Molecular Graphics on the IBM PC Microcomputer

110 Pages·1985·1.866 MB·English

by  James Henkel (Auth.)

Molecular Graphics
on the IBM® PC
Microcomputer
James C. Henkel
School of Pharmacy
University of Connecticut
Storrs, Connecticut
Frank H. Clarke
Research Department
Pharmaceuticals Division
CIBA-GEIGY Corporation
Ardsley, New York
1985
ACADEMIC PRESS, INC.
(Harcourt Brace Jovanovich, Publishers)
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COPYRIGHT© 1985, BY ACADEMIC PRESS, INC.
ALL RIGHTS RESERVED.
NO PART OF THIS PUBLICATION MAY BE REPRODUCED OR
TRANSMITTED IN ANY FORM OR BY ANY MEANS, ELECTRONIC
OR MECHANICAL, INCLUDING PHOTOCOPY, RECORDING, OR ANY
INFORMATION STORAGE AND RETRIEVAL SYSTEM, WITHOUT
PERMISSION IN WRITING FROM THE PUBLISHER.
IBM is a registered trademark of International Business
Machines Corp. PQy is a trademark of International
Business Machines Corp. Apple is a registered trademark
of Apple Computer, Inc.
ACADEMIC PRESS, INC.
Orlando, Florida 32887
United Kingdom Edition published by
ACADEMIC PRESS INC. (LONDON) LTD.
24/28 Oval Road, London NW1 7DX
Library of Congress Cataloging in Publication Data
Henkel, James 6., Date
Molecular graphics on the IBM PC microcomputer.
Includes index.
1. Molecular structure—Computer programs. 2. Computer
Ïraphics. 3. IBM Personal Computer—Programming.
. Clarke, Frank H. II. Title.
QD461.H427 1985 541.2'2'0285443 84-24530
ISBN 0-12-340820-2 (alk. paper)
PRINTED IN THE UNITED STATES OF AMERICA
85 86 87 88 9 8 7 6 5 4 3 2 1
IMPORTANT NOTICE:
READ THIS FIRST
Before you begin to use the diskette contained in this package, CON-
VERT IT TO A WORKING DISKETTE, as directed on pp. 2-7. Much
microcomputer software, especially games, will operate right out of the
package. This one will not. There are some proprietary IBM® files that
must be present on the diskette for the program to operate, and these must
be copied from your operating system diskette (DOS 1.1 or DOS 2.0).
Please do not neglect this step just to get started a few minutes sooner.
If you require technical assistance while using this package, call
collect [phone] during regular business hours (Pacific time) or write
to Dr. James Henkel, School of Pharmacy, University of Connecticut,
Storrs, CT 06268.
Preface
An understanding of chemical systems, especially living systems,
requires the ability to visualize the structures and conformations of the
often complex molecules involved. The advent of sophisticated computer
graphics has made it possible to study the interactions of complex mole-
cules at a fundamental level. Until now it has been possible to study such
processes only on very expensive equipment. With the publication of this
package, one can perform many of the same operations on the IBM®
personal computer. (A companion package is also available from Academ-
ic Press, Inc., for the Apple®.) This manual introduces the package and
provides step-by-step instructions for using it for your own study and
enjoyment.
This package has a multitude of applications, including the study of
conformations of organic molecules and the organization of organic and
inorganic crystal lattices. It can also be used by the researcher who is
studying how a substrate fits into the binding site of an enzyme or who is
comparing the structures of a series of potential ligands. A forthcoming
book to be published by Academic Press will explain how the computer
programs operate and will extend their many potential applications, only a
few of which are discussed here. Of course, the user is encouraged to find
new and creative ways to use the programs contained in this package.
We are deeply indebted to several of our colleagues who tested and
utilized preliminary versions of this program, and who have made valuable
suggestions of improvements and pointed out inconsistencies. These in-
clude Mr. Tobia Terranova, who meticulously covered the entire program
from beginning to end, as well as Dr. Bruce Tomczuk, Dr. Judith Kitchell,
Mr. Mark Rustad, and Mr. Michael Lees, all of whom have added a great
deal to the final version. We are also indebted to Professor Jon Clardy for
the algorithm for the conversion of atomic coordinates to Cartesian coordi-
nates. Any remaining problems or errors are solely the responsibility of the
authors.
v/7
INTRODUCTION
PCMODEL is a program to draw and manipulate molecules in graphic
form using the IBM® PC, PC/XT, PC/AT, PCjr, and true compatible
personal computers. The program is written in advanced BASIC (BASICA)
and requires 128K of memory under DOS 1.1 or 192K of memory under
DOS 2.0 or 2.1, as well as a graphics adapter card and a color monitor.
