UCSF *structureViz2* is a Cytoscape app that links visualization of biological networks in Cytoscape with visualization and analysis of molecular structures in UCSF Chimera. It is part of a broader effort to develop and apply tools for the visualization and analysis of biological context.
Networks consist of nodes and edges. For *structureViz2*, molecular structures are associated with nodes using the node attributes. Macromolecular structures are specified by Protein Data Bank identifiers (PDB IDs) and small molecule structures by SMILES strings. Homology-modeled protein structures can also be associated, as detailed below. In addition, protein structures can be represented as residue interaction networks (RINs), where nodes correspond to amino acid residues and edges to their covalent or non-covalent interactions. Individual residues can then be associated with RIN nodes as described below.
As an alternative to interacting with Chimera directly, *structureViz2* provides a simplified, tree-based interface to structures called the Cytoscape Molecular Structure Navigator. This interface allows selecting models, chains, and residues and adjusting their display. Basic interfaces are also provided for spatially aligning macromolecular structures and for analyzing steric clashes and hydrogen bonds.
Note that UCSF Chimera must be separately installed. Chimera may be downloaded from [http://www.rbvi.ucsf.edu/chimera/download.html].