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                    PCMODEL: MOLECULAR GRAPHICS ON THE PC

                       Advanced Shareware Version 3.03



















    Published by:     KT Consulting
                      P.O. Box 3810
                      Vernon, CT 06066

                                   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 molecules at a fundamental level, yet until recently such
    processes could be studied only on very expensive equipment. With the
    publication of the first two versions of this package ("Molecular
    Graphics on the IBM PC Microcomputer," published by Academic Press),
    one could, for the first time, perform many of the same operations on
    the IBM or compatible personal computer. Similar packages were sub-
    sequently released by other vendors, always at prices that put them
    out of reach of most chemists and biologists.

       With the release of Version 3.0 under the Shareware concept,
    molecular modeling on the personal computer has finally become avail-
    able to all who need it. As Shareware, this package may be freely
    shared with your friends and colleagues. It may be freely copied and
    distributed for trial use under the following restrictions:

       1. No charge is to be made for copying or distributing PCMODEL.
       2. No alterations may be made to the files on the diskette.
       3. The printed manual may not be copied or reproduced in any way.
       4. The commercial sale or use of PCMODEL in any manner is
          prohibited without the written permission of the publisher.

    Should you find it useful in your work, please register your copy
    using the order form on the diskette. When you register your copy you
    receive a complete, commercially printed users manual in a binder, the
    most recent version of the program, access to a library of structures,
    a coordinate conversion program, and notification of updates in the
    future. You also will become a member of the Structure Consortium when
    you register. This is a group through which data files may be shared.
    Those who create data files are encouraged to submit them to the
    Consortium. Other registered users will be able to access these files
    and receive copies for their own use. This will save substantial
    duplication of effort.

       PCMODEL is a program to draw and manipulate molecules in graphic
    form using the IBM PC, PC/XT, PC/AT, PCjr, PS/2, and true compatible
    personal computers. The program requires at least 384K of memory under
    DOS 2.x, 3.x, or 4.x. It also requires a computer with color graphics
    capability, either the Enhanced Graphics Adapter (EGA) and Enhanced
    Color Display or its equivalent, or the Color Graphics Adapter (CGA)
    and Color Monitor or its equivalent. It will use the Video Graphics
    Array adapter (VGA) at the EGA level. The EGA card must be equipped
    with 256K of graphics memory to operate in high resolution mode. The
    program requires either two floppy disk drives or (preferably) a hard
    disk, which adds significantly to the convenience and speed of the
    program operation. A 2-button or 3-button mouse cursor device com-
    patible with the Microsoft mouse protocol is highly recommended but
    not required.

       This abbreviated manual is organized into two parts: an Introduc-
    tion and Installation Section, which contains the detailed instruc-
    tions for installation of the program on your computer system, and a
    Tutorial Section containing an overview of the program operation and
    step-by-step instructions and examples to help you to learn the struc-
    ture and basic features of the program. The published version of the
    user's manual also contains a 148-page Command Reference section, where
    each of the commands used by the program is discussed in detail,
    including its use, options, and the responses produced by the program.
    Two appendices are also present. Appendix A contains a listing of all
    of the error messages you may encounter during your use of the program,
    along with explanations. Appendix B contains instructions on the use of
    the utility program, CGP, included with the package.

                              TABLE OF CONTENTS

    Introduction and Installation Section ...............................  1
       Introduction .....................................................  1
       Installation Instructions ........................................  1
          Two Floppy Drive Systems ......................................  2
          Mouse Device Installation .....................................  3

    Tutorial Section ....................................................  6
       Examining the Program Files ......................................  6
       Starting the Program .............................................  8
       Command State Display Screen ..................................... 11
          Tutorial Exercise No. 1 ....................................... 11
          Tutorial Exercise No. 2 ....................................... 15
       Introduction to Program Operation & Structure .................... 15
          Command Summary ............................................... 17
          Tutorial Exercise No. 3 ....................................... 22
          Tutorial Exercise No. 4 ....................................... 24
          Tutorial Exercise No. 5 ....................................... 27
       Mouse Device Interface ........................................... 28
          Tutorial Exercise No. 6 ....................................... 31
          Tutorial Exercise No. 7 ....................................... 36
       Data File Conventions ............................................ 40
       Entering Data from the Keyboard .................................. 42
          Tutorial Exercise No. 8 ....................................... 42

    Command Reference Section ...........................................  *

    References and Notes ................................................ 47

    Appendix A, Messages and Prompts .................................... 48

    Appendix B, Utility Programs ........................................ 55
       CCT - Coordinate Conversion and Transformation ...................  *
          Introduction ..................................................  *
          Operation of the Program ......................................  *
          The Catalog Function ..........................................  *
          File Formats and Transformation Operations ....................  *
          MM2 Files .....................................................  *
          Using the MM2 Package and the CCT Interface ...................  *
          Examining and Modifying Files with the Editor .................  *
       CGP - Coordinate Generation Program .............................. 55
          Introduction .................................................. 55
          Editing or Creating a Data Set ................................ 55
          Changing the Data Drive ....................................... 57
          The Data Entry Screen ......................................... 57
          Generating Cartesian Data Files ............................... 60
          Examples ...................................................... 61

    Help Menu Reference Card for PCMODEL ................................  *


    *Available in the registered version

    PCMODEL User's Manual                                           Page 1


                    INTRODUCTION AND INSTALLATION SECTION

       Molecular models provide one of the best means for studying chemi-
    cal structures and conformations. There are several advantages of
    placing these models on a microcomputer: we can actually see the
    relationships of the atoms of the molecule; we may easily superimpose
    the structures for comparison; we may make accurate measurements of
    interatomic distances and bond and torsion angles. All of the struc-
    tural parameters are contained within the data that is stored on
    diskette. The program uses standard cartesian atomic or X-ray coor-
    dinates 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 (1). Libraries of X-ray crystal struc-
    tures (2) also are rich sources of coordinate data. Structural infor-
    mation may 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. We obtain a great deal of
    insight 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, PC-based modeling systems
    such as this one provide a dimension of insight not previously avail-
    able except to those who work on large, expensive 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 graphic representations of
    molecules of almost unlimited size. 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 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 independently, to perform a "docking" operation in which one
    molecule may be brought into proximity with 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 high-
    light selected atoms, indicate distances between any two atoms, calcu-
    late bond and torsion angles, and edit the coordinate data.


                     INSTALLATION OF PCMODEL VERSION 3.0

       If you are reading this file, you have already installed the
    Shareware distribution version of PCMODEL. If you created floppy disk
    versions of PCMODEL, you may want to make the Working Disk self-
    booting by placing the MS-DOS system files on it. The following
    paragraph tells you how to do this. If you do not need this
    capability, skip to Section B, Mouse Device Installation.

    PCMODEL User's Manual                                           Page 2


       If you are running the program from floppy disks, you must combine
    the DOS system files with the PCMODEL program and supporting files. As
    it is supplied to you, it does not contain all of the files you need
    to run the program. Specifically, you need to combine it with (a) two
    system files if you plan to start up the computer from the PCMODEL
    diskette, and (b) the file COMMAND.COM. These are proprietary
    Microsoft or IBM products and are found on the DOS diskette.


    SECTION A. SYSTEMS WITH TWO FLOPPY DISK DRIVES AND NO HARD DISK

    1. Format a new, blank floppy diskettes by placing your DOS diskette
       in drive A (usually the upper or left-hand drive) and the blank
       diskette in drive B (usually the lower or righthand drive), then
       close the drive doors. If the system is not already on, turn on the
       power switch and enter the date and time with the DOS DATE and TIME
       commands, unless your computer has a clock/calendar board built in.
       Then type:

                format b:/s

       and press the ENTER key. The system will respond by asking you to
       insert a new diskette in drive B and press a key (the ENTER key for
       DOS 3.0 or later). Upon completion of the formatting process, the
       message:

                system transferred

       will appear, followed by a printout of the number of bytes of space
       available on the newly formatted disk. If this analysis shows any
       bad sectors, try formatting the diskette again. If it still shows
       bad sectors, replace the diskette with a new one and repeat the
       formatting procedure. Once this is done, exit from the formatting
       routine by answering no (N) to the "Format another? (Y/N)" prompt.

       The newly formatted diskette will have three files on it. Two of
       these will be hidden files that are not listed by the DOS DIR
       (directory) command. The third file is named COMMAND.COM. This file
       contains the portion of the operating system not already contained
       in memory. Label this diskette as the "PCMODEL Working System
       Diskette."

    2. Place the PCMODEL Working Disk (the one generated by the FINSTALL
       command) in drive A. Place the "PCMODEL Working System Diskette"
       (the one you just formatted with the system files on it) in drive
       B. Close the drive doors. Type the command:

                copy a:*.* b:

       The disk drive lights will alternately light up, and the files on
       the working diskette will be copied to the self-booting working
       system diskette. When the process is complete, the message:

                11 file(s) copied

    PCMODEL User's Manual                                           Page 3


       will appear. This completes the creation of the working system
       diskette. Remove it and place it in its protective sleeve.

    3. Go to Section B, "Installation of the Mouse Driver Software"


    SECTION B. INSTALLATION OF THE MOUSE DRIVER SOFTWARE

       PLEASE NOTE: While the PCMODEL program is intended to be highly
    integrated with a mouse device, it is not essential that you have a
    mouse to use the software. Some of the commands are made immeasurably
    easier and more convenient by the use of a mouse, but all except a
    very few features will work without it. If you do not have a mouse
    device, disregard this section. The PCMODEL program will still start
    up and run without the mouse interface software. The only difference
    you will see is a message, "MOUSE driver is not present" upon startup,
    and pressing function key F4, which normally toggles the mouse cursor,
    will cause a brief error message instead.

       To install the mouse, you must physically plug it into the computer
    (usually into a serial port) and load the mouse interface program
    (supplied with the mouse device) into memory. Since the mouse software
    is transparent to other applications, we recommend that you set it up
    so that it will be loaded whenever you start up the computer. The
    accompanying instructions will accomplish this.

       There are a number of mouse devices on the market, but the almost
    universal standard mouse interface protocol is the Microsoft standard
    interface. PCMODEL uses this protocol, and it should operate with any
    brand of mouse device that emulates this standard. Obviously,
    Microsoft brand mice use it. Several other suppliers have enhanced the
    Microsoft standard by outfitting a third button on the mouse device.
    We have chosen to adopt the three-button optical mouse, the PC Mouse
    from MSC Technologies, Santa Clara, California, as the mouse of choice
    for PCMODEL. This is due mostly to the added flexibility of button
    choices the three-button mouse has. Since PCMODEL uses the Microsoft
    standard interface, we have written the program to be as downward-
    compatible as possible with the two-button Microsoft mouse. There are
    some PCMODEL commands and capabilities that the two-button mouse
    cannot access due to its lack of a third button, but in those few
    instances there is a keyboard-based alternative available.

       Other mouse devices may also be used with the program if they are
    able to emulate the Microsoft mouse driver interface, and if such
    software is provided with the device. We have not tried other brands
    of mice, so we cannot offer a list of those which will or will not
    work with PCMODEL.

       There are two ways to load the mouse interface software. One is by
    running a stand-alone program either MOUSE.COM from Microsoft or
    MSCMOUSE.COM by MSC Technologies. The other way to load it is by way
    of a CONFIG.SYS file. We will address only the first method here. The
    documentation accompanying the mouse device will address the second
    method, and you should consult it if you choose to use it. Both
    methods produce the same result.

    PCMODEL User's Manual                                           Page 4


       To make sure that the mouse interface program is available to
    PCMODEL, it is good practice to load it automatically by including the
    loading statement in the AUTOEXEC.BAT file, which executes auto-
    matically upon startup. As mentioned, the PC Mouse software driver is
    named MSCMOUSE.COM, while the Microsoft driver is named MOUSE.COM.
    These programs are present on the diskettes provided with the mouse
    devices. The appropriate file must be copied to your booting diskette
    or root directory.

       The procedure for installation of this file varies, depending on
    whether or not you are using a hard disk-based system. Choose the
    appropriate set of instructions below, based on the computer system
    you are using.


    1. SYSTEMS WITH TWO DISK DRIVES AND NO HARD DISK:

    a. With the system on and the A:> prompt on the screen, place the
       mouse software diskette in drive A and the newly created working
       diskette in drive B. Close both drive doors.

    b. Type one of the following two commands, depending on the brand of
       mouse you have:

                copy a:mscmouse.com b:   (for PCMouse)
       or
                copy a:mouse.com b:   (for Microsoft Mouse)

       and press ENTER. One file will be copied to the working diskette.

    c. If you are using another diskette for a booting diskette, place
       that diskette into drive B and again type one of the following two
       commands:

                copy a:mscmouse.com b:   (for PCMouse)
       or
                copy a:mouse.com b:   (for Microsoft Mouse)

       and press ENTER.

    d. If you performed step c, use a text editor to place the command

                mscmouse/1

       into the AUTOEXEC.BAT file on your booting diskette (substitute the
       command "MOUSE/1" if you own a Microsoft mouse). It can be placed
       anywhere in the file, perhaps after the date and time prompts. The
       number 1 tells the program to place the driver on serial port 1
       (COM1:). If COM1: is dedicated to a modem or printer, substitute
       the number 2 in the command to place the driver on COM2: (COM1: is
       the default).

    e. Remove the diskettes. Place the mouse device software diskette in a

    PCMODEL User's Manual                                           Page 5


       secure place and use the working diskette for your day to day
       molecular graphics work.


    2. SYSTEMS WITH A HARD DISK:

    a. With the system on and the C:> prompt on the screen, place the
       mouse software diskette in drive A and close the drive door.

    b. Type the command:

                cd\

       and press ENTER. This will make your root directory the default
       directory if it isn't already so.

    c. Type one of the following commands (whichever is appropriate for
       your brand of mouse):

                copy a:mscmouse.com c:   (for PCMouse)
       or
                copy a:mouse.com c:   (for Microsoft Mouse)

       and press ENTER. The mouse driver file will be copied to the hard
       disk's root directory. Remove the mouse software diskette and store
       it in a secure place.

    d. The final step is to place the MSCMOUSE command in the AUTOEXEC.BAT
       file in the root directory of the fixed disk so it is executed upon
       startup. Using a text editor, place the command

                mscmouse/1

       in the AUTOEXEC.BAT file following the DATE and TIME commands if
       they are present (substitute the command "MOUSE/1" if you have a
       Microsoft mouse). Otherwise, place them at the beginning of the
       file so they are executed upon startup. The number 1 tells the
       program to place the driver on serial port 1 (COM1:). If COM1: is
       dedicated to a modem or printer, substitute the number 2 in the
       command to place the driver on COM2: (COM1: is the default).

    e. Reboot the computer by pressing Ctrl-Alt-Del.

    PCMODEL User's Manual                                           Page 6


                               TUTORIAL SECTION


    A. EXAMINING THE FILES ON THE PROGRAM DISK

       There are a number of files contained on the program and data
    diskettes (or in the PCMODEL subdirectory). You may list these files
    in the DOS environment by typing the DOS directory command

             dir/w

    then pressing the ENTER key. The listing you see on the screen repre-
    sents the disk or directory contents. We will briefly cover the names
    and purposes of the filenames you see on the screen.

    Program (.EXE) Files: The PCMODEL program is contained in the file
       PCM3.EXE. This is the program you will run when you use PCMODEL.
       There is a coordinate generating program, CGP.EXE, which is used to
       produce coordinate files from a structure's bond length and bond
       angle data. Its use is discussed in Appendix B. In the registered
       version there is also a conversion program, CCT.EXE, to intercon-
       vert data files from one format to another. Finally, there is a
       program called DTA2DT3.EXE, which converts the ".DTA" data file
       format used in the earlier Academic Press versions of PCMODEL into
       the ".DT3" data format used by the current version, Version 3.0.
       Read the name of the file as "DTA to DT3" to remember its purpose.

    Supporting Files: There are a number of files accessed by the PCMODEL
       program during its operation which must be present on the working
       diskette or in the same directory as the program files. If you are
       using a standard color graphics adapter (CGA) and monitor (or the
       color graphics emulation mode on a higher resolution system), the
       essential files are CONFIGC.PCM, which supplies configuration
       information to the program, and CONFIGC.TXT, which is a text file
       used with the CONFIGURE command to change the values of
       CONFIGC.PCM. If you are using an enhanced graphics adapter (EGA)
       with 256K of graphics memory and an enhanced color display or a VGA
       adapter, the essential files are CONFIGE.PCM and CONFIGE.TXT. The
       two sets of files contain different information, and are not inter-
       changable. By changing the values in these configuration files you
       may customize many of the presentation features of the program.
       This is done through the CONFIGURE command from within the program.
       There is also an online HELP file, PCM3.HLP, which must be in the
       same directory or diskette as the program files. This file lists
       the choices of commands available in the program. It is called by
       the HELP command within the program.