Molecular models provide one of the best means of studying chemical
structures and conformations. By placing these models on a microcom-
puter, all of the advantages of actually seeing the relationships of the atoms
of the molecule are present. In addition, models can be easily superim-
posed for comparison, and accurate measurements of interatomic distances
and bond and torsion angles can be made. All of the structural parameters
are contained within the data that are stored on the diskette. The program
uses standard Cartesian atomic or X-ray coordinates for input. These data
are available from a wide variety of sources and for a wide variety of
molecules including enzymes and other biological macromolecules (7).
Libraries of X-ray crystal structures (2) are also rich sources of coordinate
data. Structural information can also be generated directly from skeletal
molecular models, such as Dreiding stereomodels.
This program is not intended to replace physical molecular models.
Rather, it is meant to greatly augment them. A great deal of insight can be
obtained from actually handling a molecular model, turning it over, and
viewing it from several directions. Many of the features of the shape of a
molecule are apparent most readily from physical models. When used in
conjunction with skeletal models, PCMODEL provides a dimension of
insight not previously available except to those who work on large, expen-
sive molecular modeling systems. For example, PCMODEL may be used
to facilitate construction of physical models of complex molecules, since
bond lengths and angles are easily obtained from coordinate data (3,4).
Using PCMODEL, you can construct a graphic representation of
molecules having as many as 999 atoms and 999 bonds. The program
handles both small and large molecules equally well. It can easily show
enzyme active sites and other complex structures, if the atomic coordinates
7
2 CREATING A WORKING DISKETTE
are known. Once you enter the coordinates and connection tables, you can
easily manipulate the graphic image by translating it in any coordinate
direction, rotating it about any axis or bond, and enlarging or shrinking it.
You can also manipulate a selected molecule or group of molecules inde-
pendently to perform a "docking" operation in which one molecule is
brought into proximity to another molecule or group of molecules. In this
way, you can study substrate interactions with macromolecules, such as
enzyme active sites, and compare the structures of two molecules by
superposition. Using other commands you can highlight selected atoms,
indicate distances between any two atoms, calculate bond and torsion
angles, and edit the coordinate data.
This manual is loosely organized into two parts: one is tutorial and the
other is for reference. These two parts are not strictly delineated, because
we believe that the learning process is continuous and that your progress
through this manual will begin slowly, then increase later. The first sec-
tions are highly tutorial in nature because this is where you will need it
most, whereas the later sections are much less so because you will then be
more in need of detailed reference material.
CREATING A WORKING
DISKETTE
Before doing anything, you must convert the copy-protected program
diskette to a working diskette. This creates a diskette that is self-booting. In
other words, you will be able to use your working diskette to start up your
computer. The following instructions will work in conjunction with Disk
Operating Systems (DOS) Versions 1.1 (IBM #6024001), 2.0 (IBM
#6024061), or 2.1 (IBM #6024120).
The PCMODEL program diskette exists in double-sided format, eight
sectors per track, and is copy protected. Thus, you cannot make backup
copies that will function independently of the program diskette. As it is
supplied to you, it does not contain all of the files you need to run the
2 CREATING A WORKING DISKETTE
are known. Once you enter the coordinates and connection tables, you can
easily manipulate the graphic image by translating it in any coordinate
direction, rotating it about any axis or bond, and enlarging or shrinking it.
You can also manipulate a selected molecule or group of molecules inde-
pendently to perform a "docking" operation in which one molecule is
brought into proximity to another molecule or group of molecules. In this
way, you can study substrate interactions with macromolecules, such as
enzyme active sites, and compare the structures of two molecules by
superposition. Using other commands you can highlight selected atoms,
indicate distances between any two atoms, calculate bond and torsion
angles, and edit the coordinate data.
This manual is loosely organized into two parts: one is tutorial and the
other is for reference. These two parts are not strictly delineated, because
we believe that the learning process is continuous and that your progress
through this manual will begin slowly, then increase later. The first sec-
tions are highly tutorial in nature because this is where you will need it
most, whereas the later sections are much less so because you will then be
more in need of detailed reference material.
CREATING A WORKING
DISKETTE
Before doing anything, you must convert the copy-protected program
diskette to a working diskette. This creates a diskette that is self-booting. In
other words, you will be able to use your working diskette to start up your
computer. The following instructions will work in conjunction with Disk
Operating Systems (DOS) Versions 1.1 (IBM #6024001), 2.0 (IBM
#6024061), or 2.1 (IBM #6024120).
