structureViz Plugin
Version: 0.9
Release Date: January 25, 2007
Verified to work in 2.4

This plugin links the visualization of biological (and biological
relationships expressed as networks) provided by Cytoscape with the
visualization and analysis of macromolecular structures and sequences
provided by the molecular visualization package: 
<a href="http://www.cgl.ucsf.edu/chimera/">UCSF Chimera</a>. 
<i>structureViz</i> provides commands to open
structures in UCSF Chimera, align open structures using Chimera's
Sequence/Structure tools, close structures that are currently open, and
exit Chimera. In order to load a structure associated with a node, the
Protein Databank (PDB) identifier (or identifiers if there are more than
one) must be present as an attribute of that node. Currently, <i>structureViz</i>
will look for an attribute named Structure, pdb, or pdbFileName. When a
structure is opened, structureViz provides an alternative interface to
Chimera: the <b>Cytoscape Molecular Structure Navigator</b>. This interface
uses a tree-based paradigm to allow users to select and effect 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.

Released by: John "Scooter" Morris, <a href="http://www.rbvi.ucsf.edu">RBVI</a>, UCSF

[<a href="http://www.rbvi.ucsf.edu/Research/cytoscape/structureViz/">Web Site and Download</a>]