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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
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