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QCMP164. USURF:Generation of Smooth Molecular Dot Surfaces by J. B. Moon, The Upjohn Company, Kalamazoo, Michigan 49001 USURF is a FORTRAN program for generating smooth molecular dot surfaces.1It was developed primarily tocalculatesurfacesfor macromolecules, but it will work well with any molecules larger than around 30 atoms. USURF is intended to be a fast alternative to Connolly's MS program (QCPE 429)2 when only the graphical display of a molecular surface is needed. The algorithm is conceptually quite simple and proceeds in two steps. First, a "solvent- accessible"3 dot surface is calculated for a molecule. This is equivalent to a Van der Waals surface calculation in which each atomic radius has a solvent probe radius added to it. This surface can be regarded as a "solvation layer," in which each surface point represents the position of a solvent probe sphere in contact with the molecule. In the second step, the probe spheres are subjected to a Van der Waals dot surface calculation in which only the inward-facing hemispheres of each probe are surfaced. This second "Van der Waals surface" is, in fact, a close approximation to a smooth "Richards surface."4 This program is derived from QCPE 566 which originally worked on a computer with virtual memory (VAX). In order to get USURF to fit into a 640-Kb-memory PC, certain changes in DIMENSION statements had to be made. The following parameters apply to this version of the program: 1. The maximum number of atoms has been reduced to 4000. 2. The maximum number of probes is now 9000. 3. The maximum number of dots per sphere is 800. References: 1. J. B. Moon and W. J. Howe, "A Fast Algorithm for Generating Smooth Molecular Dot Surface Representations," submitted to J. Mol.Graphics, September, 1988. 2. M. J. Connolly, "Solvent-Accessible Surfaces of Proteins and Nucleic Acids," Science, 221, 709-713. 3. B. Lee and F. M. Richards, "The Interpretationof Protein Structures, Estimation of Static Accessibility," J. Mol. Biol., 55, 379-400. 4. F. M. Richards, "Areas, Volumes, Packing, and Protein Structure," Ann. Rev. Biophys. Bioeng.," 6, 151-l76. Lines of Code: 780 Microsoft 5.1 (FORTRAN 77)