    Data Files: Finally, there are several files that contain sample data.
       These files have the file extension ".DT3". (See the section "Data
       File Conventions" for details of how the system names files and
       stores data.) When you save structural data with the program, they
       will also be stored with this same file extension, unless you
       specifically override it. Thus you may list any data files on a
       disk from DOS by typing the DOS command

    PCMODEL User's Manual                                           Page 7


                dir *.dt3

       The following example data files come with the program:

       FILE NAME                    BRIEF DESCRIPTION

    ACHOLINE.DT3       Acetylcholine, a small neurotransmitter.

    EPINEPHR.DT3       Epinephrine, another neurotransmitter.

    MEPERO.DT3         Meperidine, a narcotic analgetic drug. The structure
                       was generated from Dreiding stereomodels. In this
                       structure the piperidine and phenyl rings are
                       easily seen. At the axial 4-position is the car-
                       boxyethyl group, and attached to the nitrogen at
                       position 1 is a methyl group.

    MORPHINE.DT3       Morphine, a naturally occuring narcotic analgetic
                       drug, generated from X-ray coordinate data. The
                       characteristic T-shape can be seen when the struc-
                       ture is rotated about the Y-axis.

    ADAMANT.DT3        This file contains the cartesian coordinates of the
                       carbon atoms of the symmetrical cage hydrocarbon,
                       Adamantane. These coordinates were entered from the
                       keyboard, based upon theoretically generated
                       values.

    BDNA.DT3           A 12 base-pair segment of DNA in the B conformation.

    PALTEST.DT3        A test file for palette colors. Contains at least
                       one of each atom type.

    The Chymotrypsin Active Site: There are 7 data files on the diskette
    that are part of a model of the active site of the proteolytic enzyme
    Chymotrypsin (8,9). The portions of the enzyme covered here are those
    addressed by Clarke (4) based on the X-ray structure of the enzyme
    (8). The coordinates of the atoms in each of these files are
    reproduced exactly from the X-ray data. Only a portion of the 245-
    amino acid enzyme is reproduced here.

    CTPN40.DT3         File with residues 40-43 of the Chymotrypsin active
                       site.

    CTPN56.DT3         File with residues 56-60 of the Chymotrypsin active
                       site.

    CTPN99.DT3         File with residues 99-102 of the Chymotrypsin active
                       site.

    CTPN189.DT3        File with residues 189-196 of the Chymotrypsin
                       active site.

    CTPN213.DT3        File with residues 213-228 of the Chymotrypsin
                       active site.

    PCMODEL User's Manual                                           Page 8


    FTRY.DT3           N-Formyltryptophan, a substrate for Chymotrypsin
                       (9).

    CTPNB.DT3          A file of the backbone residues (i.e., the peptide
                       chain with no side chains) from the Chymotrypsin
                       active site.

    CTPNS.DT3          A file containing the corresponding side chain
                       residues from the Chymotrypsin active site. This
                       file is a companion to CTPNB.DT3.

    The Thermolysin Active Site: Three files contain the molecules that
    represent the active catalytic site of the well-characterized enzyme
    Thermolysin (5).

    THER1.DT3          The first file contains the Zinc atom, Arginine 203,
                       and Phenylalanine 114.

    THER2.DT3          The second file contains the three ligands to which
                       the Zinc atom is bound. These molecules are His-
                       tidine 142, Histidine 146, and Glutamic acid 166.

    THER3.DT3          The third file contains the amino acid residues that
                       are involved with the hydrolytic mechanism. These
                       residues include aspartic acid and histidine 231
                       which serve to transfer a proton to the nitrogen
                       atom of the substrate as it is cleaved. Glutamic
                       acid 143 serves to transfer a water molecule to the
                       carbonyl group of the recently hydrolyzed sub-
                       strate.

    BPPP.DT3           beta-Phenylpropionyl Phenylalanine, a Thermolysin
                       substrate. The ligand has been oriented so that it
                       interacts in an optimal manner with the enzyme
                       active site (6). When the BPPP ligand is bound to
                       the active site, the carboxylic acid anion forms an
                       ionic bond with the guanidinium ion of Arginine
                       203. The amide carbonyl oxygen of BPPPO binds to
                       the zinc atom and displaces a water molecule as the
                       fourth ligand of the zinc atom. The phenyl group
                       associates with the phenyl group of phenylalanine
                       114 through a fairly weak pi-pi interaction.

    GPC.DT3            Guanyl-3',5'-cytidine, a ribonucleoside dimer gener-
                       ated from X-ray coordinate data (7). The original
                       X-ray data are contained in file GPCX.DT3 if you
                       wish to access the X-ray data file. The compound
                       crystallizes in space group C2 (monoclinic) with
                       cell dimensions a=20.987, b=16.470, and c=9.566 A.
                       The angles between the crystallographic axes are
                       alpha=90, beta=94.36, and gamma=90.



    B. STARTING THE PCMODEL PROGRAM

    PCMODEL User's Manual                                           Page 9


       The PCMODEL program runs in two modes, determined by the graphics
    hardware you have. It automatically checks for the type of graphics
    adapter present in the system.

    a. If you have an Enhanced Graphics Adapter (EGA) with 256K of
       graphics memory, the program will start up in EGA mode with a
       resolution of 640x350 pixels in 16 colors.

    b. If you have only a Color Graphics Adapter (CGA), the program will
       start up in CGA mode with a resolution of 320x200 pixels and 4
       colors.

    c. If for some reason you wish to run your EGA hardware in CGA mode,
       the program has an option to do this, as explained later.

    d. If you have a Video Graphics Array (VGA) adapter, PCMODEL will run
       in EGA mode on it as well.

       Obviously, we can operate at a much more sophisticated level with
    the added capabilities of the EGA and as you might expect, many of the
    commands are different for the two modes (EGA vs. CGA). When these
    differences are significant, we will divide the discussion into sec-
    tions devoted to each mode.

    1. STARTING PCMODEL ON A FLOPPY DISK-BASED SYSTEM:

       To begin execution of the program from a floppy disk system, place
       the PCMODEL working diskette in the A drive, and if you have two
       drives place the data diskette in drive B. Make sure that the
       default drive is A (that is, the A:> prompt is displayed on the
       screen next to the cursor). Then type:

                pcm3

       and press the ENTER key. The system will display a copyright
       notice, and then begin the session. The program is self-controlling
       from this point.

       If you are beginning with your floppy disk-based computer turned
       off, an alternate method of starting up PCMODEL is to place the
       working systems diskette (with the operating system) in the A
       drive, the data diskette in drive B (if present), close the drive
       doors, and turn on the computer. The system will start up and give
       you prompts for the date and time, then it will show the DOS
       prompt. Type

                pcm3

       followed by ENTER to begin executing PCMODEL. While this method is
       perfectly satisfactory for many situations, it will not work if
       your computer performs any special operations during startup, such
       as configuring a storage device in memory or loading a print
       spooler. In these situations, you must either start PCMODEL after
       your booting process is complete, or redefine the AUTOEXEC.BAT
       file.

    PCMODEL User's Manual                                          Page 10


    2. STARTING PCMODEL FROM A HARD DISK-BASED SYSTEM:

       If you are running the program from a hard disk, simply change to
       the directory containing the program and support files (in this
       example the subdirectory is PCMODEL) using the DOS command:

                cd\pcmodel

       followed by ENTER. Then type

                pcm3

       followed by ENTER. The program will display a copyright notice,
       then begin the session.

    3. Starting PCMODEL in an Alternate Graphics Mode:

       If you have an EGA or VGA system but want to run the program in CGA
       mode, start the program by typing

                pcm3/c

       then press the ENTER key. This option forces the program to use CGA
       mode. To switch back to EGA mode, you have to quit the program and
       start it up again without the "/c" parameter.


       The first step in learning to use PCMODEL is to start it up, as we
    just described. If you did not do so as you were reading through this
    part of the manual, go back and start up the program according to the
    directions in parts 1, 2, or 3. Once the program has begun, then
    continue reading Section C, which follows.



    C. THE COMMAND STATE DISPLAY SCREEN

       The command state display screen is the central point of the
    program. The program starts at this point and always returns there
    after performing some function. When the program first shows the
    display screen, you will see a rectangle on the screen (the display
    window), under which is a set of commands, the command list. On the
    next line under the window is the word, "Choice:", and in the lower
    right corner is the message, "H For Help." Let's look at each part of
    this screen in more detail, since it is central to the operation of
    the PCMODEL program.

       THE DISPLAY WINDOW. When you first see it, the display window
    represents a cross section of space approximately 22 Angstrom units
    wide and 10-12 Angstrom units high (depending on the graphics mode).
    The structures drawn in the display window are drawn as isometric
    projections of a 3-dimensional structure on a planar surface, i.e., on
    the front of the screen. The coordinate system is a right-handed one,
    with the positive Z-axis going away from you into the screen, the
    positive Y-axis pointing downward from the top of the screen, and the

    PCMODEL User's Manual                                          Page 11


    positive X-axis pointing to your right as you face the monitor.

       THE COMMAND LIST. The line of letters or abbreviations immediately
    below the display window is the command list. In CGA mode (FIgure 1b),
    this command list is simply a set of letters representing the first
    letters of many of the major commands understood by the program. In
    EGA mode (Figure 1a), each major command is represented by a 2 or 3
    letter mnemonic abbreviation. In either mode, not all of the commands
    are represented in the command list. For example, the function key
    commands are not displayed on the command line. They are, however,
    available from an online Help display. We will cover the operation of
    the help screens shortly. You may issue a command to the program
    either by pressing the first letter of the desired command on the
    keyboard or by placing the mouse cursor on that command and pressing,
    then releasing, the left mouse button. The details of the operation of
    each command are contained in the Command Reference Section, and
    several are addressed in the tutorial material that follows later in
    this section.

       THE COMMUNICATION LINE. At the very bottom of the screen (on the
    25th line) is the communication line. The program places most of its
    messages on this line. You have already seen an example of the use of
    this line when you started up the program. The message, "H for Help"
    appears on the right side of the communication line. Much of what
    occurs on this line is informative in nature, such as error messages
    and options available to you. If PCMODEL really needs some input, it
    will prompt you either on the communication line or on one of the
    other four lines below the display window.



                          TUTORIAL EXERCISE NUMBER 1

    We will now configure the program to set the default data directory,
    then access a data file, after which you can learn more about the
    operation of the program. Follow each of the steps carefully. We will
    not use the mouse device for this series of operations.

    1. If you have a mouse device installed, press function key F4. This
       will shut off the mouse cursor on the screen. (If you do not have a
       mouse installed, pressing F4 will generate a short error message).
       The initial part of the tutorial will use just the keyboard. Later
       we will incorporate the mouse device.

    2. If you are running the program either from a hard disk or from two
       floppy disk drives, press function key F9 to initiate the con-
       figuration reset routine.

    3. We will take this opportunity to reconfigure the default data
       directory, the place where the program looks for data files unless
       you tell it to look somewhere else. The screen will show a list of
       parameters headed by the words, "SET CONFIGURATION PARAMETERS."

       a. Press either the ENTER key or the "down arrow" key five times to
          place the cursor on the "Default Data Drive\Path" line. It

    PCMODEL User's Manual                                          Page 12


          should read "A:\DATA\" before modification.

       b. Press the Esc key to clear the line.

    4. Type in the drive and path you select for the data drive and path.
       If you are running the program from two floppy disk drives, type in
       the three characters

                      B:\

       followed by ENTER. If you are running the program from a hard disk,
       enter the hard disk drive letter and the default data path you
       defined earlier. If you followed the installation example, you
       would type

                      C:\PCMODEL\DATA\

       followed by ENTER. This denotes that the data will be in the
       \PCMODEL\DATA subdirectory on the C drive. If you chose another
       place for the data, substitute that drive and path for the one
       suggested above.

    5. Press the F2 key to refresh the screen and to save the data in the
       configuration file. Press the Y key in response to the program
       prompt. This saves the configuration file and returns to the com-
       mand state.

    6. You should now be in the command state. Press the A key. The screen
       will clear and the data files on the default data directory will
       appear in alphabetical order. The upper left file name will be
       highlighted in reverse video. Press the cursor control keys to move
       the highlighted box so that the file "MORPHINE.DT3" is highlighted
       in reverse video. Press the ENTER key. A one-line description of
       the data file appears at the bottom of the display screen. Press
       ENTER again to select the data file. The program will draw the
       structure in the display window, then return to the command state.


       Several other aspects of the display screen are now apparent, which
    we can discuss.

       THE DEPTH BAR AND DEPTH POSITION INDICATOR. When a structure is
    active a colored bar, the depth bar, appears at the left side of the
    screen, outside the window. This bar corresponds to the depth of the
    structure on the screen in Angstrom units, measured from the nearest
    Z-coordinate to the farthest Z-coordinate. The ruler scale immediately
    to the left of the depth bar is calibrated in Angstroms, and may be
    used to determine the depth simply by counting the tic marks on the
    ruler. A structure of small depth, i. e., one that is very shallow,
    will cause the depth bar to be small. Conversely, a deep structure
    will cause the depth bar to be large.

       Since there are many molecules that are more than 12 Angstroms deep
    (the limit of the depth before the bar reaches the top of the scale),
    PCMODEL has a feature that automatically changes the depth scale when

    PCMODEL User's Manual                                          Page 13


    needed. When a structure exceeds 12 Angstrom units in depth, the
    program automatically scales the depth bar to 1/6 of its normal scale
    and widens it to twice its previous width. At this higher setting,
    each scale division represents 6 angstrom units instead of 1 angstrom
    unit. This operation redefines the depth "box" from 12 angstrom units
    deep to 72 angstrom units deep, so structures up to 72 angstrom units
    deep can be represented on the Z depth scale. Depths greater than 72
    Angstrom units show as a 72 Angstrom depth, i.e., the depth bar is
    clipped at that limit.

       A vertical line, the depth position indicator, appears to the left
    of the depth scale. It denotes the absolute position of the structure
    on the Z axis. It is also calibrated to the vertical ruler, i.e., its
    length is equal to the height of the depth bar. PCMODEL places the
    depth position indicator on the ruler so that it reflects the actual
    Z-position of the structure, with the center of the scale equal to a
    Z-coordinate of 6.0 Angstroms. You may note that as you translate a
    structure along the Z-axis, its image in the display window does not
    change in appearance. This is a consequence of the isometric projec-
    tion technique the program uses for structural display. (If perspec-
    tive techniques were used, the structure would grow smaller as it was
    moved away from you in the positive Z direction.) The depth position
    indicator will move to show you the true position of the structure(s)
    in the display window. An upward motion denotes a positive translation
    along the Z-axis (into the screen) and a downward motion denotes a
    negative translation (out of the screen). If a structure is translated
    out of the 12-angstrom unit "box," the depth position indicator will
    be off the scale at either the top or the bottom of the screen. If the
    structure is only partly outside of the "box," the depth position
    indicator will be clipped by the amount lying outside. This will make
    the depth position indicator look smaller than the depth gauge. Thus
    while the depth position indicator does not always represent the depth
    of a structure accurately, the depth bar does, at least within the 72-
    angstrom unit limit.

       If you place two structures on the screen at the same time, PCMODEL
    treats these two structures independently. One of the indications of
    this independence is the appearance of a second depth position in-
    dicator at the left of the screen when the program is in Compare Mode.
    There are many advantages to this dual structure arrangement, and
    these will be apparent later in the discussion.

       DEPTH CUE CONSIDERATIONS. The techniques used to provide depth cues
    in PCMODEL vary depending on the mode in which it is operating. In the
    CGA (low resolution) mode, one technique is the use of color zones. As
    the structure is prepared for placement on the screen, PCMODEL divides
    the Z-dimension into thirds. As each atom or bond is written to the
    screen, the program colors it to reflect the color zone in which it
    resides. The net effect of this is to create a drawing that has, at
    least in its initial or default state, its near side colored red and
    its far side colored green. The area in the middle is colored
    brown/gold, the same as the border. When a structure is displayed on
    the screen in the CGA mode, you can see clearly the effect color has
    for denoting depth. In CGA mode with the color zones active, the color
    at the bottom of the bar is the color of the nearest atoms. The middle

    PCMODEL User's Manual                                          Page 14


    color in the bar represents the middle atoms, while the top color
    denotes the color of the atoms of the structure farthest from the
    screen. You may have to work with this system for a while before you
    become fully accustomed to it.

