JOHN
edited by W. MOORE
Bits and Pieces, 32 Guidelines for Authors of Bits and Pieces appeared in July
PROTEIN SYSTEM 64 Menus
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Most authors of Bits and Pieces will make available listings and/or machine-readable versions of their programs. Please read each description carefully to determine compatibility with your own computing environment before requesting materials from any of the authors. Several programs described in this article and marked as such are available from Proiect SERAPHIM. Disks are available a t $5 . ner 5lId-in. disk, $i0 per 3lI2-in. disk; program listings and other written materials are available for $2 each: 52 domestic or $10 foreign postage and handling is requirkifor each shipment. Make checks payable to Project SERAPHIM. T o order, or get a Project SERAPHIM Catalogue, write to: John W. Moore, Director, Project SERAPHIM, Department of Chemistry, Eastern Michigan University, Ypsilanti, MI 48197.
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Protein Graphics on the Commodore 64 Microcomputer Gale Rhodes
University of Southern Maine Portland, ME 04103 PROTEIN SYSTEM 64 is a set of programs for protein graphics on the Commodore 64 com~uter.This svstem allows you to create and modify structire files con&ining the coordinates of alpha carbons and cofactor atoms of moteins. to display and manipulate stereo line drawings of the struc: tures on the screen, and to print labeled stereo pairs with a dot-matrix printer.
PICFILEMAKER TYPE NEW FILE LOAD FILE FROM DISK DISPLAY FILE FOR CHECKING CHANGE COORDINATES ADD COFACTOR TO FILE SCALE COORDINATES AND SAVE SAVE UNSCALED COORDINATES
PICSYS-64 DISPLAY CURRENT VIEW ROTATE ON X-AXIS ROTATE ON Y-AXIS ROTATE ON Z-AXIS ADJUST SIZE (+ OR - 10%) DISPLAY ORIGINAL VIEW TOGGLE: MDNOISTEREO TOGGLE: COFACTOR OFFION SAVE CURRENT COORDINATES SAVE STEREO PICTURE LOAD NEW FlLE
The necessary equipment for screen displays is the Commodore 64 computer, a disk drive, and a monitor. For printing, the best equipment is a non-Commodore dot-matrix printer and a Grappler CD parallel interface; other interfaces and Commodore printers will work, hut less conveniently. The system requires one software utility: Superhasic-64 from COMPUTE!'s SECOND BOOK OF COMMODORE 64. PROTEIN SYSTEM 64 comprises three main programs, PICFILEMAKER, PICSYS-64, and STEREOPRINT. The table shows the menus for the first two programs. With PICFILEMAKER, you can load, examine, and modify existing files or you can create new files by typing in atom coordinates from the Protein Data Bank ( I ) or any other source. Coordinates may he on orthogonal axes of any scale. Files are in two parts: 1) the alpha carbon coordinates, which the display program will simply connect in sequence, and 2) the coordinates and line endpoints of selected side chains and
Figure 1. Stereo screen display of oxymyoglobin (3with PICSYS-64. The two views are arranged for convergent viewing: cross your eyes to superimpose them and see a threedimensional image.
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Journal of Chemical Education
rotactors. Once you type in and correct the conrdinates, PICFILEMAKER suves them as a disk file, then srales the coordinates for the display program I'ICSYS-64, and saves the scaled set. PICSYS-64 loads scaled coordinate files and disnlavs . a high-resolution line drawing of the structure, either as a stereo pair (Fig. 1)or as a full-screen single view. The program displays the stereo pair for convergent viewing (3);that is. vou cross vour eves to s u ~ e r i m ~ o the s e views and see a three-dimensional idage. YO; can ;mily modify the display for divergent viewing, but then the views must be closer together, smaller, and thus at lower resolution. From the PICSYS-64 menu, you can rotate the model into any orientation. When you find an instructive view you want to save, PICSYS-64 creates a new scaled file in which this view is the default. In the mono viewing mode, you see one view of the stereo pair just as it will be printed. You can label the N and C termini and every tenth alpha carbon with depth-cued lahels, and you can add a figure legend. Then the SAVE PICTURE routine saves the full-screen memory map of each view of the stereo pair, properly positioned for side-hyside printing. he program STEREOPRINT loads these bitmaps and prints a stereo pair automatically (Fig. 21, using commands to the Grappler CD interface. You can also dump the maps to a ~ r i n t e by r standard screen-dump routines, but scaling. and positioning for stereo are not automatic. The PROTEIN SYSTEM 64 disk contains these three Droerams. documentation. at least 15 structure files. and the . .. 1'AI'F:RCI.IP 64 word processor file of a 20-page user's manual. There is mace on the disk fur Sunerhasic-64 and forsurh useful utilities ns Commodore's DOS wedge. I envision these uses of PROTEIN SYSTEM fi4 in undergraduate biochemistry classes and labs: 1) A simple means of studying protein conformations. Students can disdav or print sh%ures and learn t o recognize helical and sheet regions and larger structuralfeatures. 2) A source of illustrations for handouts and exams. On tests, I often ask students, to examine a stereo view of an unfamiliar protein and describe its structural features. With PROTEIN SYSTEM 64, I have a large source of such pictures and I am not limited to published views. 3) An aid in building models. Students in
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my biochemistry laboratory select a protein for a conformational study and build a bent-wire model. Stereo views from PROTEIN SYSTEM 64 are excellent guides during the bending. 4) A simple introduction to molecular graphics. Computer graphics has almost completely replacedphysical models for fitting chemical models t o electron-density maps and for studvine conformations and interactions. " " nrotein . Because the programs in PROTEIN SYSTEM 64 are entirely in the BASIC language, you can see precisely how they use the coordinate set to produce a picture of the molecule, and how tbev mani~ulatethe coordinates to scale and rotate the structure. So these programs can be for you and your students what they have been for me: afirst step in understanding molecular graphics. All of these programs are heavily commented and easy to modify. The Commodore 64 is the cheapest commercially successful computer for which a protein graphics system is available. Among inexpensive computers, i t has the highest resolution for bitmapped graphics-320 by 200 picture elements. In addition, the Commodore 64 is quite fast, even in BASIC: PICSYS-64 rotates 100 atom coordinates in under five seconds. At current hardware prices, you can bring three dimensional screen displays and prints into your class or lab for less than $700. The PROTEIN SYSTEM 64 disk and manual are available from Project SERAPHIM on a SI4-in. disk. ~
Computer Simulated Metabolism: A StudentInteractive Program Lawrence J. Tirri and Peter W. Jurutka University of Nevada, Las Vegas Las Vegas. NV 89154 In biochemistry courses students are first introduced to metabolism through a study of the glycolytic and citric acid cycle pathways. This study usually includes discussions of the reactions and their mechanisms. Students mav studv these reactions diligently hut many experience some difficulty in understandina the factors affectine the flow of carbon through a seriesof reactions in apathwiy. In particu-
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Figure 2. Stereo print of poplar plastocyanin(4)producedby STEREOPRINT with an midata 92 printer andGrappler CD parallel interface. The two views are arranged for divergent viewing with a stereo viewer.
Volume 63 Number 12 December 1966
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