structureViz2

App to visualize macromolecular structures in a network context
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].

1.0.6

Works with Cytoscape 3.3

Release Notes

Fix a bug that prevented the settings panel from popping up.

1.0.4

Works with Cytoscape 3.3

Release Notes

This update fixes several problems with RIN generation, the parsing of PDB structures from files, and how structureViz2 determines the model number of a loaded model. New features include: 1. The Chimera path is now saved in the user's preferences 2. The information for which columns to search for various attributes is now saved in the session 3. You can now include a chimera script file in a column and send that script to Chimera via the node context menu. Just right-click on a node and ente Apps->structureViz->Execute Script in Column. Scripts can refer to data in other columns using "%*columnName*%" where *columnName* is the name of the column. If the column is a list, and you want to iterate over all of the items in the list, use "%[*columnName*]%'.

1.0.1

Works with Cytoscape 3.1

Release Notes

Fix a bug associated with newer versions of chimera which had a slightly different format for residue attributes.

1.0.0

Works with Cytoscape 3.1