computer miel, 25
edited by
w.
Eastern Michigan University.JOHN Ypsilanti, MI MOORE 48197
Bits and Pieces, 9 Most authors of Bits and Pieces willmake 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. NOTE: A revised set of guidelines for Bits and Pieces authors appears with this article; please conform to these new guidelines when submitting manuscripts.
Graphic Display of Molecular Structures from Crystallographic Data Rodney Keat
University of Glasgow Glasgow, GI2 8QQ, United Kingdom Numerous programs are available for graphics terminal disnlav . and nlottine of molecular structures using mainframe and minicomputers; however, the cost of such system for occasional use in the laboratory, or on a personal basis, is prohibitive. The wide availability of microcomputers ( I ) with moderately high resolution graphics such as the Apple I1 (280 X 192 points) now means that quite presentable results can be obtained with a display of up to -50 atoms quickly and at a relatively low cost. The program PROJECT-X described here is an approach to this problem. The data required for this program comprise unit cell dimensions, fractional coordinates for the atoms, and atomjoining information as obtained from X-ray crystallographic studies. For convenience, these data are incorporated into the program when using a cassette system, but they could be loaded as a separate array, and this arrangement would be well suited to a disk-based svstem. On runnine the nromam. fractional coordinates are converted to orthogonal c&rd&ates (2) and a set of options can be exerc~sed.The orthogonal coordinates can then be listed and a suitable origin chosen for rotation and scaline onerations. Granhic mesentation takes the form of an orthographic projectidn onto the screen of the video-monitor and requires the input of rotation angles around X, Y, and Z axes, as well as a scale. A line diagram for 30 atoms will then be completed in about 10 seconds. At this stage a series of graphics commands can be employed. These include:
-
a
a) Identification of specified atoms by a flashing cursor. h) The drawing of circles at atom positions and the redrawing of bonds to meet the c~relesat positions consistent with the viewpoint. This function is particularly useful as it gives an impression of "depth," which is reinforced hy a greater plotting density for circles "closer" to the viewer. C) The "shading" of circles representing specified atoms. d) The coordinate axes can be labelled consistent with the viewpoint. e) The screen coordinatesfor any viewpoint can he listed suitable for subsequent hand drawing purposes. As a further option, orthographic projections can be viewed 128
Journal of Chemical Education
Figure 1. Examples of the graphic displays obtained using the program PROJECT-x. Photographs (with black and white reversed) were taken directly from the video monitor. (a) A projection of an See molecule with atoms circled. (bl The same molecule viewed along one of the Se-Se bonds (marked using the "special viewpoint'' option. (c) A line projection of the molecule, N3P&N=PPhL with a viewpoim along the axis containing two of the N3P3-ring nitrogen atoms (marked "+") Phosphorus atoms are denoted by shaded circles. (d) The unit cell of diamond with carbon atoms circled.
"+"
from a special position, this being along the axis passing through any two specified atoms. The program calculates the X- and Y-axis rotations for this purpose, leaving the user to define the Z-axis rotation and scale. This facility is particularly useful in establishing conformational relat~onships.The final option permits the calculation of interatomic distances. bonded or nonbonded. The latter two options provide confirmation that the nroeram is workine correctlv and that there , ,. art. nt, misrakcs i l l t h ~ d d l aprepIir:~licm.F x n ~ ~ ~ p ~ e s ut iytplei e d rr.ult; d,tGned I)\. nhotonranhinn the s,.rcrn art. h t r w n in . Figure 1.The effects bi~imitedscreen resolution are apparent, particularly in lines which make small ( e lo oolaln L p p emenia) mster a s irom an authw, copies will be retained by the Computw Series editor and supplied by the editor toany reader who requests them at a cost of $5 for duplication, handling, and postage. (4) Transportability of the computer application. Thisbreaks dawn into three cateaories .lsee J. CHEM.EDUC.56. 146 119791for detailsl: a himware. lsabp cai narawaretgraphicr termma. m crocorn. pbler Fpecra cwcb I, elc. necessar) for r-nning the prosram7 11 90 =p ,ec)li clearl) oy manufacturer an0 mode n,moer On what make(s)and model(s) of computer has the program been run? How much memory is required to run the program (8K 36-bit words. etc.)? b. Software: In what language is the program written? Has an attemd been made to follow ANSI (American National Standards l n s ! . ~ ~ 01 e i otner trnnsportao 1, rtanoarns? c Doc.mentat an rloa man) comments are n me program lwt'"97 Are a flowchart and sample exec"! on a m l;me7 1, there separate written documentation? Is there pedagogical documentation that specifies subject matter. instructional objectives, and pedagogical techniques? ~
terns 3 ano 4 a u o e neea 0cc.p) on, a slog e paragrilpil nil plogram aescrlphm Tne lo1on ng emmp.e no cams how mrcn nformill an can oe summarized concisely: Program TISIM-Interactive ANSI-standard FORTRAN, 75 statements. 75 comments. Students run TlSlM via Tektronix 4010 graphics terminal. Execution requires 3K 36-bit words on a DEC10. Documemtion includes listing, flowchart, and several sample executions; students are given instructions via the terminal at execution time. Copies of the listing and documentationavailable free. Nocarddecks, but will supply pragramand Sample executions on your Wrack. EBCDIC. magnetic tape at 800 Bpi for $5 postage and handling charge. Send a blank tape witha check for $5 made out to: Dr. Susan Smith. Department of Chemistry. Your University. Anywhere 12345.
Volume 59
Number 2
February 1982
129