       In the high resolution (EGA) mode, both the higher quality of the
    display and the greater number of colors available provide other more
    traditional options for depth cues. The program still divides the
    structure into thirds based on the Z-coordinates of the atoms. When
    the program displays the structure in the window, it draws the bonds
    in the distal third of the structure (most positive Z-coordinates)
    with dashed lines and the bonds in the closest two-thirds of the
    structure with solid lines. This has the effect of de-emphasizing the
    bonds at the back of the structure. The colors of the atoms are as
    assigned in the configuration file.

       This latter technique can be invoked in the CGA version as well
    with the ALTERNATE DISPLAY command. In this mode the CGA display
    window has nitrogen atoms colored green, oxygen atoms colored red, and
    all other atoms colored yellow/brown. The most distal third of the
    bonds are then drawn with dashed lines. When the ALTERNATE DISPLAY
    command is invoked in the high resolution (EGA) state, the dotted
    lines of the bonds become more exaggerated. The most distal bonds
    become more highly broken up, while the middle depth zone uses dashed
    lines. Bonds in the most proximal zone remain as solid lines.

    PCMODEL User's Manual                                          Page 15


                          TUTORIAL EXERCISE NUMBER 2

    Now try the ALTERNATE DISPLAY command on the structure in the display
    window. Hold down the Alt key and press the D key. The structure is
    redrawn in the alternate display mode. If you are in the CGA (low
    resolution) mode, the colors of the atoms change. If you are using the
    EGA (high resolution) mode, the bonds between the atoms are drawn in
    increasingly more broken lines, as discussed. Toggle back to the
    normal display mode by again pressing Alt-D. Decide which image looks
    best to you and select that mode with the Alt-D command. If you are
    operating in CGA mode leave the program in the alternate display mode,
    where the color zones are turned off and some of the bonds are present
    as broken lines.



    D. INTRODUCTION TO PROGRAM OPERATION AND STRUCTURE

       The following portions of the manual will take you through many of
    the functions of the PCMODEL program. One of the most important pieces
    of information you can have before beginning the program is how to
    recover from an error, and how to get out of the program when you want
    to. There is nothing more frustrating than to have a computer program
    waiting for some response and not knowing what to type in. Before you
    continue to use PCMODEL, let's review five important points:

    1. The program is driven from a short list of commands used to perform
       the program's functions. You may issue these commands by simply
       typing the first letter of the command.

    2. When it begins, PCMODEL automatically sets the keyboard into upper
       case mode, so that any alphabetic characters you type while in the
       program appear in upper case. If you type commands or responses in
       lower case, the program will not usually understand them and will
       issue an error message. However, there are some points in the
       program where lower case letters are acceptable and these are
       covered under the EDIT command in the Command Reference Section.

    3. When the program requires a Yes or No answer, type just Y or N or
       press the appropriate mouse button as prompted. You do not normally
       need to press the ENTER key following a letter response.

    4. If you are in the middle of executing one of the commands and you
       become uncertain of where you are in the program or what you are
       doing, you can usually return to the command state in one or more
       of the following three ways: (1) press the ENTER key several times
       until the command state is restored; (2) press the F1 function key;
       or (3) hold down the Ctrl key and pressing the F1 key. You may
       think of this third option as a kind of "panic button" which will
       always return you to the command state. While there are places in
       the program where the ENTER or F1 keys have other meanings, Ctrl-F1
       will always return to the command state.

    5. To terminate the program it must be in the command state. To exit,
       press the Q (QUIT) key. You may then choose either to return to the

    PCMODEL User's Manual                                          Page 16


       operating system (DOS) or to clear the structures and restart the
       program. If you have modified a structure but not saved it, the
       program will warn you of this fact and ask if you want to quit
       anyway. If you do, press the Y key, otherwise press the N key to
       return to the command state. The structure(s) in memory will be
       lost unless you file it on disk before quitting.


       Each of the Command List choices executes a unique command that
    accomplishes a defined task. To help orient you to the way that
    PCMODEL operates, we will take some care here to outline the framework
    within which the commands operate. Most of the purposes of the com-
    mands are essentially self-explanatory. For example, the ADD FILE
    command brings a structure from the diskette into the display window
    and the ROTATE command causes the structures on the display to be
    rotated about either a principal or nonprincipal axis.

       Obviously, many of the commands require more information than
    simply the command itself. For example, you must have a way to specify
    a filename when you ADD a file to the display. Likewise, to ROTATE a
    structure you must provide both the axis of rotation (X, Y, Z, or one
    defined by any two atoms), and the angle over which the structure is
    to rotate. PCMODEL has two ways to obtain this information: (1) menus
    and (2) separate prompts.

       The program operates in a multilevel command format, with the
    display screen and its command list at the highest level. When you
    type a command letter on the display screen, the program will begin to
    implement that command.

       We will use the ROTATE command to illustrate the multilevel nature
    of the command structure. The ROTATE command is represented on the
    command list by the letter R or the mnemonic "Rot." When you invoke
    the command by pressing the letter R, the program immediately clears
    the command list and the input ("Choice:") line as well as the com-
    munication line. It then asks you for a rotation axis. The program is
    now on a second level of operation, one that is more specific than the
    first level. Instead of accepting any of the possible command list
    choices, it is now concentrating only on the ROTATION function and
    asking for guidance from you. From this second level, you can either
    return to the first (more general) level by pressing the ENTER key, or
    you can continue by specifying either a principal axis (X, Y, or Z) or
    a nonprincipal axis (by typing B, for a bond).

       If you choose an axis of rotation, the program now moves to a
    third, still more specific level of operation by prompting you for an
    angle through which to rotate. After you enter the value to rotate,
    the program implements the task, then waits for input of another
    angle.

       You can move up and down through these levels. A response moves to
    the next level down, while pressing the ENTER key moves to the next
    higher level. In this example, you would press the ENTER key to return
    to the second (rotation axis) level and press the ENTER key again to
    return to the command state. You will find that with practice, both

    PCMODEL User's Manual                                          Page 17


    the command structure and the resultant program operation are quite
    intuitive.

       To review to this point, you now know the following:

    1. The display screen consists of a display window, a depth gauge,
       four text lines, and a communication line at the bottom.

    2. The program uses a multilevel mode of operation for its commands.

    3. The levels of operation move from the highest or most general (the
       command state) to the lowest or most specific (such as choosing the
       precise angle of rotation).

    4. Move down the levels by responding to the prompts with some form of
       input, either letters or numbers, thus telling the program that you
       want it to continue carrying out the command on which it is work-
       ing.

    5. Move up the levels toward the command state by pressing the ENTER
       key with no other letters or numbers.

    6. When the program requests input, it will be a request for either a
       letter or a number. Generally, responses to a letter request do not
       need to be followed by the ENTER key. Responses to a request for a
       number do need to be followed by the ENTER key.

    7. The Function keys (F1-F10) are active for input of predefined
       values on occasion. When they are, the menu of choices represented
       by the keys is displayed on the communication line and the line
       above it. All function keys are also active in the command state.

       We will now consider all of the commands available with PCMODEL.
    The commands can be grouped into 5 categories based on function. These
    five functions include (1) System and Control Functions, (2) Display
    Functions, (3) File Manipulation Functions (4) Structure Manipulation
    Functions and (5) Printing Functions. Initially most of the commands
    we will discuss and illustrate are from the display and manipulation
    groups.

    SYSTEM AND CONTROL FUNCTIONS

       There are nine commands that make up this group. The commands are:

    Q or Qt          Quit the current structure. The program gives you the
                     options of clearing memory to begin a new structure,
                     stopping the program, or continuing with no change.
                     This is the way you leave the program and return to
                     DOS.

    Alt-Q            This Alternate-Quit key combination serves as a RESET
                     command. The program quits the current structure and
                     restarts the program. It differs from the QUIT com-
                     mand in that it does not present you with the prompts
                     or warn you if the data set has not been filed.

    PCMODEL User's Manual                                          Page 18


    Ctrl-Q           This command serves as an Immediate and Unconditional
                     QUIT command. It causes the program to terminate
                     immediately and return to DOS. It does not check for
                     modified data sets or give you a chance to change
                     your mind. Use it with extreme care!

    Ctrl-F1          This command acts as a "panic button" that, when
                     pressed in response to a prompt, immediately stops
                     the program and returns to the command state.

    F4               The F4 key toggles the mouse cursor on or off, if a
                     mouse device is present.

    F9               The F9 key resets the program configuration
                     parameters. You saw a use of this command when we
                     reset the default data drive and path earlier. There
                     are a number of other parameters that can be set.

    Alt-F9           The Alt-F9 key also changes the default data drive and
                     path, but on a temporary basis. It does not save the
                     changes to the disk, so the change remains in effect
                     only for the current session.

    Alt-L            The limits of the data arrays are defined dynamically
                     in PCMODEL. The default array size is 1000 atoms and
                     1000 bonds, but you can change this limit using the
                     Alt-L command.

    Alt-F1           The Alt-F1 key suspends operation of the program and
                     loads another copy of DOS into memory (i.e., it
                     creates a DOS SHELL). You can run any DOS application
                     (if there is enough memory), then return to the
                     program where you left off by typing EXIT, followed
                     by the ENTER key. Systems running DOS 2.x may behave
                     abnormally using this command. Under DOS 2.x the
                     system can hang up, requiring a power down to restart
                     the system.


    DISPLAY FUNCTIONS

    C or Col         The COLOR command toggles between the two color
                     palettes defined for the program. In CGA mode, the
                     palettes are fixed as either red/green/brown or
                     magenta/cyan/white, and are not very useful. In EGA
                     mode, however, the two palettes assign the screen
                     colors of the atoms and other screen components.

    K or Kmp         The COMPARE command (accessed by the letter K, because
                     the letter C was taken) highlights the last structure
                     from the previous structures on the display.

    Alt-K            The ALTERNATE COMPARE command modifies the way in
                     which the Compare command displays the structures.
                     When toggled on, it removes depth cueing from the

    PCMODEL User's Manual                                          Page 19


                     normal display window and displays the second struc-
                     ture in dashed lines in the expanded display window.

    M or Mot         The MOTION command sets the structure(s) in the dis-
                     play window into rotational MOTION. You can choose to
                     rotate the image about any axis, X, Y, or Z.

    S or Siz         The SIZE command is used to zoom in or out. You can
                     zoom in by giving the program a larger size and zoom
                     out by providing a smaller size value. The number you
                     enter serves as a multiplier for the screen coor-
                     dinates.

    Z or Zpl         The Z-PLANES command sets the positions of the front
                     (Hither, toward the user) and back (Yon, away from
                     the user) Z-clipping planes for the display window.
                     This does not turn the clipping planes on, it just
                     sets the position.

    F8               The F8 key actually toggles the Z-clipping planes on
                     and off.

    F3               The F3 key toggles the CIRCLES option. When this
                     option is on, each atom is circled to produce a "ball
                     and stick" model in the display.

    Alt-F3           The Alt-F3 key combination invokes the ATOM ID Mode,
                     in which each atom is labeled by a letter repre-
                     senting the atom type. The letters used are based on
                     the first letter of the identifier string associated
                     with each atom (C or carbon, H for hydrogen, etc.).
                     Pressing the key combination again toggles the ATOM
                     ID mode off.

    Alt-2            Another way of representing a structure in 3-D is to
                     draw two slightly rotated images next to one another.
                     The image then appears in stereo perspective when
                     viewed with a viewer or by bringing the images together
                     with your eyes. The Alt-2 key combination toggles this
                     display mode.

    Alt-3            The program can display a structure in a 3-dimensional
                     viewing mode in which two slightly rotated images of
                     the structure are drawn - one in red and one in
                     green. You can then view this through red/green
                     glasses that produce the 3-D image. The Alt-3 key
                     combination toggles this display mode on and off.

    Alt-D            The depth cueing options can be toggled with this key
                     combination. In CGA mode the alternate depth cues
                     assign colors on the basis of atom type instead of
                     depth. In EGA mode, the alternate depth cue option
                     causes the distant bonds to be drawn in broken lines.

    Alt-H            The Alt-H key combination hides any hydrogen atoms

    PCMODEL User's Manual                                          Page 20


                     that may be present on the structure in the window.
                     It does not remove them from the structure.

    Alt-E            This key combination expands the display window to
                     fill nearly the whole screen. Since the text lines
                     are gone in this mode, the program cannot stay in
                     this mode, and when you press any key PCMODEL returns
                     to the normal display state, i.e., the command state.
                     The Expanded display state is useful if you wish to
                     photograph the screen or capture the screen image
                     with one of the many "screen grabber" utilities on
                     the market.

    Alt-S            PCMODEL simulates a solid model by drawing overlapping
                     spheres (actually disks) for the atoms of a struc-
                     ture. This key combination toggles this function.

    Alt-A            This key combination does both an Alt-E (expanded
                     screen) and an Alt-S (solid model) command at the
                     same time. Pressing any key restores the screen to
                     the normal display state.

    Alt-N            There are times when you will wish to prevent the
                     program from sorting the coordinates of a structure
                     before displaying it. This option allows you to shut
                     off automatic coordinate sorting.


    FILE MANIPULATION FUNCTIONS

    A or Add         The ADD command reads a structure file from the disk
                     and loads it into memory. It also serves to examine
                     the contents of the various disks and directories for
                     data files. If a data file contains a comment line,
                     that line can be displayed without loading the file
                     itself.

    F or Fil         The FILE command does the opposite of the ADD command
                     - it writes or files one or more of the structures in
                     memory to disk.

    G or Get         The GET command is used to enter the cartesian coor-
                     dinates for a new structure by typing them at the
                     keyboard.

    U or Un          The UNADD command is used to remove the last (most
                     recently added) structure from memory.

    Alt-U            The ALTERNATE UNADD command removes the first (pre-
                     vious) of two structures from memory.

    X or Xry         If the cartesian coordinate data of a structure are
                     given in unit cell fractional coordinates you can use
                     the X-RAY command to convert them into cartesian
                     coordinates so they may be displayed.

    PCMODEL User's Manual                                          Page 21


    Alt-C            The CLONE command produces an identical second copy of
                     a structure in the display window. This is useful for
                     comparisons of both a modified and an unmodified
                     structure.


    STRUCTURE MANIPULATION FUNCTIONS

    D or Dis         The DISTANCE command calculates the interatomic dis-
                     tance between any two atoms. One of the options of
                     this command is to print selected distances on the
                     printer.

    E or Ed          The EDIT command is a very complex one, with many
                     options. These include changing atomic coordinates &
                     bonds by modifying the raw coordinate data, as well
                     as adding and deleting other atoms and identifier
                     labels.

    I or Inv         The INVERT command changes the current structure's
                     stereochemistry by inverting one or more of the
                     coordinate dimensions or atom centers. There are
                     options for each of the three axes plus a center of
                     inversion.

    J or Jn          The JOIN command establishes a bond between any two
                     atoms. If the atoms are parts of two previously
                     unconnected structures, the two structures become
                     one.

    Alt-J            The alternate-J key selects the UNJOIN command, which
                     does the converse of the JOIN command by breaking a
                     bond between two atoms. The command does not create a
                     fragment, however.

    N or Num         The NUMBER command is used mostly without a mouse to
                     determine the internal atom number and identity label
                     of an atom.

    O or Ori         The ORIENT command has options to center a structure
                     by placing a designated atom at the center of the
                     screen and to orient a structure by placing desig-
                     nated atoms at the center, and on the cartesian axes
                     of the display window.

    Alt-O            The ALTERNATE-ORIENT command marks the current orien-
                     tation of a structure so that it can be restored
                     using an option of the ORIENT command.

    R or Rot         The ROTATE command causes a structure to rotate about
                     a major axis (X, Y, or Z), and causes all or part of
                     a structure to rotate about a bond or axis formed by
                     any two atoms.

    T or Trn         The TRANSLATE command moves a structure along any of

    PCMODEL User's Manual                                          Page 22


                     the major (X, Y, Z) axes.

    V or Vgl         The V key selects the ANGLE command. Remember it by
                     thinking of the relationship of the sides of the "V."
                     Using this command you can determine the bond angles
                     and torsion angles wothin a structure.

    F2 (Alt-M)       The F2 key selectes the Dynamic Motion environment.
                     This requires a mouse device. One or more structures
                     can be rotated and translated in real time in
                     response to the mouse movements. This capability adds
                     tremendous convenience to "docking" and superimposi-
                     tion experiments.

    F7               Using the FIT STRUCTURES command you can designate up
                     to four atom pairs (three in CGA mode) between which
                     the interatomic distances can be monitored. This
                     capability is most useful for structure fits and
                     comparisons.

