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594. PAP: A Protein Analysis Package
by Timothy Callahan, W. B. Gleason and Terry P. Lybrand, Department of Medicinal Chemistry and Minnesota Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455 PAP is a program package for the analysis of protein coordinates which are in the Brookhaven Protein Data Bank (PDB) format. These programs can be used to make two types of phi-psi plots:a Ramachandran-style scatter plot, and a plot of phi and psi values as a function of the linear sequence. Programs are also available for the display of distance diagonal plots for proteins. Two protein structures can be compared and the resulting rms differences in the structures plotted as a function of their linear sequence. In addition, various utilities are supplied for splitting PDB files which contain multiple subunits into individual files and also for renumbering PDB files. A utility is also provided for converting AMBER-style PDB files into standard PDB files. Priestle's program RIBBON [J. Appl. Cryst., 21, 572-576 (1988)] has been converted to run in a stand-alone mode with interactive rotation of the 3D ribbon picture. Programs are Silicon Graphics 4D level and have been tested on 4D70/GT and personal Iris workstations; programs which give Postscript output have been converted to run on Digital Equipment Corporation VAX computer and SUN workstations. RIBBON programs run only on SGI. NOTE:QCPE is supplying this program for the Silocon Graphics IRIS Workstation only. FORTRAN 77, C Lines of Code: 12,000 |