The PCMODEL program diskette exists in double-sided format, eight
sectors per track, and is copy protected. Thus, you cannot make backup
copies that will function independently of the program diskette. As it is
supplied to you, it does not contain all of the files you need to run the
MOLECULAR GRAPHICS ON THE IBM PC 3
program. Specifically, you need to add (1) two system files, and (2) the file
COMMAND.COM. These are proprietary IBM products and are found on
the DOS diskette. To create a working diskette with these files on it,
carefully follow the instructions below. Your computer will have one disk
drive, two disk drives, or a fixed disk and the procedure is slightly different
for each. Choose the set of instructions below that matches the configura-
tion of your computer. For detailed instructions and explanations concern-
ing the DOS commands, please refer to the Operating System Instruction
and Reference Manual provided with your DOS diskette.
IF YOU HAVE TWO DISK DRIVES, perform the following steps:
1. Place your DOS diskette in Drive A (the left-hand drive) and the
program diskette in Drive Β (the right-hand drive), close the drive doors,
and turn on the system. Enter the date and time in response to the prompts.
Then type
b: install
and press the ENTER key («*). [Remember that the colon (:) is a necessary
part of the DOS command format. You must include it whenever you are
specifying a disk drive.] The system will respond by alternately activating
each disk drive, then will conclude with the message:
System transferred
followed by
1 file(s) copied
2. Remove the DOS diskette from Drive A and replace it in its
storage sleeve. Your PCMODEL program diskette has now been converted
to a working diskette.
3. Place the working diskette in Drive A and make sure that it is the
default drive (i.e., that the A) prompt is displayed). If some other letter
besides A) is displayed, reset the default drive to A by typing
A:
then press ENTER. Go to the section, Using the PCMODEL Program on
p. 7.
4 CREATING A WORKING DISKETTE
IF YOU HAVE ONLY ONE DISK DRIVE, perform the following
seven steps:
1. Place your DOS diskette in the disk drive, close the drive door,
and turn on the system. Enter the date and time when you are prompted.
You will see the A) prompt on the screen adjacent to the cursor. Type:
reinstall
and press the ENTER key You will see the message:
Insert diskette for drive B: and strike
any key when ready
2. Remove the DOS diskette and place the PCMODEL program dis-
kette in the disk drive and close the drive door. Then press the space bar.
The drive light will come on, and this message will appear:
A>A:SYS B:
Insert diskette for drive A: and strike
any key when ready
Remove the PCMODEL program diskette from the disk drive and place the
DOS diskette in the drive and close the door. Then press the space bar.
3. The disk drive light will again come on, followed by the message:
Insert diskette for drive B: and strike
any key when ready
Remove the DOS diskette from the drive and replace it with the
PCMODEL program diskette, close the drive door, and press the space
bar. The system will respond with the message:
System transferred
followed by the message:
Insert diskette for drive A: and strike
any key when ready
4. Again remove the PCMODEL program diskette, place the DOS
diskette in the drive, and close the drive door. Press the space bar. This
message will again appear:
MOLECULAR GRAPHICS ON THE IBM PC 5
Insert diskette for drive B: and strike
any key when ready
5. Once more, remove the DOS diskette and place the PCMODEL
diskette in the drive and close the door. Press the space bar. The system
will respond with the message:
A>COPY A : COMMAND. COM B:
Insert diskette for drive A: and strike
any key when ready
6. Remove the PCMODEL diskette and place the DOS diskette in the
drive, then close the drive door. Press the space bar. The system will
respond with the message:
Insert diskette for drive B: and strike
any key when ready
7. Again swap the DOS diskette in the drive for the PCMODEL
diskette. Press the space bar once more. The system will respond with the
message:
1 file(s) copied
This completes the generation of the working diskette. With the diskette
you have just created, proceed to the section, Using the PCMODEL Pro-
gram on p. 7.
IF YOU HAVE A FIXED DISK (A PC/XT OR EQUIVALENT), you
may copy the PCMODEL diskette to the fixed disk and run it from there,
as long as you have the master program diskette in the Drive A when the
program starts up. The copy protection scheme used by PCMODEL does
not render the files contained on the disk inaccessible for copying. In fact,
they can all be copied to other disks. Those copies will not run, however,
without the presence of the master program diskette, as mentioned above.
Thus, PCMODEL can be placed on the fixed disk, as follows:
1. Start up your system as usual, entering the date and time in the
normal manner. (Most users have their systems configured to boot from the
fixed disk rather than from the floppy drive.)