    Alt-F            The FRAGMENT command causes two connected atoms to be
                     separated and if the residues are not connected in
                     any other way, causes two independent fragments to be
                     formed. This command is especially useful in gener-
                     ating molecular building blocks and functional
                     groups.


    PRINTING FUNCTIONS

    L or Lst         The LIST command is used to print a hard copy of a
                     structure's atomic coordinates and bond connections
                     on the printer.

    F5               The F5 key sends a line feed character to the printer.
                     This is useful when you want to advance the paper
                     without reaching over to the printer.

    F6               The F6 key sends a page eject (form feed) character to
                     the printer. This permits you to start a new page
                     without having to reach to the printer.

    P                The Print command is a specialized one, active in high
                     resolution mode. When the expanded display screen is
                     present, the print command saves a high resolution
                     image of the display screen to disk, which can then
                     be printed on a laser printer.



                          TUTORIAL EXERCISE NUMBER 3

       Let's now manipulate the Morphine structure in the window, to
    illustrate some of the capabilities of the program. We will begin with
    several of the commands that change the display options of the

    PCMODEL User's Manual                                          Page 23


    program. As you view the screen (in either CGA or EGA mode) the struc-
    ture should appear as a series of connected lines. Some of the lines
    are broken, denoting bonds at the back of the molecule. Perform each
    of the following steps.

    1. Press the F3 key to call the CIRCLES command. The program will
       redraw the structure to include circles representing each atom of
       the molecule. This CIRCLES command produces a "ball and stick" type
       representation. Press the F3 key again to return to the "stick"
       display. The F3 key toggles the CIRCLES command. Notice that the
       program takes longer to display the structure when it draws the
       circles, so you will probably want to leave the CIRCLES mode off
       during normal operation.

    2. Hold down the Alt key and press the S key. The program will redraw
       the structure to simulate a SOLID model. It makes use of a simple
       "kissing spheres" (actually "kissing contoured disks" technique to
       produce a quasi-solid image. It will give you an approximation of a
       solid model without taking the extended time to calculate a true
       solid display. Press the Alt-S keys again to return to the normal
       display state.

    3. Hold down the Alt key and press the E key. PCMODEL will EXPAND the
       display screen to the point where it almost fills the physical
       screen. This expanded display screen mode makes no difference for
       morphine, since it is completely visible in the display window, but
       the expanded state is useful for larger molecules. Press ENTER or
       any other key to return to the command state.

    4. Press the S key, which changes the SIZE of the image. The program
       will ask you for a size factor. Type the number 2 followed by
       ENTER. The program will redraw the image at twice its original
       size. Type the number 0.5 followed by ENTER. The image becomes half
       its previous size, i.e., it becomes the size it was when you
       started. Press the + key followed by ENTER. The program redraws the
       image larger by 10%. Repeat this step. The image becomes 10% larger
       again. Press the - key followed by ENTER. The image becomes 10%
       smaller. Notice that neither the depth bar nor the depth position
       indicator has changed, meaning that the structure has not changed
       position, but that the view has "zoomed" in, then out. Press ENTER
       to return to the command state.

    5. Press the M key, which initiates the MOTION command. The program
       redraws the structure in an expanded display screen and prompts you
       for an axis (X, Y, Z, or S to stop). Press the Y key. The image
       begins to rotate about the Y-axis. The rotation is relatively
       smooth in the EGA mode and somewhat "blinky" in the CGA mode. This
       is a consequence of the capacity of the graphics display hardware.
       While the image is rotating press the X key. The direction of
       rotation changes to produce a "tumbling" about the X-axis. Press
       the Z key, which causes the structure to rotate about the Z-axis in
       a "twisting" motion. Press the S key to stop the motion. Press
       ENTER to return to the command state.

    6. Rather than trying to restore the rotated structure to its original

    PCMODEL User's Manual                                          Page 24


       state, we will simply reload another copy of it. Press the Q key to
       call the QUIT command. If you wish to continue to the next lesson
       Press the R key in response to the "(R)estart, (C)ontinue, or
       (E)nd" prompt. The program clears the display window and returns to
       the command state. If you want to end the program, press the E key
       to return to DOS.



                          TUTORIAL EXERCISE NUMBER 4

       We will now cover several of the structure manipulation features of
    the PCMODEL program. As you did previously, follow each of the steps
    in the tutorial. This sequence does not show all of the features
    available, but illustrates the basic capabilities and organization of
    the program. If you are starting up the program again at this point
    after leaving off with Exercise Number 3, be sure to toggle off the
    mouse device (if it is present) by pressing function key F4, then
    begin:

    1. Load the MORPHINE.DT3 data file again, as you did in Tutorial
       Exercise 1, step 6, if the structure is not in the display window.

    2. Press the N key, which initiates the NUMBER command. The numbers of
       the atoms are the internal numbers assigned by PCMODEL when it read
       in the coordinate data. They are assigned in the order they are
       read and may or may not have any relevance to the atom numbers
       assigned by IUPAC or other official body.

       a. At the atom number prompt type the number 1 and press ENTER. The
          atom at the lower right edge of the phenyl ring is highlighted
          with a green box. The number of the atom and its identifier
          label (in this case C1) are presented below the window.

       b. Press the + key. The box moves to the next higher atom (in this
          case atom 2) and the respective information is printed below the
          window.

       c. Press the - key. The box moves to the next lower atom number,
          atom 1, again.

       d. Press the - key again. The box moves to the H atom on the
          nitrogen, atom number 24. This wrap-around feature works when-
          ever the "+/- active" prompt is on the screen.

       e. The program can also search by atom identifier label. Press the
          L key followed by ENTER.

       f. At the prompt for the label type the characters C15 followed by
          ENTER. The program locates the atom corresponding to that label
          at the top of the molecule, highlights it with a highlight box,
          and displays the coordinate information below the window.

       f. Press ENTER to return to the atom number prompt, then a second
          ENTER to return to the command state.

    PCMODEL User's Manual                                          Page 25


    3. Press the D key to invoke the DISTANCE command. Press the D key
       again to choose to DRAW the distances in the display window.

       a. Choose atom number 1 as the base atom by pressing the 1 key
          followed by ENTER in response to the prompt. Choose atom number
          3 as the target atom by pressing the 3 key followed by ENTER.
          The program draws a dotted line between the atoms and prints the
          atom numbers, identifiers, and the distance between them (2.43
          angstroms) below the window.

       b. Press the + key. The target atom number increases by 1 and the
          program draws a new line from the base atom (atom 1) to atom 4,
          the new target atom. A distance of 2.80 angstroms appears below
          the window.

       c. Press the ENTER key twice to return to the command state

    4. Press the V key to invoke the ANGLE command. Press the S key to
       select the simple angle option.

       a. Press the number 1 followed by ENTER, then the number 2 followed
          by ENTER, then the number 3 followed by ENTER. Note that all
          three atom numbers are on one line below the window. The program
          highlights the three atoms with boxes and prints the identifier
          labels and the C1-C2-C3 angle of 121.80 below the window. The
          center atom of the angle is always highlighted by the yellow
          box.

       b. Press ENTER to clear the boxes and angle information. Press
          ENTER again to return to the angle option prompt.

       c. Press the T key to select the torsion angle option. Once again
          press the 1 key followed by ENTER, then the 2, 3, and 4 keys,
          each followed by ENTER. The program highlights atoms 1 and 2
          with green boxes and atoms 3 and 4 in red boxes, then prints the
          torsion (dihedral) angle and the atom identifiers below the
          window. The angle of 2.2 degrees indicates that the four atoms
          are essentially planar.

       d. Press the ENTER key three times to return to the command state.

    5. Press the T key to invoke the TRANSLATE command. Type X to select
       the X-axis for translation.

       a. Type the number 2 followed by ENTER. The structure moves 2
          angstroms to the right.

       b. Press the function key F5, which moves the structure 2 angstroms
          to the left. For this command the function keys are programmed
          to produce ten predefined translations, as stated in the prompts
          at the bottom of the screen.

       c. Change the axis of translation by pressing the Y key followed by
          ENTER.

    PCMODEL User's Manual                                          Page 26


       d. Press the F6 key to move the structure 2 angstroms lower in the
          window. (Remember the origin is in the upper right corner.)

       e. Press the F5 key to raise the structure by 2 angstroms.

       f. Change to the Z-axis of translation by pressing the Z key fol-
          lowed by ENTER.

       g. Press the F4 key to move the structure 1 angstrom in the +Z
          direction. Note that while the appearance of the image did not
          change, the depth position indicator at the left of the screen
          moved up the scale.

       h. Press the F4 key again and watch the depth indicator. Press the
          F5 key to return the structure to its previous position.

       i. Press ENTER to return to the command state.

    6. Press the R key to select the ROTATE command. Press the Y key to
       choose the Y-axis for rotation.

       a. Press the F6 key. The structure rotates +30 degrees, with the
          left side of the structure moving toward you. Just as for the
          TRANSLATE command the function keys are predefined for the
          values at the bottom of the screen.

       b. Press the F5 key to restore the original image with a -30 degree
          rotation.

       c. Press the X key followed by ENTER to change the axis of rotation
          to the X-axis.

       d. Type the number 60 followed by ENTER. The structure "tumbles"
          forward by +60 degrees.

       e. Press the F7 key to restore the original image by a -60 degree
          rotation about the X-axis.

       f. Press Ctrl-F1 to return directly to the command state.

    7. Press the Q key to invoke the QUIT command. Press the Y key to tell
       the program not to save the modified structure. If you want to
       continue with the next exercise, press the R key to restart the
       program. If you want to quit and return to DOS at this point press
       the E key.

    PCMODEL User's Manual                                          Page 27


                          TUTORIAL EXERCISE NUMBER 5

       We will now look at a couple of the printing capabilities of the
    program. If you do not have a printer connected to the parallel
    printer port (LPT1:) then you should skip this section. If you are
    using a serial printer, use the DOS MODE command to redirect the
    default line printer output to the serial port. Consult your DOS
    manual for instructions on how to do this.

    1. If you are starting fresh from this point, begin the program in the
       usual way and toggle the mouse device off, if one is present, by
       pressing the F4 function key. Load the morphine molecule by press-
       ing the A key, then typing MORPHINE followed by the ENTER key.

    2. Make sure the printer is turned on and is on line. Make sure the
       paper is set to the top of the page.

       a. Press the L key to invoke the LIST command.

       b. Press the C key to choose the coordinate listing option. A
          listing of all of the coordinates and bond connections by atom
          number will be printed on the printer. When the program is
          finished printing the information it returns to the command
          state.

       c. Press the L key to invoke the list command once again.

       d. Press the B key to choose to list the bond lengths for each of
          the connected atoms of the structure. The program will print out
          a list of the connected atoms and the bond distance between each
          atom pair, then return to the command state.

    3. Press the D key to invoke the DISTANCE command. Press the L key to
       choose to send a list of interatomic distances to the printer.

       a. At the prompt for the first base atom, type the number 18 fol-
          lowed by the ENTER key.

       b. At the prompt for the second base atom, again type the number 18
          followed by the ENTER key. This limits the atoms over which
          distances are calculated to one atom - the nitrogen atom.

       c. At the prompt for the first target atom, type the number 1
          followed by the ENTER key.

       d. At the prompt for the second target atom, type the number 24
          followed by the ENTER key. This specifies that the distances of
          all of the atoms of the molecule from the nitrogen atom will be
          covered in the printout.

       e. At the prompt for a minimum distance, type the number 1.0 fol-
          lowed by ENTER.

       f. At the prompt for the maximum distance, type the number 8.0
          followed again by the ENTER key. This specifies that the program

    PCMODEL User's Manual                                          Page 28


          should report all interatomic distances larger than 1.0
          angstroms and smaller than 8.0 angstroms.

       g. The program will list a series of distances between each atom of
          the molecule and the nitrogen atom on the printer. While this
          list does not have much use for morphine, you can see that if
          two molecules are in proximity, this feature is very useful for
          determining the distances between the atoms of the two struc-
          tures. It is most useful for docking experiments.

    4. Press the Q key to QUIT the program. If you want to continue with
       the tutorial material, press the R key to restart the program. If
       you want to exit and return to DOS, press the E key.



    E. MOUSE DEVICE INTERFACE

       If you do not have a mouse device attached, you may skip this
    section. Version 3.0 of PCMODEL is heavily enough integrated with a
    mouse cursor device that you are at a significant disadvantage without
    it. Nevertheless, the program will run without it in a somewhat com-
    promised state. For the purposes of this program, the three buttons of
    the standard 3-button mouse device will be denoted as buttons [1],
    [2], and [3], moving left to right across the top of the device (the
    "tail" of the mouse will be above the buttons).

       The main or dominant button is the left one, button [1]. It is this
    button that you will use to invoke all of the commands from the com-
    mand line and to activate the atom searching algorithm. It may also be
    used to provide an affirmative answer to a "yes or no" program prompt.

       The third or right button (button [3]) is usually used to exit or
    withdraw from a command environment (much like a blank ENTER key press
    on the keyboard). It may also be used to provide a negative response
    to a command or program request, i.e., a "No" answer to a "Yes or No"
    prompt. In the command state the right mouse button selects the
    Alternate-Command, just as if you had held down the Alt key while
    pressing the command letter on the keyboard. For example, the UNADD
    (U) command removes the second or most recently added structure from
    the display, while the ALTERNATE UNADD (Alt-U) command removes the
    first or previous structure from the display. You may invoke the UNADD
    command by clicking the U or Un with the left mouse button and the
    ALTERNATE UNADD command by clicking the U or Un with the right mouse
    button.

       The center button (button [2]) is used less frequently and is of
    lesser importance than the other two. This is intentional since the
    center button is the one that is missing from the two-button mouse,
    not the right button ([3]). Any function accessed exclusively by this
    button is unavailable to those systems equipped with a two button
    (Microsoft type) mouse. In many instances where a response on the
    center button is necessary, you may press the numeral "2" on the
    keyboard, which has the same effect. There are, however, a couple of
    occasions where this is not possible. In one instance, discussed

    PCMODEL User's Manual                                          Page 29


    later, both the left and right buttons are pushed together to simulate
    the center button.

       If the mouse and its device interface are present, the program
    starts up with the mouse active and the mouse cursor in the middle of
    the screen. As you now know, you may toggle it off by pressing the F4
    function key. With the mouse activated, the graphics arrow cursor may
    be placed anywhere on the display screen by moving the mouse device.
    To invoke one of the commands, move the mouse to place the cursor
    arrow tip so that it is in contact with the appropriate letter or
    mnemonic abbreviation on the command line. Activate the command by
    clicking the left mouse button (button [1]). Clicking is the act of
    pressing, then releasing, a mouse button. This has the same effect as
    pressing the command letter key on the keyboard. All of the displayed
    letter commands may be invoked with the mouse cursor device in this
    way. The function key commands are not accessible with the mouse
    device, but are invoked with a single press of the appropriate func-
    tion key. The Alternate commands are invoked by placing the cursor
    arrow on a command letter or mnemonic combination, then clicking the
    right mouse button (button [3]).

       There are three different types of commands involved in the opera-
    tion of the software, (1) those that take no argument and are imple-
    mented immediately upon a keypress, (2) those that require an atom
    number or other simple choice following command input, and (3) those
    that require text or other complex or extensive input. The mouse
    interface interacts with these three types of commands differently. It
    offers the most dramatic improvement for the type 1 and (especially)
    type 2 commands. For example, if a response requires entry of an atom
    number, rather than typing that atom number on the keyboard, you may
    simply point to the atom of interest with the mouse cursor and press
    the appropriate mouse button, usually the left one.

       The key component to effective communication between the user and
    the screen display is the ability of PCMODEL to search, detect, and
    identify a given atom based on its screen coordinates. The routine to
    perform this function will identify an atom if the tip of the mouse
    cursor is within an area represented by the circle that is drawn
    around the atom when the CIRCLES command is active. (Actually, the
    area searched by the routine is the box which circumscribes the
    circle). If you direct the program to search for an atom identity when
    the cursor is not within an area bounded by the circle, you will hear
    a two-tone sound from the speaker. Moreover, the size of this target
    area for atom matching grows and shrinks with the size of the atoms in
    the display window, as determined by the SIZE (S) command. If the
    structure is magnified by "zooming in", then the target area (as
    circumscribed by the resulting larger circle) is proportionately
    larger than it is when the structure is smaller.

