Amiga ISO Collection/AmigaDemoCD2.iso/ASCII/TEXTE/c.s.a.reviews/software/science/MoG

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Path: menudo.uh.edu!usenet
From: [e-mail] (Augustus W. Fountain)
Newsgroups: comp.sys.amiga.reviews
Subject: REVIEW: MoG, Molecular Graphics software for the Amiga
Followup-To: comp.sys.amiga.applications
Date: 13 Jan 1994 20:59:29 GMT
Organization: The Amiga Online Review Column - ed. Daniel Barrett
Lines: 296
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Reply-To: [e-mail] (Augustus W. Fountain)
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Keywords: science, graphics, molecular, commercial


PRODUCT NAME

    MoG, Molecular Graphics Software for the Amiga.


BRIEF DESCRIPTION

    MoG is a molecular graphics software package, actually consisting of
three major parts:  MoG, CPK, and PLT.  This software allows for the viewing,
building, manipulating, and printing of high quality, three dimensional,
space filled, molecular structures.  This program is best utilized when
working with organic molecules and protein structures.  Although utilizing
its own molecular file format, MoG does support CSSR and PDB molecular file
formats by means of a conversion program.  Output from MoG can be in either
IFF-ILBM, Postscript, EPSF, or HPGL formats.  From CPK, the IFF-ILBM format
supports HAM and Extra Half Bright (EHB) displays.


AUTHOR/COMPANY INFORMATION

    Name:        SciTech Software
    Address:    23, Stag Leys
            Ashtead
            Surrey
            England
            KT21 2TD

    Telephone:    [phone]


LIST PRICE

    Version     Full Price    Academic Price    Comments
              ($US)           ($US)
    ===================================================================
    Basic        $200.00     $135.00
    CoPro         $300.00     $185.00     Requires 68020+ and
                            68881 or 68882
                            co-processor
    Library     $475.00     $300.00     Linkable Library

    In order for a buyer to qualify for the academic price, SciTech
Software requires that the order be placed on university letterhead and
countersigned by the department head or some other university representative.

    The version evaluated in this review is the "CoPro" version.


SPECIAL HARDWARE AND SOFTWARE REQUIREMENTS

    HARDWARE

        At least 1 Meg of Fast RAM.
        If you desire to create space-filling pictures with CPK from
        within the program, at least 1.5 Meg of Fast RAM is
        necessary. The software is fully compatible with the enhanced
        chip set.

        A hard drive is not required, but is highly recommended.
        Fully loaded, MoG will occupy approximately 1.2 Meg of hard
        disk space.

        The Basic version does not require a CPU faster than the
        68000.  However, the CoPro version and Link library require
        a 68020 or 68030 CPU and a 68881 or 68882 math co-processor.
        The co-processor version is recommended for larger molecules
        and faster imaging.

        Some form of flicker-free video is an absolute must with this
        program.  Without it, you will not be able to exploit fully
        the ability to manipulate large molecules easily.

    SOFTWARE

        AmigaDOS V1.3 or higher is required to run MoG, with
        AmigaDOS V2.0 or higher being recommended.  (I tested
        this program with AmigaDOS 2.1)

        MoG comes packaged with PLT version 1.3B, a spooled HPGL
        printer driver, written by Rich Champeaux and Jim Miller.
        PLT is a quality driver which can also be used by other
        programs, such as Gnuplot and Multiplot.  This utility is
        freely distributable, but is not in the public domain.


COPY PROTECTION

    Serial numbered for company reference only.


MACHINE USED FOR TESTING

    Amiga 2000
    AmigaDOS 2.1
    8 Meg Fast RAM, 1 Meg Chip RAM
    GVP Series II 68030 CPU, 68882 FPU, 68030 MMU [33 MHz]
    Quantum ELS85S hard drive, 85 Meg
    Flicker Fixer
    Panasonic PanaSync C1381! monitor
    Hewlett Packard DeskJet 500


INSTALLATION

    The software does not use the Commodore Installer program.  An
installation script named Install-HD is provided; however, it assumes the
destination drive name is dh0:.  Instructions are provided to describe
changes to the script needed prior to installation to a different drive or
onto a floppy based system.  The process was fairly simple; however, it does
require a minor editing job to the S:Startup-Sequence or S:User-Startup file.


INTRODUCTION

    The major function of this software is to produce high quality,
three dimensional, space filled images of organic molecules and protein
structures.  MoG performs its primary task exquisitely.  Extremely high
quality, three dimensional images that are publication ready can easily be
produced.  The graphical user interface (GUI) uses simple buttons to rotate,
translate, and magnify a structure in an easy, stepwise fashion.  You have
full control of the molecule's movement by setting default rotation angles
and step increments.  A translation matrix can even be called to perform
specific symmetry operations on the molecule.

    MoG uses several text-editable configuration files to give the user
full control over the MoG environment.    Most of these defaults can be saved
directly from the program, but several require specific definition in the
configuration file.

HOW THE PROGRAM WORKS

    Once the program is activated from the Workbench, the user can then
load a MoG structure for viewing.  Conversion from CSSR and PDB formats is
allowed from within the program, but MoG will not automatically read one of
these files.  I was able to check the conversion of PDB files only, since
CSSR files are not in the public domain and out of my financial reach.  PDB
files are available from the Protein Data Bank at Brookhaven National
Laboratory via ftp from pdb.pdb.bnl.gov.  The default conversion program can
be changed to another if the user desires.  SciTech Software provides the
source code for the conversion program as well as the MoG file structure in C
for those ambitious computer chemists.

