP.DAT
SB - Toggles Bond lines on/off. Bond lines are only available
in graphic mode with 16 colors.
SC - Toggles electronegativity scale on/off. When on, a color
scale is shown at the bottom of the display window (EGA
mode only). The atom colors are changed to correspond to
the electronegtivity of the atom. When off no scale is
shown and the colors are changed to have more contast.
SE - Toggles expanded view on/off.
SG - Toggles grid on/off.
SN - Toggles atom numbering on/off.
V - (View) This command will show the view of the chemical
that has been selected by the up/down cursor keys.
The horizonal axis and vertical axis are shown in the
upper right hand corner of the screen. Lines are
shown to indicate bonds. The upper right hand corner of
the screen shows which axis (X, Y, or Z) is aligned
with the vertical and horizontal view shown.
Atoms are listed on the left. In 16 color modes, the
color is used to designate the atoms. In 2 and 4 color
modes, the atoms are labeled.
W - (Not on Menu) The Write command write the buffer to
the file TEMP.DAT. The Write and the Read commands
can be used to recover from an error during
construction of a chemical.
Contruction of Ring Structures
Ring structures are difficult to make because of the large number
of possible bonds. Also the angles need adjustment to make a
closed ring. Special hybrids ending in _5 or _6 are provided in
CHEMICAL for constructing 5 and 6 flat ring structures. The ' and `
bonds should be selected to form rings. CHEMICAL defaults (high-
lights) to this choice to simplify ring formation.
The formation of combined six and five ring structures such as
Purine requires adjustment of the angles for the atoms to meet
correctly. CHEMICAL will make this adjustment if the six atom
ring (using _6 hybrids) is made first (don't forget to bond the
1st and 6th atoms before added the 7th). Then three _5 hybrids
should be selected. The default bonds should then form the correct
double ring structure. The first ring is generated clockwise and
the second ring is generated counter-clockwise.
The angles in the sp3 hybrid do not allow a flat ring. A
twisted ring can be made by selecting the default bond
selection sequence.
Example 1: Make Water Molecule
1) Use the A command to show periodic table
2) Select O,H, and H using the cursor keys and Enter Key
3) use esc to exit A command
4) Select the Bond Command
5) Select O and H
6) Select shared (default) bond
7) Select one of the O-H bonds
8) Use the Bond Command to make the other O-H bond
(Two atoms always need to be selected to make a bond)
Note: The angle between the Hydrogen atoms can be made closer
to the actual angle by selecting the sp3 hybrid for Oxygen.
Example 2: Benzene C6H6
1) Clear previous entries with (C)lear
2) Enter 6 Carbon Atoms using (A)tom
3) Select the sp2 hybrid for each Carbon Atom using (H)ybrid
4) Use the Up/Down cursor key to set view to TOP
5) Bond Atoms 1-2, 2-3, 3-4, 4-5, 5-6, 1-6 (selecting highlighted bond)
6) Make a pi bond between atoms 1-2, 3-4, and 5-6 using (B)ond
7) Enter 6 Hydrogen Atoms using (A)tom
8) Bond each hydrogen atom to a carbon atom
Example 3) [Co(NH3)6]3+ Coordination Compound
1) Select Co and six N atoms
2) Select the +3 ionization and d2sp3 Hybridization of Co using
the Ionize and the Hybrid commands
3) Select the sp3 Hybrization of N using the Hybrid command
4) Bond the six d2sp3 orbitals on Co with the six N atoms using
the dative bond
5) Select 18 hydrogen atoms
6) bond the hydrogen atoms to the six nitrogen atoms
CHEMICAL, CHEMVIEW, and CRYSTAL are placed in the Public Domain
and may be freely copied and distributed. The latest version of
including source code can be obtained from the author for $20.
Updates are $10 for registered users. The source code is not
for public distibution and is only available from the author.
The following programs are also available:
PLANETS computes information relating to the position,
distance, magnitude, orbit view, skyview, etc. for the major
planets, four minor planets, and halley's comet on a specified
date and time. Also, orbital data for any desired planet or
comet can be entered and saved in a disk file. Skyview and
orbital views can shown in forward or backward motion. The moons
for each planet can be displayed. This program requires a
graphics display and 256K bytes of memory. The latest
version is 4.1.
CHARACTER is a computer program designed to draw faces. The
drawings consist of lines of different color and thickness. The
age, weight, and emotions (Anger, Disgust, Fear, Happiness,
Sadness, Surprise) can be changed by adjusting scales on the left
side of the screen. Individual features, such as eye seperation,
nose position, or nose width, can be changed by accessing
additional menus. The detailed positions of the lines can be
changed by using a mouse. CHARACTER requires 512K bytes of
memory, and a CGA, EGA, VGA, or Hercles monitor. A mouse is
required to access all the features of CHARACTER.
Larry Puhl
6 Plum Court
Sleepy Hollow, Ill. 60118
ORDER FORM:
CHEMICAL/CHEMVIEW/CRYSTAL (price is for all 3) $20 ____
BIOCHEM $10 ____
PLANETS $10 ____
CHARACTER $20 ____
Shipping outside of USA $5 ____
3 1/2 inch disks $2 ____
(Updates for registered users are half price)
TOTAL ____
send to: ______________________________________________
______________________________________________
______________________________________________
______________________________________________
Comments:
FILE0938.TXT
Disk No: 938
Disk Title: Chemical Molecular Modeling
PC-SIG Version: S1.4
Program Title: Chemical
Author Version: 4.2
Author Registration: $20.00
Special Requirements: 640K RAM, and CGA or EGA.
CHEMICAL is a molecular-modeling program for 3-D representations of
chemical elements.
Select atoms from the Periodic Table and the program retrieves the
electron orbital information. The atoms can be bonded into molecules,
and the molecules bonded with other molecules to make large chemical
structures. The chemical is displayed as it is constructed, and when
formed, can be rotated and viewed. The hybrid and ionize commands can
be used to alter the orbitals before bonding. Read, write and view a
chemical data file from the disk. CHEMICAL also has a help function and
a tutorial.
Included is CHEMVIEW (an EGA-only function), a companion program that
shows three-dimensional animation of the models made with CHEMICAL.
PC-SIG
1030D East Duane Avenue
Sunnyvale Ca. 94086
(408) 730-9291
(c) Copyright 1989 PC-SIG, Inc.
GO.TXT
╔═════════════════════════════════════════════════════════════════════════╗
║ <<<< Disk No 938 CHEMICAL >>>> ║
╠═════════════════════════════════════════════════════════════════════════╣
║ To start the program, type: CHEM (press enter) ║
║ ║
║ To start CHEMVIEW, type: CHEMVIEW (press enter) ║
║ ║
║ To print the documentation, type: COPY CHEM.DOC PRN (press enter) ║
╚═════════════════════════════════════════════════════════════════════════╝
Directory of PC-SIG Library Disk #0938
Volume in drive A has no label
Directory of A:\
CGA BGI 6221 6-21-88 2:00a
CHEM DOC 13036 2-24-90 10:47a
CHEM EXE 265804 2-20-90 9:10p
CHEM TUT 4584 4-24-88 3:17p
CHEMVIEW EXE 48868 11-24-88 10:10a
EGAVGA BGI 5363 6-21-88 2:00a
FILE0938 TXT 2147 3-23-90 8:59p
GO BAT 38 3-23-90 1:17p
GO TXT 694 3-23-90 8:49p
H2SO4 DAT 928 11-17-89 6:28p
HERC BGI 6093 6-21-88 2:00a
WATER DAT 405 12-03-88 3:37p
12 file(s) 354181 bytes
2048 bytes free