       All of the usual prompts are also compatible with the mouse device.
    For example, with more than one file on the display screen, certain
    operations cause the "(P)revious, (L)ast, or (A)ll?" prompt, which
    asks if you want the operation to be performed on the previously added
    atoms, the last-added structure, or on all of the structures in
    memory. When the mouse is active, you may respond to this prompt by

    PCMODEL User's Manual                                          Page 30


    pressing button [1] for Previous, button [2] for Last, or button [3]
    for All. When it is feasible, information is provided on the com-
    munication line to inform you of the mouse choices. Most of the com-
    mands are identical in their operation either with or without the
    mouse. Exceptions to this are the DISTANCE and ANGLE commands, which
    will be covered in more detail later.

    PCMODEL User's Manual                                          Page 31


                          TUTORIAL EXERCISE NUMBER 6

       We will now go through some of the more useful operations using the
    mouse device. Follow each of the instructions as you work through the
    exercise.

    1. Start the program or perform a QUIT/RESTART to clear the screen.
       The mouse cursor, a green arrow on the EGA screen, should be
       present in the lower center of the display window.

    2. Move the mouse device about the table or pad surface, checking that
       the cursor arrow follows the motion of the mouse. If it does not,
       check the connections to the mouse. Refer to the mouse user's
       manual for further instructions on trouble shooting.

    3. Invoke the ADD FILE command as follows:

       a. Move the mouse cursor to point to the Add or A command at the
          left of the command line and click the left mouse button.

       b. The screen will clear and the catalog for the default data
          directory will appear on the screen, along with a small block
          mouse cursor.

       c. Move the mouse cursor so that it lies on top of the file name
          "EPINEPHR.DT3." Click the left mouse button. The program will
          retrieve the file and display the epinephrine molecule in the
          display window.

    4. Invoke the NUMBER command either by (1) placing the mouse cursor on
       the Num or N command and clicking the left button, or (2) moving
       the mouse cursor into the display window and clicking the left
       button.

       a. Place the mouse cursor tip on the blue nitrogen atom at the end
          of the side chain. Click the left mouse button. The program
          highlights the atom with a green box and prints the atom number,
          the identifier label, and the coordinates of the atom in the
          text area.

       b. Place the mouse cursor somewhere on the display screen where it
          is not in contact with the structure. Click the left button. The
          program produces a two-tone sound indicating that the cursor was
          not in close enough proximity to an atom to capture its iden-
          tity.

       c. Place the mouse cursor on any of the other atoms and click the
          left button to familiarize yourself with the behavior of the
          program.

       d. Click the right mouse button to return to the command state.

    5. Place the tip of the mouse cursor on the Dis or D and click the
       left button to call the DISTANCE command. This command works dif-
       ferently when called by the mouse instead of the keyboard, in that

    PCMODEL User's Manual                                          Page 32


       the program does not give you an option to print the distances on
       the printer.

       a. At the prompt for a base atom, place the tip of the cursor on
          atom 1, which is the benzene ring atom to which the side chain
          is connected. Click the left button.

       b. At the next prompt (for a target atom on button [1]), place the
          tip on the ring position para to atom 1. Click the left button.
          The program draws a dotted line between the atoms, identifies
          the atoms by their numbers and their identifier labels in the
          text area, and below that line it prints the distance between
          them (2.77 A).

       c. Place the cursor tip on the other ring carbon atom bearing a
          hydroxyl group, atom 3. Click the left button. The dotted line
          is moved to the new target atom and a new set of atoms and a new
          distance (2.48 A) appears in the text area.

       d. If you have a three button mouse, place the cursor tip on the
          nitrogen atom and click the center button. This selects a new
          base atom. If you have a two-button mouse, press the "2" key on
          the keyboard. This returns to the base atom selection prompt.
          Place the mouse on the nitrogen atom and click the left button.

       e. Place the cursor tip on the hydrogen atom of the beta-hydroxyl
          group on the side chain. Click the left button. The program
          identifies the distance with a dotted line, then prints the atom
          numbers and identifiers along with the distance between the
          atoms (3.29 A).

       f. Click the right button to return to the command state.

    6. Invoke the DYNAMIC MOTION command by pressing the F2 function key
       or clicking the Mot or M command letter with the right mouse but-
       ton. This command allows you to manipulate a structure by linking
       its rotation and translation to the movement of the mouse device.
       The program goes into expanded screen mode and prints a prompt
       under the expanded display window.

       a. Press and hold the right mouse button. While holding the button
          down, move the mouse device on its pad or surface. As you move
          the mouse back and forth the structure in the window moves along
          the X-axis. As you move the mouse along the axis of its attached
          cord ("up and down") the structure will move along the Y-axis,
          i.e., up and down on the screen. Return the structure to the
          center of the screen and release the mouse button.

       b. Press and hold the left mouse button. Move the mouse device left
          and right on its pad or surface. The structure will rotate about
          the Y-axis in step with the mouse. Move the mouse device forward
          and backward on its pad or surface. The structure will rotate
          about the X-axis in step with the mouse. Release the left mouse
          button.

    PCMODEL User's Manual                                          Page 33


       c. Press and hold both the left and the right button together. Move
          the mouse from side to side. The structure will rotate about the
          Z-axis, i.e., it will twist clockwise and counterclockwise in
          conjunction with the mouse. Release the buttons.

       d. If you have a 3-button mouse, you can translate the molecule in
          the Z-direction by holding down the center button and moving the
          mouse forward or backward. You will not see a change in the
          display, even though the Z-coordinates are changing. To invoke
          this command with a 2-button mouse, press the T key. In the
          DYNAMIC MOTION state this key assigns the Z-translate operation
          to the left-right button combination. Pressing the T key again
          reassigns the Z-rotate operation to the left-right chord.

       e. Continue to manipulate the structure until you are comfortable
          with the operations just discussed. When you are finished,
          orient the structure to roughly the same position it was in when
          you started, then press ENTER to return to the command state. If
          you have a 3-button mouse, you may return to the command state
          by pressing all 3 buttons simultaneously.

    7. We will now look at the JOIN and UNJOIN commands vs. the FRAGMENT
       command. We will use the DYNAMIC MOTION command to make these
       differences apparent.

       a. Hold down the Alt key and press the F key to invoke the FRAGMENT
          command. You may also invoke the FRAGMENT command by clicking on
          the Fil or F command with the right mouse button.

       b. Position the tip of the mouse cursor on atom 1, the point on the
          phenyl ring where the side chain is connected. Click the left
          mouse button.

       c. Position the tip of the cursor on atom 7, the atom of the side
          chain connected to the phenyl ring. Click the left mouse button.
          The program will separate the two parts of the structure by
          deleting the bond between them. These two parts are independent
          and can be manipulated separately.

       d. Press the F2 key to enter the DYNAMIC MOTION mode.

       e. Press the A key to select both (i.e., All) fragments for motion.

       f. Press and hold the right mouse button. Move the mouse about on
          its surface. Note that both fragments move together. Release the
          button.

       g. Press the P key to select the previous structure, i.e., to
          select the former part of the original structure. The former
          part is the part behind the bond that was broken, looking from
          the first to the second atom of the bond.

       h. Press and hold the right mouse button. Move the mouse device
          about on its surface. Note that the phenyl ring is the only part
          that moves. Release the button.

    PCMODEL User's Manual                                          Page 34


       i. Press the L key to select the latter structure or fragment.

       j. Press and hold the right mouse button again. Move the mouse
          device about on its surface. Note that the side chain is the
          only part that moves. Position the side chain next to the phenyl
          ring in roughly the same relative position it was in when the
          bond was broken. Release the button.

       k. Press either the ENTER key or all three buttons to return to the
          command state.

       l. Press the J key or click the left button on the Jn or J command
          to invoke the JOIN command.

       m. Place the cursor tip over atom 1 (the point on the phenyl ring
          where the side chain was originally connected). Click the left
          mouse button.

       n. Place the cursor tip over the atom of the side chain which was
          originally connected to the ring. Click the left mouse button.
          The program reconnects the two fragments.

       o. Either click the right mouse button or press the ENTER key to
          return to the command state.

       p. Hold down the Alt key and press the J key to invoke the UNJOIN
          command. Alternatively, click the Jn or J command with the right
          mouse button.

       q. Place the tip of the mouse cursor on atom 1 again (the ring atom
          to which the side chain is attached). Click the left button.

       r. Place the tip of the cursor on atom 7 (the connection point on
          the side chain). Click the left mouse button. The bond between
          the two parts of the molecule becomes broken. Press the right
          button or the ENTER key to return to the command state.

       s. Either press the F2 function key or click on the Mot or M com-
          mand with the right mouse button to enter the DYNAMIC MOTION
          state. Repeat steps e. through j. Note that the two parts are
          not independent as they were before. Press ENTER to return to
          the command state.

       t. Repeat steps l. through o. to reconnect the two pieces of the
          molecule.

    8. We will now use the program's editing capabilities to restore the
       geometry of the modified epinephrine. To do this we likely will
       need to adjust both the C1-C7 bond distance and the C2-C1-C7 bond
       angle. In doing so we need to make sure that both the phenyl ring
       and atom 7 are in the XY plane so they will end up planar when
       connected. Since they were not all in the XY plane when we
       separated them into fragments, we will first regenerate the frag-
       ments, then use the ORIENT command to place them in the XY plane.
       We will then edit the bond length and bond angle to produce a

    PCMODEL User's Manual                                          Page 35


       realistic geometry.

       a. Repeat steps 7a.-c. to produce two fragments again.

       b. Either press the O key or click on the Ori or O command. This
          invokes the ORIENT command.

       c. Click the left mouse button to select the previous fragment,
          i.e., the phenyl ring.

       d. Place the cursor tip on atom 1 (the point where the disconnec-
          tion was made) and click the left mouse button to select it as
          the centered atom.

       e. Place the cursor tip on the ring carbon para to atom 1 (the atom
          with the para-hydroxyl substituent. Click the left mouse button
          to select it as the X-axis atom.

       f. Place the cursor tip on the meta ring carbon (containing the
          other hydroxyl substituent). Click the left mouse button. The
          program will orient the phenyl ring to lie in the XY plane, then
          return to the command state.

       g. Click again on the Ori or O command to again invoke the ORIENT
          command.

       h. If you have a three-button mouse, click the center button to
          select the latter fragment for orientation. If you have a two-
          button mouse, press the "2" key on the keyboard to accomplish
          the same step.

       i. If you have a three-button mouse, click the center button to
          select the Centering Only option. If you have a two-button
          mouse, you can accomplish the same thing by pressing either the
          2 key or the C key.

       j. Place the cursor tip on atom 7 and click the left mouse button.
          The program will move the latter fragment so that atom 7 is at
          the center of the screen (directly on top of atom 1), then it
          will return to the command state. Both the phenyl ring and atom
          7 are now in the XY plane.

       k. Either click on the Jn or J command or press the J key to invoke
          the JOIN command.

       l. Type the number 1 on the keyboard followed by ENTER. Type the
          number 7 on the keyboard followed by ENTER. Press the ENTER key
          to return to the command state.

       m. Either press the E key or click the left mouse button on the Ed
          or E command to enter the EDIT environment.

       n. Click the left mouse button to select the Edit option. Click the
          right button to select the Bond Length option.

    PCMODEL User's Manual                                          Page 36


       o. Since the atoms of interest are on top of one another, use the
          keyboard to enter the atom numbers. Type 1 followed by ENTER,
          then 7 followed by ENTER. The program will report that the
          current bond length is 0.00 and ask for a new bond length. Type
          1.45 followed by ENTER. The bond length becomes 1.45 A. Press
          ENTER to return to the command state.

       p. Invoke the EDIT command again as in step m. Select the Edit
          option again as in step n. Click the middle button to select the
          Bond Angle option. If you have no center button press the 2 key.

       q. Place the cursor tip on one of the ring carbons ortho to the
          side chain connection. Click the left mouse button. Place the
          cursor tip on atom 1 (the ring carbon to which the side chain is
          connected). Click the left mouse button. Place the cursor tip on
          atom 7 (the side chain atom connected to the ring) and click the
          left mouse button again.

       r. The program will print the angle value and prompt you for a new
          one. Type 120 followed by ENTER. The program will redraw the
          structure with the correct angle. Press ENTER to return to the
          command state.

    9. Terminate the session by pressing the Q key or clicking on the Qt
       or Q command. Answer Yes to the "OK to quit?" prompt by clicking
       the left mouse button or pressing the Y key. Then select either the
       End option to return to DOS or the Restart option to clear the
       screen.



                          TUTORIAL EXERCISE NUMBER 7

       Using a number of files on the disk we can now recreate the active
    site of the enzyme Chymotrypsin, a well-characterized proteolytic
    enzyme (8,9). Rather than place all of the atoms of a macromolecule
    into one file at one time, it is often more convenient and accurate to
    assemble the larger model from component parts. This is the strategy
    we will follow here. We will construct two parts of the active site,
    then fit a substrate, N-formyltryptophan, to the partial active site.
    This strategy gives us maximum responsiveness, since we are manipulat-
    ing only those residues that are actively interacting. Once we get a
    reasonable fit, we will then add the remaining segments of the active
    site.

    1. There are five fragments of the chymotrypsin active site in the
       data directory on the disk. We will now combine two of these frag-
       ments to produce the partial active site.

       a. Press the A key or click on the Add or A command to invoke the
          ADD FILE command and to display the default data directory.

       b. Move the mouse cursor to the file CTPN189.DT3 and click the left
          button. A comment line describing the contents of the file will
          be displayed at the bottom of the screen, along with a prompt to

    PCMODEL User's Manual                                          Page 37


          select it or reject it. Click the left mouse button again to
          select the file. The program will add the CTPN189.DT3 file to
          the display window and return to the command state.

       c. If the CIRCLES are present on the screen, press the F3 key to
          toggle them off.

       d. Invoke the ADD FILE command again as in step 1a. Select the file
          CTPN213.DT3 by the procedure outlined in step 1b. The program
          will add the file to the display window and return to the com-
          mand state.

    3. Invoke the ADD FILE command again as in step 1a. Select the file
       FTRY.DT3 as in step 1b. The model substrate N-formyltryptophan will
       be added to the active site residue in the display window.

    4. Invoke the ALTERNATE DISPLAY command either by pressing the Alt-D
       key combination or clicking the Dis or D command with the right
       mouse button. If you are in EGA mode the depth cueing will be
       enhanced. If you are in CGA mode the color depth zones will be shut
       off.

    5. Press the K key or click on the Kmp or K command to invoke the
       COMPARE command. The substrate is now highlighted against the
       enzyme residue. You can see from the depth indicators at the left
       that the substrate is significantly closer to you than the enzyme
       residue.

    6. Invoke the FIT STRUCTURES command by pressing the F7 function key.
       Use the keyboard to enter specific atom numbers, rather than the
       mouse device.

       a. Type the number 174 followed by ENTER when you are prompted for
          base atom 1. Type the number 15 followed by ENTER when you are
          prompted for target atom 1. This distance is from the indole
          nucleus to one side of the hydrophobic cleft on the enzyme
          (Cysteine 191).

       b. Type the number 174 followed by ENTER in answer to the prompt
          for base atom 2. Type the number 87 followed by ENTER at the
          prompt for target atom 2. This represents the distance from the
          indole nucleus to the other side of the hydrophobic cleft
          (Serine 218).

       c. Type the number 162 followed by ENTER at the prompt for base
          atom 3. Type the number 44 followed by ENTER for target atom 3.
          This measure is the distance from the formyl carbonyl to the
          Serine 195 hydroxyl.

       d. EGA mode only: type the number 173 followed by ENTER when the
          prompt for base atom 4 appears. Type the number 158 followed by
          ENTER for target atom 4. This is a measure of the distance from
          the edge of the indole ring to the bottom of the enzyme
          hydrophobic cleft (Tyrosine 228).

    PCMODEL User's Manual                                          Page 38


       e. Press ENTER to return to the command state. The four distances
          (3 in CGA mode) are labeled in four colors (3 in CGA) and
          printed in the text area.

    7. We will now fit the substrate molecule into the active site using
       the DYNAMIC MOTION command.

       a. Either press the F2 function key or click the Mot or M command
          with the right mouse button to enter the DYNAMIC MOTION mode.

       b. Press the T key. Press the L key to select the last structure
          (the substrate) for translation.

       c. Depress both the left and right mouse buttons and move the mouse
          slightly away from you. This moves the substrate in the +Z
          direction. Release the right button. Wait for the program to
          recompute the new positions and draw them in the window. Note
          the distances, all of which should have decreased. Continue this
          process until both distance C and distance D (if present) are in
          the range of 4 Angstroms.

       d. Depress the right mouse button and slowly move the mouse to
          bring the substrate molecule into the cleft, then release the
          button. As you do so, the distances A and B will become nearly
          equal in the range of 5-6 Angstroms. Repeat the process as
          needed to bring distances A and B into the range of 5-6
          Angstroms.

       e. Fit the molecule into the cleft by alternately rotating and
          translating it as needed.

       f. Press ENTER to return to the command state.

