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SBEVSL

Structural Biology Extensible Visualization Scripting Language

Herbert J. Bernstein
Dept. of Mathematics and Computer Science, Dowling College, Oakdale, NY 11769 USA
(yaya at dowling dot edu)

Paul A. Craig
Dept. of Chemistry, Rochester Institute of Technology, Rochester, NY 14623 USA
(pac8612 at rit dot edu)

Work supported in part by grant 1R15GM078077-01 from the National Institute of General Medical Sciences (NGMS). The content is solely the responsibility of the authors and does not necessarily represent the official views of NIGMS.

Copyright © 2006, 2007, 2008 Herbert J. Bernstein and Paul A. Craig, All Rights Reserved

Before using this software, please read the

for important disclaimers and the IUCr Policy on the Use of the Crystallographic Information File (CIF) and other important information.

RESEARCH PLAN: There are many excellent visualization packages in structural biology. Unfortunately, no single package meets the needs of the entire community and even an individual researcher may have to use several different packages in the course of an experiment. One package may be used during structure solution to work with electron density maps and models, another package to interactively review configurations to achieve an understanding of the interaction of structure and function and to select views that will help to illustrate those points to others. Yet other packages may be used for high quality publication renderings, movies and instructional tutorials. Despite many decades of effort at integrating software for structural biology into comprehensive suites, the transition from program to program can still be clumsy and time-consuming. This unnecessary loss of time is compounded when one structural biologist communicates their findings or ideas to another structural biologist who uses different visualization and modeling software tools.

The goal of the SBEVSL project is to combine the full power that is currently available in molecular visualization with a level of ease of use that has not previously been achieved. We will make tools available to the broadest possible audience in such a way that users familiar with one program can transport their scripts to another program without having to learn the subtleties of the command language for the new program.
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PROGRESS REPORT: We are trying to take a program-independent, general view of functions and features required to do molecular graphics, drawing on best practices from existing packages. Initial efforts were directed at identifying the abilities of various molecular modeling programs to determine which functions in each would have a corresponding counterpart in each of the other programs. Ar RIT, the molecular modeling programs PyMOL and Rasmol were the first programs addressed in this manner. At Dowling College, the programs RasMol, PyMOL, DINO and ccp4mg were considered. Collectively the major focus in coding for the two groups has been on changes to PyMOL at RIT and changes to RasMol at Dowling College.
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DEVELOPMENT SITE: The SBEVSL development site is a gforge site at Dowling College. A clone of the CVS repository is available as an SVN repository on sourceforge.
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MEETING PRESENTATIONS:

B. Hanson, C. Westin, L. Slatest, P. A. Craig, "EZ-Viz Version 2.0", Northeastern Regional Meeting of the American Chemical Society, Binghamton, NY, October, 2006.

C. Westin, B. Hanson, P. A. Craig, "Using PyMOL's Align Feature to Create a Database of Ligand Binding Site Files for the Structural Analysis of Proteins," ASBMB Annual Meeting, Washington, DC, April 28 -- May 3, 2007.

B. R. Hanson, C. Westin, P. A Craig, "Using PyMOL's Selection Algebra for Enzyme Catalytic Site Prediction," ASBMB Annual Meeting, Washington, DC, April 28 -- May 3, 2007.

B. Hanson, C. Westin, L. Slatest, P. Craig, "ProMOL, Simplification and Increased Functionality of PyMOL," presentation at session SP.01.06, American Crystallographic Association Meeting, 21 -- 26 July 2007, Salt Lake City Utah, abstract W044.

H. J. Bernstein, I. Awuah Asiamah, G. Darakev, J. Jemilawon, P. Kamburov, "Support for Maps in RasMol," poster T174, American Crystallographic Association Meeting, 21 -- 26 July 2007, Salt Lake City Utah, abstract W0059.

C. Westin, B. Hanson, H. J. Bernstein, I. Awuah Asiamah, D. Boycheva, G. Darakev, N. Darakev, J. Jemilawon, N. Jia, P. Kamburov and G. Todorov, P.A. Craig, S. Mottarella, "SBEVSL: Communicating Scripts Between Molecular Visualization Programs" poster T172, Crystallographic Association Meeting, 21 -- 26 July 2007, Salt Lake City Utah, abstract E0003.

J. Jemilawon, I. Awuah Asiamah, H. J. Bernstein, G. Darakev, N. Darakev, P. Kamburov, "Use of CBFlib for Map Support," poster presentation at poster session B, 9th International Conference on Biology and Synchrotron Radiation (BSR 2007), 13 -- 17 August 2007, Manchester, UK.

S. E. Mottarella, C. Wischmeyer, B. Hanson, C. Westin, P. A. Craig, "Execute RasMol Scripts in PyMOL", poster American Society for Biochemistry and Molecular Biology, San Diego, CA, 5 -- 9 April 2008.

S. Mottarella, B. Hanson, C. Westin, P. Craig, H. Bernstein, "A Rasmol to PyMOL Translator," poster TP161, American Crystallographic Association Meeting, 31 May -- 5 June 2008, Knoxville, TN, abstract W0049

C. Wischmeyer, P. Craig, H. Bernstein, "Homology Exploration with ProMOL," poster SP169, American Crystallographic Association Meeting, 31 May -- 5 June 2008, Knoxville, TN, abstract W0050.

P. A. Craig, S. E. Mottarella, C. Wischmeyer, H. J. Bernstein, I. Awuah Asiamah, D. Boycheva, G. Darakev, N. Darakev, P. Gozo, J. Jemilawon, N. Jia, P. Kamburov, G. McQuillan, D. O'Brien, G. Todorov, "Using RasMol, PyMol and Jmol with the Structural Biology Extensible Visualization Scripting Langauge (SBEVSL)," poster MP054, American Crystallographic Association Meeting, 31 May -- 5 June 2008, Knoxville, TN, abstract W0073.

H. J. Bernstein, I. A. Asiamah, G. Darakev, N. Darakev, J. Jemilawon, N. Jia, P. Kamburov, G. McQuillan, G. Todorov. "SAXS, Lee-Richards Surfaces and a Simplified Command Set for Maps," poster MP039, American Crystallographic Association Meeting, 31 May -- 5 June 2008, Knoxville, TN, abstract W0070.

Meeting at RIT 9 Sep 2006 On 9 Sep 2006, H. Bernstein, I. Awuah Asimah, G. Darakev, N. Darakev and J. Jemilawon from Dowling travelled to RIT to meet with P. Craig, B. Hanson and C. Westin to discuss work to be done in starting up the project.
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SBEVSL Presentations at ACA 2007

Brett Hanson and Charlie Westin from RIT and Herbert J. Bernstein from Dowling College attended the summer 2007 meeting of the American Crystallographic Association in Salt Lake City Utah from 21 to 27 July 2007. This is a report on the aspects of their attendance that relate to the SBEVSL project.
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