StructureViz

John (Scooter) Morris

University of California, San Francisco

UCSF structureViz is a Cytoscape plugin that links the visualization of biological networks (and biological relationships expressed as networks) provided by Cytoscape with the visualization and analysis of molecular structures and sequences provided by UCSF Chimera. structureViz provides commands to open structures in UCSF Chimera, align them using Chimera's Sequence/Structure tools, or use any of the other Chimera analysis and visualization capabilities. Structures may be PDB identifiers, ModBase identifiers, or SMILES strings. When a structure is opened, structureViz provides an alternative interface to Chimera: the Cytoscape Molecular Structure Navigator. This interface uses a tree-based paradigm to allow users to control the display of models, chains, and residues, mostly through the use of context menus. Additional commands allow for selection by chemistry (Ligand, Ions, Solvent, Secondary Structure, and in the model context menu, Functional Residues). Users can also take advantage of Chimera's structural alignment capabilities by using the "Align" command. structureViz is available from the Cytoscape plugin manager or at http://www.rbvi.ucsf.edu/research/cytoscape/structureViz.

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