    As a brief aside, another conversion program that is in the public
domain called Babel is available via ftp from joplin.biosci.arizonia.edu.
This compressed tar archive is actually a file of Unix source code in C for
the program.  Once compiled, it runs via the Shell on the Amiga, providing
conversion routines for a dozen or so popular molecular structure formats,
like MoPac, and simple xyz models.  I have contacted Pat Walters at the
Laboratory for Artificial Intelligence in Chemistry, University of Arizona,
and informed him that Babel runs on the Amiga.  He has agreed to include MoG
conversion in future versions of the archive.

    Inside MoG, atoms are displayed as "x"'s and bonds as thin lines in
simple wire diagrams.  Labels showing the identity of specific atoms can be
displayed to aid in viewing the structure.  Simple bond angle and distance
calculations can be made on loaded structures.  Bonds can be broken and
twisted, and atoms moved, all by using the mouse.  A fragment library
of molecular and protein "backbone" structures is also provided.

    I found building a molecule very difficult.  MoG provides no easy
way to do this.  Even if the molecule you build or manipulate looks "right",
there is no way to perform energy minimization or reference known bond
angles and distances to be sure.

    Once you have your structure the way you want it, colors for the
individual atoms or protein residues can be assigned.  The easiest way to
do this is to read in a color list.  Your alternative is to assign each
type of atom or residue a color from the pallet requester.  Now that each
atom can be distinguished, CPK can be invoked to draw the space filled
image.

    Production of high quality images is painfully slow.  The best route
to follow is to produce only "preview" quality images in MoG, since the
image will have to be rendered again through CPK to save it as an IFF file.
CPK's only function is to render and save spaced filled image files
generated by MoG.  As a default, MoG saves a ".cpk" file each time a
molecule is rendered.  The ".cpk" files can be rendered and saved in batch
sequence by using a script, or done individually.  Currently, MoG and CPK
are not ARexx compatible.  Only wire diagrams can be saved as EPSF,
Postscript, HPGL or IFF files from within MoG.

    An uuencoded IFF-HAM image of morphine appears in a separate posting
after this review, as an example of what these images look like.

    [MODERATOR'S NOTE:  This example image also appears in the
    c.s.a.review archives in the file software/science/MoG-example.uu.
    - Dan]


DOCUMENTATION

    MoG comes with a bound manual which fully explains the many
functions of the software.  The documentation is adequate to assist you in
installing and learning the software.  The authors do assume you have some
understanding of organic chemistry and especially amino acid types.


LIKES AND DISLIKES

    LIKES:

    - The ease with which molecules can be rotated and translated for
      viewing.
    - The ability to create publication quality, spaced filled images of
      relatively large organic molecules.

    DISLIKES:

    - No ARexx interface.
    - The inability to perform energy minimization calculations on
      organic molecules.
    - The difficultly in building molecules from fragments or protein
      residues.
    - The inability to save IFF images of space filled images from
      within MoG itself.
    - The inability to produce other types of molecular images, such as
      ball and stick images, or pi-orbital displays.
    - The silly, amateurish looking icon for MoG.


COMPARISON TO OTHER SIMILAR PRODUCTS

    MoG is a long way from being comparable to commercial molecular
graphics packages available on the Macintosh, Unix, or (do I even dare say)
MS-DOS platforms.  The best and closest program available for comparison on
the Amiga is a public domain program entitled Molec 3D, by Stefan Abrecht,
available on Fred Fish 482.  This little program will display only three
dimensional ball and stick images, and uses a very simple yet awkward GUI.


BUGS

    None found.  MoG caused no Enforcer hits during any of its
functions, operations, or routines.


VENDOR SUPPORT

    MoG is available only from SciTech Software directly.  I was
extremely pleased with the courtesy and treatment I received from the
company when I contacted them with my order.  Upgrades are available from
the company as they are developed.  Future additions to MoG are expected to
have ARexx support, least-squares fitting, and simple energy calculations.


WARRANTY

    None offered.


CONCLUSIONS

    As a chemist, my first impression is that I wish there had been
more guts to be package than glitz.  All the effort in development seems to
have gone into producing the spaced filled images with little thought into
what chemists actually need.

    This program is the only commercial molecular graphics program
available for the Amiga.  Although it has its limitations, it still provides
students, teachers, and researchers in Chemistry and Biochemistry with a
valuable tool.    Overall I would rate MoG as Good.  I rate this product
perhaps 3 stars out of 5.  I am looking forward to future enhancements of
this software.

    For another review, see:

        Martin, Andrew C. R.; Journal of Molecular Graphics, Vol.
        11, No. 3, 1993, pages 53-55.


COPYRIGHT NOTICE

    This review is freely distributable.


Augustus W. Fountain III               ///
Captain, Chemical Corps             AMIGA
Assistant Professor of Chemistry         \\\/// [68030]
United States Military Academy              \XX/
    Researcher at Florida State University
email: [e-mail]
voice: [phone]

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! Any opinions expressed are my own and do not reflect those of the         !
! U.S. Army, the Federal Government, or the Analytical Chemistry Dept of FSU.!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

---

   Daniel Barrett, Moderator, comp.sys.amiga.reviews
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