Path: menudo.uh.edu!usenet From: afountai@garnet.acns.fsu.edu (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 Sender: amiga-reviews@math.uh.edu (comp.sys.amiga.reviews moderator) Distribution: world Message-ID: <2h4cnh$9nl@menudo.uh.edu> Reply-To: afountai@garnet.acns.fsu.edu (Augustus W. Fountain) NNTP-Posting-Host: karazm.math.uh.edu Keywords: science, graphics, molecular, commercial PRODUCT NAME MoG, Molecular Graphics Software for the Amiga. BRIEF DESCRIPTION MoG is a molecular graphics software package, actually consisting of three major parts: MoG, CPK, and PLT. This software allows for the viewing, building, manipulating, and printing of high quality, three dimensional, space filled, molecular structures. This program is best utilized when working with organic molecules and protein structures. Although utilizing its own molecular file format, MoG does support CSSR and PDB molecular file formats by means of a conversion program. Output from MoG can be in either IFF-ILBM, Postscript, EPSF, or HPGL formats. From CPK, the IFF-ILBM format supports HAM and Extra Half Bright (EHB) displays. AUTHOR/COMPANY INFORMATION Name: SciTech Software Address: 23, Stag Leys Ashtead Surrey England KT21 2TD Telephone: +44 372 275775 LIST PRICE Version Full Price Academic Price Comments ($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/morphine.iff. - 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: afountai@chem.fsu.edu voice: (904) 644-7799 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! 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 Send reviews to: amiga-reviews-submissions@math.uh.edu Request information: amiga-reviews-requests@math.uh.edu Moderator mail: amiga-reviews@math.uh.edu Anonymous ftp site: math.uh.edu, in /pub/Amiga/comp.sys.amiga.reviews