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623. MD Display: Program for Displaying Molecular Dynamics
Results
by T. Callahan, E. Swanson and T. P. Lybrand, Molecular
Bioengineering Program, University of Washington,
Seattle, Washington 98105
MD Display has been designed to allow the user to
create a colored, animated display of a molecular
system from the data produced by a molecular dynamics
program. Rotation, clipping, translation, coloring,
and scaling are all controlled by the user through the
mouse and keyboard. Additional display features
include stereo, half-bond coloring, and control of
animation speed and direction. Atoms which are not
involved in any bonds are represented by a three-
dimensional cross (axes). This package also allows the
user to monitor distances, bond angles, dihedrals, and
hydrogen bonds during animation. There are options to
superimpose a reference structure on the animation
sequence, display a solvent-accessible molecular
surface (only for static structures), display
Ramachandran plots that correspond to protein/peptide
conformation in each frame, perform frequency filtering
of trajectories in "real time", and generate color or
B/W PostScriptİ files (of individual frames) suitable
for printing or display by other programs.
A second program, NM Display, is available for
visualization of normal mode displacements. This
program contains many options and features available in
MD Display and employs the same graphical user
interface.
Data preparation is performed using the preprocessor
program, Preproc. The preprocessor reads formatted
ASCII parameter and coordinate files (or a Brookhaven
PDB file) and produces 3 or 4 binary files: an atom
attribute file, a bond file, a coordinate file, and
(optionally) a molecular surface file. These files in
turn are read by the display programs. Also included
is a utility program, pdb2cor.c, which reads in a
number of PDB files and writes out an equivalent Amber
format trajectory file. This program allows MD Display
to be used with MD programs which dump coordinates in
PDB format (or even allows the user to look at any
arbitrary sequence of PDB files with the same
topology).
NOTE:This system will be distributed on a DC 6150
tape cartridge only. Silicon Graphics 4D GT, GTX,
Personal Iris, and Indigo workstations (with 24-
bit color) are currently supported.
Lines of Code: 20,000
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