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QCMP124. SIMVOL/PLTSIM Package
by Brian T. Luke, IBM Kingston, Neighborhood Road,
Kingston, New York 12401
SIMVOL: A Program to Calculate the Volumes, Areas, RMS
Overlap and Percent Similarity and Identicality of Two
Molecules
The program SIMVOL is written to perform each of the
following tasks:
1. Read a structure from a disk file that contains
its coordinates in Protein Data Bank (PDB) format.
2. Calculate its surface area and volume. This
includes a listing of the percent of the surface area
covered by each type of atom, as determined from the
atom's label in the input file, and for each type of
residue listed in the PDB file.
3. Read a second structure from a disk file in PDB
format.
4. Minimize the root-mean-squared (RMS) error in the
positions of a set of atoms from each structure.
5. Calculate the surface area and volume of the
second structure. This also includes a listing of
the percent of the surface area covered by each type
of atom, as determined from the atom's label in the
input file, and for each type of residue listed in
its PDB file.
6. Calculate the overall percent similarity and
percent identicality of the two structures.
7. Calculate the percent similarity and percent
identicality of each atom in each structure.
8. Calculate the percent similarity and percent
identicality for each atom name in each structure, as
determined by the atom labels in each PDB file.
9. Calculate the percent similarity and percent
identicality for each residue in each structure, as
determined by the residue names in each PDB file.
10. Generate a plot file, in addition to a file of
overlapped structures in PDB format, which can be
used to graphically display regions of similarity or
differences in the structures.
SIMVOL lets you scale the Van der Waals radius of each
atom and include a constant "probe" radius in all
calculations. A molecule's volume and surface area,
and the degree of similarity of two structures are
determined using the procedure described by M. Marsili,
P. Floersheim, and A. S. Dreiding, Computers &
Chemistry 7(4), 175-181 (1983).
Lines of Code: 1927
FORTRAN 77 (VS FORTRAN, XL-FORTRAN and SVS C3 FORTRAN)
PLTSIM: A DOS Program to Graphically Display SIMVOL
Plot Files and Show the Similarities and Differences of
a Pair of Molecules
PLTSIM reads both the overlapped structures file and
the plot file generated by SIMVOL. It graphically
displays the overlapped structures and dots that are
either:
1. within the volume of the first or second
structure, or both structures
2. within the volume of the first or second
structure, but not both structures
3. within the volume of both structures, but not a
single structure
4. within the volume of the first structure, but not
in the volume of the second structure.
5. within the volume of the second structure, but not
in the volume of the first structure.
PLTSIM is distributed with both a source file,
"pltsim.f", and an executable file, "pltsim.exe", that
contains the virtual memory manager and the plot
functions developed by Silicon Valley Software. The
program first reads a data file that tells the program
what the display type is (e.g., Hercules Monochrome,
CGA 4-Color, VGA 16-Color, etc.) and certain other
parameters that control the location of the plot on the
terminal.The purpose is to provide as much
flexibility as possible without having to recompile the
program.
In addition, PLTSIM lets you generate PostScript files
that contain the current display. Hardcopy is
generated by simply sending this file to a PostScript
printer.
Due to the requirements of the program and compiler,
PLTSIM will only run on a 386-class Personal Computer,
or higher, with 8M or more of memory and a graphics
display.
Acknowledgment
The author would like to acknowledge Silicon Valley
Software's policy of royalty-free distribution of SVS
C3 FORTRAN 77 compiled applications. This allows for
distribution of an executable that contains a DOS-
Extender Virtual Memory Manager and an i387 Coprocessor
Emulator (if necessary). If you want to modify the
source and use this compiler, the company can be
reached at the following address:
Silicon Valley Software
1710 South Amphlett Blvd., Suite
100
San Mateo, CA 94402
Telephone:(415) 572-8800
FAX: (415) 572-1685
Lines of Code: 575 + 1927 = 2502
SVS C3 FORTRAN 77 (v. 2.8.1)
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