VISUALIZING SYMMETRIC MOLECULAR MODELS AT THE PROTEIN DATA BANK

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This project develops software for the Protein Data Bank for visualizing and validating structures of molecular complexes containing tens to thousands of molecules. The initial aim of the project was to correct errors in the symmetry matrices used to specify virus capsid assemblies. The symmetry specifications in Protein Data Bank virus models used a variety of undocumented coordinate systems and omitted data or include incorrect symmetries, mistakes that were difficult to catch because no readily available tools used that information. Software has been written to view the molecular assemblies using the symmetry information in PDB files and also to detect and display severe clashes between protein subunits of such models that may indicate incorrect symmetry. The capabilities have been extended to validate crystallographic symmetry that describes the packing of biomolecules in crystals used for xray diffraction. Refinements to the symmetry visualization and clash detection are ongoing.