Friday, 6 October 2006
South Ballroom (Binghamton Regency Hotel and Conference Center)
394

EZ-Viz version 2.0, Further Simplification and Increased Functionality to Pymol

Charles Westin, Rochester Institute of Technology, Rochester, NY, Brett Hanson, Rochester Instittue of Technology, Rochester, NY, Paul Craig, Rochester Instittue of Technology, Rochester, NY, and Len Slatest, Brookhaven National Laboratory, Upton, NY.

PyMol, a powerful open source molecular visualization tool, has a notoriously difficult user interface. In order to decrease the steep learning curve associated with PyMol, Laura Grell and Chris Parkin developed PyMol made EZ, (EZ-Viz), a plug-in user interface, to simplify the use of PyMol. We have enhanced the EZ-Viz plug-in to incorporate many of PyMol's powerful features, including: Easy movie making, multiple view modes, electron density mapping, Ramachandran plots, ray trace options, amino acid reference, mouse modes, and perspective options. Instead of issuing multiple character commands into PyMol's command line, the push of a button now renders the same outcome. Beyond these implementations, over 35 known catalytic active site motifs have been defined in EZ-Viz and are shown differentiated from the rest of the enzyme. Once the motif has been selected and returned for a PDB file, the user can easily show surface contacts, polar contacts, residue labels, and bound substrates. It is also possible for a user to define their own motif and exert a great deal of selectivity in searching for their domain of interest. Further pursuits regarding EZ-Viz will entail the implementation of algorithms for the prediction of ligand and protein docking, protein fold motifs, and hydrophobic pocket motifs. Other efforts may be made to enhance PyMol's source code, and to recompile it with EZ-Viz, both fixing inherent bugs in PyMol and integrating EZ-Viz directly into PyMol's user interface.


Web Page: ez-viz.rit.edu

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