    8. File the substrate structure by pressing the F key or clicking on
       the Fil or F command. Answer the "Previous, Last, or All" prompt by
       pressing the L key or clicking the middle button. Answer Y to the
       "File Exists. Replace?" prompt. The program will display the com-
       ment line associated with the FTRY.DT3 file, then prompt you for
       any changes. Press the ENTER key or click the left mouse button to
       leave the existing comment line intact. The optimally positioned N-
       formyltryptophan is saved to disk.

    9. Remove the substrate from the display by either pressing the U key
       or clicking on the Un or U command (the UNADD command).

    10. Add the remainder of the active site residues using the following
        steps.

        a. Invoke the ADD FILE command. The program will display the
           default data directory. Position the mouse cursor on the
           CTPN40.DT3 file and click the left mouse button.

        b. Invoke the ADD FILE command again. Position the mouse cursor on
           the CTPN56.DT3 file. Click the mouse button to select the file.

    PCMODEL User's Manual                                          Page 39


        c. Invoke the ADD FILE command once more, position the cursor on
           the CTPN99.DT3 file, and select it with the left mouse button
           as before.

    11. Press the F key or click on the Fil or F command to invoke the
        FILE command.

        a. Click the right mouse button or press the A key to select the
           ALL option.

        b. The last-added file name (CTPN99) will appear after the prompt
           for the file name. Turn this into the file name "CTPN" by
           pressing the backspace key twice. The program will display the
           comment associated with the first file you added (the
           CTPN189.DT3 file) and ask you if you want to modify it. Press
           the Esc key to blank the line. Then type in a comment describ-
           ing the file, such as, "Chymotrypsin active site assembled from
           the 5 data files supplied." Press the ENTER key or click the
           left mouse button. You have now filed the assembled active site
           of chymotrypsin in your data directory.

    12. Invoke the ADD FILE command again as in step 1a. Select the file
        FTRY.DT3. The recently positioned model substrate N-
        formyltryptophan will be added again to the active site residue in
        the display window.

    13. Note: If you do not have a printer connected to your computer,
        skip this step and go to step 14. Press the L key or click on the
        Lst or L command to invoke the LIST command, then press the C key
        or click the left button to list the coordinates on the printer.
        This operation will print a complete list of all of the coor-
        dinates and bonds of the enzyme active site, along with the iden-
        tifier labels.

    14. Enter the EXPANDED SCREEN mode by pressing the Alt-E key combina-
        tion or clicking on the Ed or E command with the right mouse
        button. The mechanistic machinery of the enzyme can be seen in
        this view, as discussed by Blow (9).

        a. If you are in CGA mode and have a graphics printer connected,
           press the Shift-PrtSc key combination to produce a screen dump
           on the printer. If you are in EGA mode and have access to a
           laser printer, press the P key. The program will produce a
           file, PCM3DUMP.1 in the current directory. This file can be
           copied to the laser printer for printing.

        b. Press the ENTER key to return to the command state.

    15. Leave this problem by pressing the Q key or clicking on the Qt or
        Q command to invoke the QUIT command; press either the E key or
        the R key or the appropriate mouse button, depending on whether
        you want to END the session or RESTART the program for another
        exercise.

    PCMODEL User's Manual                                          Page 40


    F. DATA FILE CONVENTIONS

       There are several points of information that must be considered
    while naming data files and saving them on disk.

    1. In the MS-DOS system, a file is named with a string of eight
       characters or less, followed by a period (.) and an extension of up
       to three characters. Thus, a valid filename could be

                MYFILE1A.TXT

       The filename need not take up all eight allowed spaces, but it must
       begin with a letter or one of a small number of other special
       characters. Similarly, the extension need not take up all three
       allowed spaces. Certain special characters are also allowed in the
       extension. If possible, use only letters and numbers for filenames.
       For further details on naming of files consult the DOS reference
       manual.

    2. The PCMODEL program utilizes the extension part of the filename to
       denote the type of file it is. For example, structural data are
       saved with the extension ".DT3". The program automatically appends
       the proper extension to the filename when it needs to. When you
       specify a filename for the program, you do not need to add the .DT3
       extension to the filename. PCMODEL will do it for you.

    3. A drive designation letter may be associated with a filename. This
       takes the form of a letter and a colon (:) placed in front of the
       filename. For example, if the file in paragraph 1 were on the disk
       in the B drive, the full designation of the filename would be

                B:MYFILE1A.TXT

       If no drive letter is present in the filename, the system assumes
       that the file is on the currently active drive (the current or
       logged drive in DOS terminology). You are not restricted to reading
       or writing a file only on the disk in the current drive. You may
       specify any drive letter that is valid in your system simply by
       placing it as a prefix to the filename. The operating system will
       then access that drive instead of the current or default drive. For
       example, if drive A is the current drive, a file "MYFILE1A.TXT" on
       the disk in drive A could be accessed either by its name or by its
       name with the drive letter prefix, "A:MYFILE1A.TXT." If drive B is
       the current drive however, the file name without the "A:" drive
       prefix will not permit DOS to find it.

       If you wish to name a data set as "FILE1.DT3" and drive A is the
       current drive, you could specify the file name as "FILE1.DT3" on
       the disk in the A drive by typing

                FILE1

       then pressing the ENTER key in response to the "Enter filename:"
       prompt. However, you could file the structure on a diskette in
       drive B by placing the prefix "B:" in front of the filename by

    PCMODEL User's Manual                                          Page 41


       typing

                B:FILE1

       then pressing the ENTER key. It would then be stored as "FILE1.DT3"
       on the B disk drive. When you begin to create large numbers of
       files, you may wish to maintain a separate diskette or hard disk
       directory for those files.

       The PCMODEL program does not restrict you to writing a file only
       once. The structure remains in memory and its coordinate data may
       be written to multiple disks by repeating the FILE command.
       Specifying a drive designation identical to the default drive does
       no harm to the program or data files.

    4. A path name also may be associated with the file name and drive
       designation letter. The path name tells the operating system the
       name of the subdirectory in which the file resides. For example, if
       you installed PCMODEL on your system's hard disk, you likely did
       not place it in the disk's root directory, but in one of the
       "branches" of the root directory called a subdirectory, called
       "PCMODEL" in this case. Since the operating system nromally cannot
       detect the contents of these subdirectories from the root direc-
       tory, you must include the names of the subdirectories on the
       "path" from the root directory to the file of interest. A file
       named "FILE1" in this subdirectory would have a complete name of

                C:\PCMODEL\FILE1

       where the center part of the string, separated by the backslashes,
       is the path name. Please consult your DOS reference manual for a
       greater discussion of subdirectories and path names.

    5. The standard PCMODEL Version 3.0 file format maintains the coor-
       dinates in Angstrom units. Each data file is composed of four types
       of information. The first line contains a comment in free text
       format, describing the contents of the file. The first character of
       the first line is an asterisk (*), which signals to the program
       that it is a comment line. If the program does not find an asterisk
       in column 1, it assumes that there is no comment line associated
       with the file. The second line (which is the first line if no
       comment is present), is composed of two integer numbers. The first
       denotes the number of atoms in the file and the second denotes the
       number of bond connections present in the file.

       The next part of the file contains a number of lines of coordinate
       data, one line for each atom. The atomic coordinates are in car-
       tesian format, with the first representing the X value, the second
       the Y value, and the third the Z value. Following these three
       numbers is an identifier string of up to eight alphanumeric charac-
       ters. This string contains the atom type (denoted by the first
       character in the string), and other useful identification informa-
       tion. The count of these atomic coordinates lines corresponds to
       the first number on line 2 of the file.

    PCMODEL User's Manual                                          Page 42


       The third part of the file contains a series of number pairs, each
       pair representing a bond between two atoms. The number of lines of
       atom pairs corresponds to the second number on line 2. The numbers
       making up each pair are the atom numbers assigned by the program in
       the order they were read from the preceding section.



    G. ENTERING DATA FROM THE KEYBOARD

       The most obvious way to generate new structures is by typing the
    corresponding coordinate data in by way of the keyboard, although
    there are other more convenient ways to generate it (see Appendix B).
    Coordinate data to be displayed using PCMODEL must be in the program's
    memory before they can be used, and since much of the available data
    are present only in printed form, we will take a few minutes to ac-
    quaint you with the keyboard data entry operation. At the same time
    you will gain some insight into the program's data format and command
    operation. As you have seen, once the coordinate data are on a disk,
    they can be loaded into the program quickly with the ADD FILE command.
    For the moment, the data we want is not on a disk and it will have to
    be generated at the keyboard.



                          TUTORIAL EXERCISE NUMBER 8

       We will now create the structure of cyclohexane from its cartesian
    coordinates by entering the coordinates from the keyboard. For
    simplicity, we have eliminated the hydrogen atoms from the molecule,
    but we will add them later. The program should now be in the command
    state, i.e., the state it is in immediately after it is started up.
    The display window should be empty and the command list should be
    immediately under the display window. Carry out the following steps:

    1. Press the G key to invoke the GET COORDINATES command.

    2. The program clears the screen and asks if the data are in X-ray
       (unit cell) format. Press the N key, since these data are in stand-
       ard cartesian coordinate format.

    3. The program again clears the screen and prints the prompt

                Number of atoms in structure:

       Specify the number of atoms to be entered by typing the number 6,
       then press the ENTER key.

    4. The program clears the screen and gives you the message

                Number of bonds in structure:

       appears. Respond in this case by again typing the number 6, fol-
       lowed by ENTER. This number represents the number of atomic connec-
       tions in the cyclohexane molecule.

    PCMODEL User's Manual                                          Page 43


    5. After clearing the screen, the program prompts you for the car-
       tesian (X, Y, & Z) coordinates and an identifier label for each
       atom by printing

                Enter Coordinates
                No.      X      Y      Z      ID

       PCMODEL now is looking for the coordinates of exactly 6 atoms - the
       number you specified earlier. It is looking for an X, a Y, and a Z
       value for each atom and an optional (but highly recommended) iden-
       tifier label. Each value is entered individually. After you enter
       each value, press the ENTER key. The cursor will then move to the
       next field.

       The identifier label is a string of up to eight characters that
       identifies the atom with which it is associated. You may place
       almost any character or characters in this field, but the first
       character should be the element abbreviation for the atom, e.g., C
       for carbon, H for hydrogen, etc. The program uses the first letter
       of the identifier string to assign the atomic radius and the dis-
       play color for the atom.

       During coordinate data entry PCMODEL automatically activates the
       keypad input by activating the Num Lock key from within the
       program. With the numeric keypad activated, you do not often need
       to look at the monitor screen during input. Moreover, as you are
       typing in the coordinate data the program will sound a tone at the
       end of every row, i.e., after every identifier label you type. This
       feature is intended to keep you informed of where you are in the
       input process. Using this feature you will not have to watch the
       input list, the screen, and the keyboard at the same time.

       Now type in the numbers in Table 1. Notice that the numbers are all
       positive. This is nothing to be concerned about. As you will learn
       later, the program considers the screen to be a window on the side
       of a cube, and the center of the cube (at the center of the screen)
       is the point X=12, Y=6, Z=6 rather than (0,0,0). Thus atom number 1
       is at the center of the screen in the present model.

       Due to the nature of the input process in this part of the program,
       you can only make corrections to the number you are currently
       typing. To correct a number you are currently typing, backspace
       over the mistake and retype it. Once you press the ENTER key, the
       number you entered cannot be corrected until later. If you find a
       number with an error in it after you have pressed the ENTER key,
       don't panic, just make a note of it. You can correct it at a later
       point in the program, using the EDIT command.

    6. The bond connection table is now entered. PCMODEL prints the mes-
       sage

                Enter Connectivity Table
                No.    K    L

       and waits for you to enter the atom numbers of each bonded pair of

    PCMODEL User's Manual                                          Page 44


       Table 1. Cartesian coordinates of cyclohexane.

                 X        Y        Z     ID

               12.00     6.00     6.00   C1
               12.56     5.22     7.18   C2
               14.02     5.63     7.43   C3
               14.85     5.31     6.18   C4
               14.29     6.10     4.98   C5
               12.82     5.69     4.74   C6

       atoms. The atom number is the number the program assigned to the
       atom as you entered it in the previous coordinate data entry step.
       The program behaves here exactly as it did during coordinate entry
       - after each number entry, press the ENTER key. Again, if you make
       a mistake, you can correct it before you press the ENTER key, but
       not afterward. Also as above, you may correct any errors discovered
       after the fact using the EDIT command. Once more, the program will
       BEEP after the last entry on a line, in this case after the second
       entry. Now type in the data in Table 2.

       Table 2. Connection Table for Cyclohexane.

               K      L

               1      2
               2      3
               3      4
               4      5
               5      6
               1      6

       Please note: if you make a mistake in entering either a coordinate
       value or a connection value, the structure that the program con-
       structs on the screen may be somewhat bizarre, unless the error is
       a very small one. For example, if atom 6 is paired with atom 4
       instead of atom 1 in the connectivity table, a different, strange
       looking molecule will be formed. This is because the coordinates
       are correct but the connection is not. When you correct the error
       using the EDIT command, the structure will be restored to its
       intended appearance.

    7. The last step in the data entry process is to file the data on the
       disk. The program prompts you for a filename under which the data
       will be filed by the prompt:

                Enter filename:

       For this example, type

                CYCLOHEX

       then press the ENTER key. The program will file the cyclohexane
       coordinates on the disk you specified in the configuration file
       under the filename "CYCLOHEX.DT3," then draw the graphic image on

    PCMODEL User's Manual                                          Page 45


       the screen and return to the command state. At this point you will
       see the cyclohexane molecule in the display window.

    PCMODEL User's Manual                                          Page 46


                          COMMAND REFERENCE SECTION






                     [Present Only in Registered Version]

    PCMODEL User's Manual                                          Page 47


                             REFERENCES AND NOTES


    1. F. C. Bernstein, Protein Data Bank, Chemistry Department, Brook-
       haven National Laboratory, Upton, NY 11973.

    2. S. R. Wilson and J. C. Huffman, "Cambridge Data File in Organic
       Chemistry. Applications to Transition-state Structure, Conforma-
       tional Analysis, and Structure-activity Studies," J. Org. Chem. 45,
       560 (1980).

    3. C. L. Strong, "The Amateur Scientist: How an Amateur Can Construct
       a Model of an Enzyme Molecule at Modest Cost," Scientific American,
       234, 124 (1976).

    4. F. H. Clarke, "New Skeletal-Space Filling Models: A Model of an
       Enzyme Active Site," J. Chem. Educ. 54, 230-235 (1977).

    5. B. W. Matthews, L. H. Weaver, and W. R. Kester, "The Conformation
       of Thermolysin", J. Biol. Chem. 249, 8030 (1974).

    6. W. R. Kester and B. W. Matthews, "Crystallographic Study of the
       Binding of Dipeptide Inhibitors to Thermolysin: Implications for
       the Mechanism of Catalysis," Biochemistry 16, 2506 (1977).

    7. A. Aggarwal, S. A. Islam, R. Kuroda, M. R. Sanderson, S. Neidle,
       and H. M. Berman, Acta Cryst. B39, 98 (1983).

    8. D. M. Blow, "Structure and Mechanism of Chymotrypsin," Accts. of
       Chemical Research 9, 145 (1976); D. M. Blow, J. J. Birktoft, and B.
       S. Hartley, Nature 221, 337 (1969).

    9. T. A. Steitz, R. Henderson, and D. M. Blow, "Crystallographic
       Studies of Substituents and Inhibitors Bound to the Active Site of
       Alpha Chymotrypsin," J. Molec. Biol. 46, 337 (1969).

    PCMODEL User's Manual                                          Page 48


                       APPENDIX A - MESSAGES & PROMPTS

       Built into the PCMODEL program are several checks for data,
    response, and hardware integrity. If the program encounters a user
    response that is inappropriate, a hardware condition that is incom-
    patible with operation, or data that is defective, it halts execution
    and presents you with one or more brief error messages describing the
    problem. Depending on the severity of the problem, the program will
    either wait for you to correct the problem or return to the command
    state. The following compilation is an alphabetical listing of the
    possible error messages you may see during operation of the program,
    along with discussions of their meanings and steps to take to correct
    the associated error conditions.

    ARRAYS FULL. REDIMENSION MEMORY TO ###. This error occurs when you invoke
    any of the automatic commands that increase the use of the data arrays
    and the arrays have insufficient room to accomodate the increase.

