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QCMP051. Display of Space-Filling Models of
Proteins (includes programs MOLVIEW4,
CONVERT2, QUIKDIS4 and CONV1/CAC)
by Roger Rowlett, Department of Chemistry,
Colgate University, Hamilton, New York 13346
Purpose: MOLVIEW 4 creates color space- filling model representatons of the non- hydrogen atoms of proteins based on atomic coordinate data deposited in the Protein Data Bank.MOLVIEW4 also provides for a semiinteractive rotational transformation of the image about any of the orthogonal axes. CONVERT2 is supplied to modify the format of atomic coordinate files from the Protein Data Bank (F. C. Bernstein et al., J. Mol. Biol. 112, 535 (1977)) and generate the atomic color scheme for use by MOLVIEW. The algorithm is described by R. S. Rowlett, Computers & Chemistry, 9, 301 (1985). General Description: MOLVIEW4 uses a simple modified painter's algorithm to produce color space-filling model images of protein molecules based on atomic coordinate data available from the Protein Data Bank. MOLVIEW4 is an updated version of MOLVIEW (QCMP016) that takes advantage of EGA-ECD color graphics display to produce 640 x 350 images in 14 of 16 possible colors. MOLVIEW4 is also written in QuickBASIC to maximize execution speed and exploit 8087 math coprocessor support. QUIKDIS4 is a simplified version of MOLVIEW4 that executes much faster than the parent program. QUIKDIS4 does not perform calculations toaccount forthe interpenetration of atoms in space-filling models, but otherwise functions much like MOLVIEW4. There is a slight degradation of image precision in QUIKDIS4 displays compared to MOLVIEW4, but the images are accceptably correct for displaying whole protein molecules. QUIKDIS4 displays images many times faster than MOLVIEW4 for machines not equipped with a math coprocessor. CONVERT2 is a program provided to convert Protein Data Bank atomic coordinate files into more compact random-access files for use by the programs MOLVIEW4 and QUIKDIS4. Only ATOM, HETATM and CONECT records of Protein Data Bank atomic coordinate files are used. A description of the format of both Protein Data Bank atomic coordinate files and the files created by CONVERT are described by R. S. Rowlett, Computers & Chemistry, 9, 301 (1985). CONV1CAC is a program provided to convert Protein Data Bank atomic coordinate files for 1CAC only to the format used by MOLVIEW4 and QUIKDIS4. The Protein Data Bank structure file for 1CAC contains an error which CON1CAC corrects in the conversion. NOTE:MOLVIEW4, QUIKDIS4, CONVERT2 and CONVICAC are not compatible with QCMP016. Minimum Hardware: IBM-PC or compatible, 512 Kb memory, EGA color graphics, dual floppy disk drives or hard disk. Recommended Minimum Hardware: IBM-PC/XT compatible 512 Kb memory, 128 Kb RAM disk, 8087 Math coprocessor, EGA/Enhanced Color Display graphics. Mass Storage Required: CONVRT2 (20 Kb), MOLVIEW4 (11 Kb), QUIKDIS4 (7 Kb). Also, approximateley 200 Kb for each Protein Data Bank file and 60 Kb for each converted Protein Data Bank file. Execution/Display Time: CONVERT2 (15 min.), MOLVIEW4 (13 min.), QUIKDIS4 (4.5 min) for a a 2000 atom coordinate file at 8 MHz with 8087 coprocessor. Without the 8087 coprocessor, MOLVIEW4 (~120 min.) and QUIKDIS4 (7. min.) take considerably longer to execute. Microsoft QUICKBASIC 4.0 Lines of Code: 3647 |