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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 C |