    ATOM OFF SCREEN. This message occurs during the NUMBER (N) and ANGLE (V)
    commands, when the requested atom is not within the viewing window. It
    has no effect on the accuracy of the calculated values, but simply
    appears as a point of information.

    BAD FILENAME: FILENAME. This error is generated if you try to name a data
    file with a name that is inconsistent with the conventions used by the
    computer operating system and PCMODEL. Review the section "Data File
    Conventions" on page 48 for more information. The program will accept
    letters and numbers of from 1 to 8 characters in length as a filename.
    The program automatically appends the filename extension ".DT3" to the
    name of each file it creates. The program returns to the command state
    following this error.

    CAN'T ADD FILE. MAXIMUM OF 20 REACHED. While PCMODEL can handle a very
    large number of atoms and bonds, they must be contained in no more
    than 20 data files. This message appears when you try to ADD a file to
    memory after you have already added 20 separate data files with the
    ADD command.

    CONFIGC.PCM FILE MISSING. DEFAULT USED. When PCMODEL begins execution in
    the CGA graphics mode, it reads several configuration parameters from
    a disk file named CONFIGC.PCM. If this file is not present on the
    current drive, this error appears. Rather than terminating, PCMODEL
    warns you of this condition and assigns a set of default parameters to
    the values normally read from CONFIGC.PCM. To eliminate this error,
    make sure that the CONFIGC.PCM file is present on the current drive.
    Execution continues after this error, although the default configura-
    tion parameters may be different than you usually use.

    CONFIGE.PCM FILE MISSING. DEFAULT USED. When PCMODEL begins execution in
    the EGA (high resolution) mode, several configuration parameters are
    read from a disk file named CONFIGE.PCM. If this file is not present
    on the current drive and directory, this error appears. Rather than
    terminating, PCMODEL warns you of this condition and assigns a set of
    default parameters to the values normally read from CONFIGE.PCM. To
    eliminate this error, make sure that the CONFIGE.PCM file is present

    PCMODEL User's Manual                                          Page 49


    on the current drive. Execution continues after this error, although
    the configuration parameters may be different than you usually use.

    CONFIG.TXT MISSING. When you press the F9 key in the command state,
    PCMODEL begins a routine to reset the configuration parameters con-
    tained in the CONFIG.PCM file. To do this it must access another file,
    either CONFIGC.TXT or CONFIGE.TXT, which also must be present on the
    current drive and directory. If it is not present, this error is
    generated. Make sure that the current drive contains copies of the
    files CONFIGC.TXT and CONFIGE.TXT. The program returns to the command
    state after this error occurs.

    DATA FILE IS NOT PRESENT. This message appears when you attempt to ADD a
    file that doesn't exist on the indicated drive and directory. Check to
    be sure that you used the correct drive designator when specifying the
    filename. The program returns to the command state after this error
    occurs.

    DISK I/O ERROR. CHECK DISK. This message is generated when the operating
    system senses that the disk is bad, that it is not formatted, or that
    it is formatted incorrectly. To find the source of the error, first
    check to make sure that the diskette in the drive has been formatted.
    If the diskette in question has functioned well previously, then you
    should consider the possibility that the diskette is faulty or im-
    properly installed. Reinsert the existing diskette in the drive. If
    this does not solve the problem, replace the diskette with the backup
    copy. Be sure to create another backup copy of the disk from your
    existing backup copy before using it. If this message appears when
    writing to your hard disk, you have our condolences - it could mean
    that the hard disk is failing.

    DISK IS WRITE PROTECTED. REMOVE THE TAB. A write protection tab has been
    placed on the diskette to which you have attempted to write a file
    with the FILE command. Also, you may have tried to update the Con-
    figuration file on the default drive and that diskette has a write
    protect tab in place. To correct the error, remove the tab from the
    diskette. On rare occasions, a hardware failure can generate this
    error. The program returns to the command state after this error.

    DISK MEDIA ERROR. RETRY OR REPLACE DISK. This error occurs for the same
    reasons the "Disk I\O error" does - the operating system cannot read
    the disk for some reason. Follow the advice given under the "Disk I/O
    error."

    DRIVE OR PRINTER DOESN'T EXIST. If you issue a command that prints
    material on the printer, but you don't have a printer and the printer
    adapter card does not exist, you will get this message. You cannot
    correct it, except by installing the device. If you get this message
    even though you have the device installed, check the installation,
    since the computer is not recognizing its presence. Control is
    returned to the command state after this error.

    DUPLICATE ATOM SPECIFIED. REENTER. You have entered the same atom number
    twice during input for an angle calculation. PCMODEL cannot calculate
    a simple or torsion angle unless three or four unique atoms, respec-

    PCMODEL User's Manual                                          Page 50


    tively, are specified. The program returns to the atom input line of
    the ANGLE (V) command.

    EMPTY DISPLAY. USE GET COMMAND. You have invoked the EDIT command with no
    structure in memory, i.e., the coordinate and bond arrays are empty.
    Use the ADD FILE command to place a data file in memory before invok-
    ing the EDIT command. The program remains in the command state after
    this message.

    END OF FILE REACHED. CHECK FILE MAKEUP. This error is generated when
    PCMODEL is reading a data file and reaches the end of the file before
    all of the data it is expecting is assimilated. It may mean that the
    data file is damaged in some way, or more likely, that the data file
    is not in PCMODEL format. The program reads in four values from each
    coordinate data line of the data file: the X, Y, and Z coordinates and
    the atom identifier label. If no identifier label is present, a ques-
    tion mark (?) is present as the fourth variable on each line. If the
    data file is an external one (i.e., not generated by PCMODEL or one of
    its utility programs), it may not have these question marks present.
    This condition will generate the indicated error. To correct it,
    modify the data file with a text editor, placing a space and a ques-
    tion mark at the end of every line of coordinates. Do not add anything
    to the bond connectivity lines.

    The other possibility is that the data file is damaged in some way.
    Check this by examining the data file structure with a text editor.
    The first line of the file will contain either a comment line which
    begins with an asterisk or two numbers, the number of atoms (N) and
    the number of bonds (M). If the comment line is present, the second
    line then contains the two numbers. Following this line there should
    be N lines of coordinate data and M lines of bond connection data. If
    there is not, then the file has been damaged. Reconstruct the file
    from your backup copy.

    FILE ALREADY EXISTS. REPLACE? (Y OR N). This cautionary message appears
    when you invoke the FILE command and the named file already exists on
    the specified directory. It warns you that an existing file is about
    to be overwritten.

    FILE MODIFIED. QUIT ANYWAY? (Y OR N). You have tried to QUIT the program
    after you have made a change to the current structure. The commands
    that trigger this message include EDIT, INVERT, ORIENT, ROTATE, TRANS-
    LATE, and X-RAY TRANSFORM. If you wish to save the data as a new or
    replacement data file, press the N key, then use the FILE command to
    save the data. If you wish to quit without saving the changes you have
    made, press the Y key. The normal QUIT sequence will then continue.

    FILE PRESENT. USE QUIT/RESTART FIRST. You have tried to invoke the GET
    COORDINATES (G) command while another file is already in memory. The
    GET COORDINATES command will only function when no other structures
    are present in the display. To correct the situation, restart the
    program with the QUIT command followed by the Restart option, or use
    the RESET (Alt-Q) command.

    FILENAME IS TOO LONG. REENTER IT. You have typed in a filename that is

    PCMODEL User's Manual                                          Page 51


    greater than eight characters in length. The maximum length for a
    filename in the DOS operating system is eight characters. Control
    remains in the FILE environment, and you are prompted for another
    filename.

    HARDWARE ERROR (CHECK THE PRINTER). This error is caused when the program
    finds a device fault, a hardware error sensed by one of the interface
    cards, such as the printer card inside the computer. While the error
    could be due to any of several devices, the most likely situation in
    which you will encounter this error is when you are performing a
    command that accesses the printer, and if the printer is detached or
    defective in some way. The solution is to check the printer to be sure
    it is functional. If the error occurs at some other place in the
    program, it is likely that one of your hardware components needs
    service or replacement. The program returns to the command state after
    this error is generated.

    ILLEGAL FUNCTION CALL, LOC ###. The program has come upon an internal
    error that was not anticipated. An error such as this one indicates a
    bug in the program that has not been corrected. Please report the
    circumstances of the error to the author, along with the location
    number reported by the program.

    INVALID ATOM TYPE. REENTER. While adding hydrogen atoms in the semi-
    automatic mode, you have specified an atom type that is not carbon,
    nitrogen, oxygen, or sulfur. No other atom types can be processed
    semi-automatically. Control remains in the EDIT environment, and you
    are prompted for a valid atom type.

    INVALID CHARACTER IN FILENAME. REENTER. You have included an invalid
    character in the filename while executing the FILE command. Identify
    the character, then remove it from the filename. Control remains in
    the FILE command and you are again prompted for a valid filename.

    INVALID CHARACTER IN NUMBER FIELD. During an input operation from either
    the keyboard or from a file, the program encountered a letter or other
    character when it was expecting a number. This error should occur
    infrequently, if at all, and may be corrected by reentering the number
    correctly. The program returns to the command state when this error is
    encountered.

    INVALID VALUE. This response is the general one that occurs when an
    incorrect data value is entered in response to a prompt from PCMODEL.
    The invalid value may be a negative number or zero, or it may be a
    number greater than the range of numbers acceptable to the program.
    For example, the program cannot operate on atom numbers higher than
    the total presently in memory. This message may also result from
    inclusion of a nonnumeric (e.g., alphabetic) character when the
    program is expecting a number. Also, you may have entered a number
    that is already in use, e.g., an atom number for an angle that has
    already been specified for that angle. In each case where this error
    occurs, the program sounds a tone, then prompts you again for a valid
    response.

    OUT OF MEMORY. ARRAYS RESET TO 1000. This message appears if you set the

    PCMODEL User's Manual                                          Page 52


    coordinate data arrays at a level too large for the available memory
    in your computer. It may also occur if your computer has several
    utility programs (e.g., print spoolers) loaded along with PCMODEL,
    such that you are operating very close to the limit of the memory
    needed by PCMODEL. You may need to acquire more memory or eliminate
    one or more of the co-resident programs.

    OUT OF STRING SPACE. You have added so many atoms with their identifier
    strings that the program has no more room to store the strings. This
    error should be seen rarely if ever, since the coordinate data iden-
    tifier strings are handled dynamically.

    OVERFLOW. USE SMALLER NUMBER. A program integer variable has been set to
    a value greater than 32,768. The most likely occurrence of this mes-
    sage is in the case of an unreasonably large size factor, put in with
    the SIZE command. While the SIZE command has a built in check for size
    factors greater than 10, it is possible to put in multiple SIZE com-
    mands that will eventually cause this error. The program returns to
    the command state after it recovers from this error. If the error
    condition is due to an unreasonably large cumulative size factor, it
    may be avoided by using smaller SIZE factors.

    PATH NOT FOUND. CHECK THE PATH SPECIFICATION. You have specified a path
    name which does not exist on the drive indicated. Make sure you have
    spelled the path correctly and that the disk drive is the one you
    intended to access.

    PATH/FILE ACCESS ERROR. CHECK THE PATH SPECIFICATION. See the "Path not
    found" error for a discussion of this error.

    PRINTER IS OUT OF PAPER OR TURNED OFF. If the printer is not ready,
    either by being out of paper or in a disabled state (such as not being
    on), this error will appear. Correct the error by loading the printer
    with paper or make sure it is turned on, then reissue the command. The
    program returns to the command state after this error.

    PRINTER TIMEOUT. CHECK THE PRINTER. This error occurs when the printer is
    not on line. Place the printer on line, then reinitiate the command.

    REACHED ARRAY LIMIT. USE ALT-L. You have tried to read a data file that
    contains too many coordinates. This error only appears if a structure
    already exists in memory. If the memory arrays are blank, the program
    will automatically rescale itself to accomodate the larger coordinate
    requirement. To rectify the situation, use the QUIT and RESET command
    sequence, then increase the array limits with the Alt-L command.

    THE DISK DRIVE IS NOT READY. This message occurs if either the disk drive
    door is open or there is no diskette in the drive. To correct the
    error, close the door or make sure the desired disk is in the drive.
    The program returns to the command state after this message is dis-
    played.

    THE DISK IS FULL. PLEASE REPLACE IT. If nearly all of the space on a
    diskette is in use and you attempt to save another file on it that is
    larger than the space remaining, the program will generate this error.

    PCMODEL User's Manual                                          Page 53


    The program returns to the command state, at which point you should
    replace the diskette with one containing enough space to hold the new
    data file.

    THE PCM3.HLP FILE IS MISSING. When you request the more detailed second
    help screen by pressing the H key from the primary help screen,
    PCMODEL reads in a file from the default drive named PCM3.HLP. If that
    file is absent, this message results. Make sure that the current drive
    and path contains the PCM3.HLP file.

    TOO MANY FILES OR BAD FILE SPEC. A diskette directory will hold only a
    finite number of filenames, and if the files are all small ones, it is
    possible to fill up the directory on the diskette before you actually
    fill up the space on the diskett itself. If this happens, the stated
    error will be generated. Replace the diskette with either a new,
    formatted one or one with enough room in its file directory to hold
    the file you are attempting to save. The program returns to the com-
    mand state after it encounters this error.

    SIZE FACTOR TOO LARGE. USE 10 OR LESS. You have tried to zoom in too far
    with the SIZE command. To safeguard the data integrity against ac-
    cidental errors, you cannot expand the scope of the display window
    more than 10-fold at one time. There is normally no reason to enlarge
    the image this much anyway, since the useful range of the SIZE command
    is from 0.1 to 10. The program returns to the command state following
    this error, and the display window is left unchanged.

    TOTAL EXCEEDS SPECIFIED VALUE. While performing a nonprincipal rotation,
    you have input a range of atom numbers that exceeds the number of
    atoms you originally specified. Control remains in the ROTATION en-
    vironment, and you are prompted for a new atom total. Be sure to
    specify the proper total of atoms to be rotated. Moreover, remember
    that the range you specify for the atom numbers is inclusive.

    UNANTICIPATED ERROR ### LOC ###. Despite the inclusion of extensive error
    checking capability, it is possible that unanticipated errors may
    occur during the use of PCMODEL. If such a situation arises, you will
    see this message. In place of the ### characters will be two numbers.
    Please record these numbers and the conditions under which they arose,
    then contact the author with the information. PCMODEL will hold the
    screen display until you press any key, in order to give you an oppor-
    tunity to record the error code information and the conditions. With
    your help, we can make the program even more robust than it currently
    is.

    VALUE MUST BE >0. REENTER. You have tried to enter an atom number with a
    value less than 1 into the connection table during editing. The values
    in the connectivity table must be integers greater than zero.

    VALUE MUST BE GREATER THAN CURRENT TOTAL. Using the Add option of the
    EDIT command, when you add one or more atoms to the current model, the
    new total of atoms must be larger than the previous total. In other
    words, you cannot delete an atom with the Add option by specifying a
    total that is less than that with which you started. Use the Delete
    option to remove atoms from the model. Control remains in the EDIT

    PCMODEL User's Manual                                          Page 54


    environment, and you will be prompted for a new atom total.

    YOU NEED A GRAPHICS CARD TO RUN PCMODEL. This error appears if you at-
    tempt to run PCMODEL on a system equipped with only a monochrome
    monitor. There is no corrective action to take, except to obtain an
    appropriate graphics card and monitor.

    X-RAY FORMAT FILE. DO QUIT+RESTART FIRST. You have tried to add a data
    file that is in X-ray (unit cell) coordinate format to a display
    already containing a cartesian coordinate file. The two formats are
    not compatible. You must convert the X-ray file to cartesian format
    first.

    PCMODEL User's Manual                                          Page 55


                  APPENDIX B - COORDINATE GENERATION PROGRAM



    INTRODUCTION

       The CGP program is intended for use in conjunction with PCMODEL. It
    generates a PCMODEL data set for a molecule of up to 100 atoms, based
    only on the identities of the atoms contained in the molecule and the
    bond lengths and bond angles between the atoms. The program is full-
    screen oriented, and the files generated may be saved and freely
    edited.

       Start the program by typing

     CGP

    followed by ENTER, at the DOS prompt. It is completely self-contained,
    and you do not need any other files or libraries present on the dis-
    kette. Because of the close synergy between CGP and PCMODEL, it is
    convenient to keep them in the same directory if you are using a hard
    disk.

       The program begins by presenting the menu screen. On this screen
    are six choices, numbered 1 through 6, as follows:

    1. Edit a data set

    2. Create a new data set

    3. Disk data files

    4. Generate a coordinate file

    5. Help

    6. Quit

    To select one of the choices, press either the corresponding number or
    the first letter of the choice. For example, you may receive help by
    pressing either the number 5 or the letter H. Both upper and lower
    case letters are acceptable. You may also quit and return to DOS by
    pressing function key F1.

       The data sets for the CGP program are in the form of string data
    containing atom identifiers, bond lengths and bond angles. All data
    files for CGP have the extension ".CGS" (for Coordinate Generation
    String) and can be identified as such. Any CGP data set can be edited
    by the CGP program itself or read by a word processor that can handle
    ASCII text files.


    EDITING OR CREATING A DATA SET

    PCMODEL User's Manual                                          Page 56


       When you select either choice 1 (Edit) or choice 2 (Create), you
    are prompted for a file name. The program prints the current drive and
    colon, eight spaces, and the extension ".cgs." You may now type in a
    filename of up to eight characters. Several editing keys are active at
    this point, in addition to the normal keyboard letters and numbers:

       1. The right and left cursor keys allow you to scan over the entire
          filename space, except the ".cgs" extension.

       2. The Esc key will erase the entire field, again except for the
          ".cgs" extension. The F2 function key will perform the same
          function.

       3. The Backspace key will perform the usual destructive backspace
          function, erasing the letter to the left of the cursor and
          placing the cursor there.

       4. The Del key will remove the character directly above the cursor
          and fill in the blank by shifting the remaining characters to
          the right of the cursor one space to the left.

       5. The F1 function key will cancel the entry process and return to
          the initial menu screen.

       6. The F6 function key will erase all characters above and to the
          right of the cursor.

       7. The Ctrl-F1 key combination cause the program to immediately
          terminate and return to DOS. No data will be saved and no prompt
          will appear.

       8. The ENTER key sends the file name to the program. If the file
          name line is blank, either because you did not enter a name or
          you erased the name using the Esc key, the program returns to
          the initial menu.

       When you specify the file name and press ENTER, the program checks
    for the existence of that file. If you have selected Choice 2 (Create
    a new data set), the program will make sure that the file does not
    already exist. If it does, you will be so informed and asked if you
    want to overwrite it. If you press N for no, the program will return
    to the initial menu. Otherwise, the program will move to the data
    entry screen.

       If you have selected Choice 1 (Edit an existing data set), the
    program will load that file and move to the data entry screen. If the
    specified data set is not present, an error message will be generated
    and you will be prompted for another file name.

       The CGP program maintains the current file name in memory until it
    is erased or replaced with another. This means that when you choose
    Edit a subsequent time, the program prompt will contain the name of
    the previous file. You may either edit this file name to specify the
    new file name or you may blank the line with the Esc (or F2) key, then
    type the new name.

    PCMODEL User's Manual                                          Page 57


    CHANGING THE DATA DRIVE

       When a file name is requested by CGP, it is prefaced by the default
    drive designator. This is a letter, usually in the range A-E, that
    represents the disk drive that DOS considers to be the active drive.
    This drive is the same one that shows in the DOS system prompt. Al-
    though the current drive is specified automatically at the prompt,
    followed by a colon (:), you may change this letter by moving the
    cursor to the left and typing a new letter over the original one. This
    will cause DOS to look for the file name on the newly specified drive,
    rather than the default drive. Please note that by changing the drive
    letter in the file name line, you are not changing the current drive.
    You are simply redirecting the search for the present file name to
    another disk drive.

       The program as currently configured does not support path names and
    subdirectories, so if you are using a hard disk, make sure that the
    desired subdirectory is already current by changing to it before
    beginning CGP. Since the disk drive letter is an integral part of the
    file name, CGP will not allow you to omit it from the filename. If you
    do so, the program will detect its absence and place the current drive
    letter back into the file name before it begins to search for the
    specified data set.


    THE DATA ENTRY SCREEN

       Entry of atom identifiers and bond length and bond angle data with
    CGP takes place in full-screen mode. When the data entry screen comes
    up, there are seven columns across the screen and 20 rows down the
    screen. There is also a title line at the top of the screen and a row
    of prompts at the bottom of the screen. The active file, i.e., the
    file serving as the current data set, is printed just above the prompt
    legends. The cursor may be moved to any position on the data entry
    screen where data may be entered.

       There are actually five pages of data entry screens, which may be
    thought of as windows on the data file. When the data screen first
    appears, page one is in the window and the numbers are from 1 to 20.
    If you press the PgDn key, the screen will clear and the second page
    of data will appear. The atoms on this page are numbered from 21 to
    40. Similarly, there are three more pages that may be accessed by
    consecutively pressing PgDn. You may return to the previous pages by
    pressing the PgUp key. The window is decreased by one page each time
    the PgUp key is pressed, until the first page is reached. At that
    point the PgUp key has no effect.

       Several editing keys and functions are active on the data screen,
    besides the usual letters and numbers. Following is a list of the
    active keys:

       a. The cursor right and cursor left keys move the cursor across the
          screen. The cursor will move only to those fields where data
          input is allowed. Each field on the screen is seven columns wide
          except the Atom Identifier field (the leftmost one), which is

    PCMODEL User's Manual                                          Page 58


          eight characters wide. As you move the cursor horizontally
          across a field, it will skip from the last column in one field
          to the first column of the next field. When it reaches either
          the end or the beginning of a row, it will wrap around to the
          next or previous row, respectively.

       b. The Backspace key serves the usual destructive backspace func-
          tion, deleting the character immediately to the left of the
          cursor and closing up the remaining data in the field. It has no
          effect at the beginning of a field, i.e., it will not move
          across fields to delete characters.

       c. The Esc key and the F2 function key perform the same function.
          Both serve to erase the field in which the cursor is placed and
          replace it with blanks.

       d. The ENTER key and the Tab key perform the same function - to
          move the cursor to the next field in the row. If the cursor is
          already in the last field, it moves to the first field of the
          next row. Before CGP leaves a data field it checks to make sure
          that the data in the field are left justified and contiguous,
          i.e., with no spaces or gaps in the characters.

       e. The Shift-Tab key performs the reverse of the Tab key, that is,
          it moves the cursor to the previous field. Again, if the cursor
          is already in the first field of the row, it is moved to the
          last field of the previous row.

       f. The Home key moves the cursor to the top leftmost field of the
          screen.

       g. The PgUp and PgDn keys have been discussed previously. They move
          the displayed page up or down, respectively. The PgDn key, when
          pressed, displays the next 20 rows of data in the data set,
          while the PgUp key displays the previous 20 rows of data.

       h. The Cursor Up and Cursor Down keys move the cursor between rows
          of data. It is this capability that contributes to the full-
          screen capability of the program. You are not limited to moving
          from field to field in one row.

       i. The Del key performs the usual function, deleting the character
          above the cursor and moving all subsequent characters to the
          left by one space.

       j. The F1 function key exits the data screen and returns to the
          initial menu. If any changes have been made in the data, CGP
          will save the data on disk before exiting. This is to safeguard
          the data from loss. If no changes have been made, the program
          returns directly to the initial menu.

          Before saving the file, CGP will prompt you for the file name.
          The default file name is the same as the active file. You may
          press ENTER to save the data in this file. You may, however,
          change the name of the data file at this point so that it will

    PCMODEL User's Manual                                          Page 59


          be saved under a different name. The major use for this is to
          create one or more similar but different files. Using this
          option, you may change an existing file and save it as a new one
          without retyping redundant data. The same keys are active for
          the specification of a new file name as are active in the file
          name input section, previously discussed.

       k. The Shift-F2 function key is a line erase key. Pressing this key
          combination will cause the current line of data to be erased
          from the current cursor data field to the end of the row.

       l. The Ctrl-F1 function key unconditionally terminates the program
          and returns to DOS. In this sense it serves as a kind of "panic
          button." When you press this key combination, the program is
          immediately terminated. No prompts are displayed, no messages
          are given, and no files are saved.

       m. The F3 function key toggles between the two data modes possible
          in CGP. One is based on both a bond angle and a dihedral angle
          to specify the coordinates of an atom, while the other depends
          on two bond angles. The former is the default mode. This will be
          discussed further in a later section.

       n. The F4 function key duplicates the data in the field above the
          current one. This capability is a useful one and saves con-
          siderable time. For example, many of the bond angles in a
          molecule will be standard tetrahedral ones of 109.5 degrees.
          Rather than typing the same number so many times, it can be
          copied down a column using the F4 key. To do this, move the
          cursor to the field below the field you want to copy, then press
          F4.

       There are a few other aspects of data entry that need to be dis-
    cussed. One of these is the form of the data. Due to the way the data
    are handled by CGP, all of the fields must be filled in if the cal-
    culation algorithm is to perform without error. This means that no
    blank rows can be included within the data set. Moreover, each atom
    must have at least one character that identifies it in the leftmost
    column of each row. If you leave any blank rows on data input, say by
    skipping a row with the Cursor Down key, the program will protest, as
    it will if you try to fill in any of the data fields without first
    filling in the atom identifier field. We suggest that each atom iden-
    tifier begin with one of the capital letters used by PCMODEL for atom
    assignment (C, H, O, N, S, P, B, F, G (for Cl), E (for Br), or I). In
    this way, the atoms will be displayed in the appropriate colors and
    sizes when the coordinate file is read into PCMODEL.

       The program checks for a blank "Atom ID" field in order to know
    when the end of the file has been reached. If you were to find a way
    to place a blank row in a data set, all the data below the blank field
    would be lost when the data set were saved.

       The algorithm used to calculate the cartesian coordinates is based
    on that used in the FORTRAN program MBLD, available from the Quantum
    Chemistry Program Exchange (Dept. of Chemistry, Indiana University).

    PCMODEL User's Manual                                          Page 60


    For input it uses seven data values. Each atom (except the first
    three) has associated with it:

       1. An atom identifier containing up to eight characters. It may be
          composed of letters and numbers, and the letters may be upper or
          lower case.

       2. The number of a previous atom in the data set to which it is
          attached. This number is handled as an integer.

       3. The bond length between the atom whose number was stated in
          Field 2 and the current atom.

       4. The number of a previous atom in the data set which forms a bond
          angle with the current atom. This number is also an integer.

       5. The bond angle between the atom whose number was stated in Field
          4 and the current atom.

       6. The number of a previous atom in the data set which forms a
          dihedral angle with the current atom, or less preferably, the
          number of a second previous atom (different from the atom stated
          in Field 4) which forms a simple bond angle with the current
          atom.

       7. The value of the angle denoted by the number of the atom in
          Field 6. Note that a dihedral angle has a sign, and the use of
          the wrong sign will produce bizarre (and occasionally almost
          unrecognizable) results in the final coordinate data file. To
          denote whether this angle is a dihedral angle or a simple bond
          angle, the F3 function key is used. In the default state, the
          angle is assumed to be a dihedral angle. If it is a second
          simple bond angle, let the program know this by pressing the F3
          function key with the cursor in the angle field. The field will
          be written in reverse video and the data file on the disk will
          also be marked to reflect this status when it is written. If you
          later decide to use a dihedral angle and change the atom number
          in Field 6 and the value for the angle in Field 7, be sure to
          toggle the field back to the default state by pressing F3 again
          while the cursor is in Field 7.

       The first three atoms of the data set are unique, since they are
    treated specially by the program. The first atom is specified only by
    the Atom ID. It is defined as having the coordinates 0,0,0, that is,
    at the origin. The second atom must have both an Atom ID and a bond
    length by which it is attached to the first atom. The third atom is
    specified by a bond length from the second atom and a bond angle it
    forms with the first atom. The data screen is equipped with protected
    fields for these first three atoms, so that they may be treated in
    this manner.


    GENERATING CARTESIAN COORDINATE DATA FILES

    PCMODEL User's Manual                                          Page 61


       To generate a Cartesian coordinate data file, select Choice 4 from
    the initial menu. You will then be prompted for a file name exactly as
    you were when you chose a file to edit or to create. If you have
    already edited a file during the session, that file name will be
    displayed. You may change it or enter a new name at this point, then
    press ENTER. You may also accept that file name (the usual case) just
    by pressing the ENTER key. The program will then generate a file of
    that name on the drive specified, with the standard PCMODEL ".DT3"
    extension. If the file already exists, it will be overwritten by the
    program. This coordinate data file is in the standard PCMODEL Version
    3.0 format. There is no bond information in the data file generated by
    CGP. PCMODEL will add the bond connections when it reads the data
    file.

       The molecule as generated has atom 1 placed at the coordinates
    12,6,6, rather than 0,0,0. This translation permits the displayed
    structure to appear at the center of the PCMODEL display window. Once
    you display the molecule in PCMODEL, rotating it about the X axis
    helps to visualize it. This is because of the nature of the bond
    generation process. The view initially presented is "end on," and is
    not easily visualized.


    EXAMPLES

       Included with the CGP program are four data set files. These are
    for the molecules Ethyl Chloride (ETHCHLOR.CGS), Cyclohexane
    (CYCLOHEX.CGS), Adamantane (ADAMANT.CGS), and Meperidine
    (MEPERID.CGS). These files may be loaded and studied to become
    familiar with the CGP program. To illustrate the use of CGP, here are
    the step by step instructions for generating a coordinate file from
    the Cyclohexane data set:

       1. Place all the files on the default drive, on either a diskette
          or a hard disk. Make sure that the drive containing the files is
          the default drive.

       2. Begin the program by typing CGP and pressing the ENTER key. The
          initial menu will appear.

       3. If you wish to edit the file, select Choice 1 from the menu by
          pressing either the number 1 or the letter E, otherwise go to
          step 6, below.

       4. Type the file name CYCLOHEX at the file name prompt (upper or
          lower case) and press ENTER.

       5. Edit or browse the data. When you are finished, press F1. If you
          have changed the data, you will be prompted for a file name
          before the program saves the changes. If you receive this
          prompt, press ENTER.

       6. Select Choice 4 from the menu by pressing either the 4 key or
          the G key. You will be prompted for a file name. If you have
          already edited or browsed the CYCLOHEX.CGS file, it will appear

    PCMODEL User's Manual                                          Page 62


          in the file name space. If this is the case, just press ENTER.
          Otherwise, type in the name CYCLOHEX and press ENTER. The
          program will inform you that the file is being generated, then
          tell you that the file has been generated. The initial menu will
          reappear on the screen.

       7. Select Choice 6 from the menu by pressing either the 6 key or
          the Q key. The program will exit to DOS.

       8. Run the PCM3 program, either from the diskette or from the hard
          disk. After it is running, ADD the file CYCLOHEX by pressing the
          A key, then selecting it from the catalog listing with the mouse
          device or the cursor arrow keys. Be sure to select the right
          drive and path for the directory. When this process is complete,
          the structure will appear on the screen. It may be manipulated
          in the usual way at this point.

    PCMODEL User's Manual                                          Page 63


                               PCMODEL ORDER FORM


    Remit to:  KT Consulting             Disk Size:   _____ 5.25" 360K
               P.O. Box 3810                          _____ 5.25" 1.2M
               Vernon, CT 06066                       _____ 3.5"  720K



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     (does not include manual, includes disks,
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    Supplemental:
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    PCMODEL User's Manual                                          Page 64


                               LICENSE

    PCMODEL is a shareware (user supported) product and is not in the
    public domain. You are free to use, copy and distribute PCMODEL for
    noncommercial use if no fee is charged for use, copying, or distri-
    bution, and if it is not modified in any way. Clubs and user groups
    may charge a nominal fee (less than $6) while distributing PCMODEL.

    The PCMODEL software package and manual are distributed on an "As Is"
    basis, without warranty. Neither the authors nor KT Consulting shall
    have any liability to any person or entity with respect to any
    liability, loss, or damage caused or alleged to be caused directly or
    indirectly by the instructions in the manual or the software itself.
    In no event shall KT Consulting be liable for any damages, including
    loss of profits, savings, or other incidental or consequential
    damages arising out of the use or misuse of the program, or for any
    claim by any party.

    If you have any questions, comments, or suggestions about PCMODEL,
    send them to Jim Henkel at the address below or at Compuserve ID
    73277,762.

    If you find PCMODEL to be useful in your research, teaching, or other
    activities, a registration of $69 (+ $6 shipping) would be
    appreciated. Upon full registration, you will receive a 250-page
    printed user's manual, the most recent version of the program, a
    coordinate conversion and transformation program, notice of updates,
    and access to the Coordinate Data Consortium, a depository of
    structures generated and contributed by users of the program. Lower
    cost registration options are available, as listed on the order form.

                                    KT Consulting
                                    P.O. Box 3810
                                    Vernon, CT 06066