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Abstract W0073

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Abstract W0073

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  1. The SBEVSL dictionary is central repository of commands common to molecular visualization programs that employ a scripting interface. We begin with a scene consisting of a variety of objects that include the molecules themselves as well as other actions on the molecules and perspectives of the molecules. Using RasMol, PyMOL and Jmol with the Structural Biology Extensible Visualization Scripting Language (SBEVSL)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^*Rochester Institute of Technology, Rochester NY 14623, ^Dowling College, Oakdale, NY 11769 RasMol PyMOL Jmol Chime RasMol PyMOL Jmol Chime SBEVSL One of the major challenges in translating scripts between programs is that some of the scripts resemble natural language (Rasmol, Jmol, Chime) while other scripts resemble programming languages (PyMOL, VMD). Therefore, it is necessary to match the intention of the command extracted from each program to the common core dictionary, then translate it to the command style (natural or programming) for the application. Native SBEVSL Support Rasmol Add mapping Create an interface for PyMOL scripts PyMOL Build a command for hydrogen bonds Create the ConScript plug-in for PyMOL Our approach with Rasmol and PyMOL is to actually modify their code so that each can accept scripts designed for the other program. This has included adding features to both programs. Abstract W0073 There are many useful molecular graphics programs, but moving among them can be challenging. The Structural Biology Extensible Visualization Scripting Language (SBEVSL) project is working to simplify the task of starting a graphics presentation under one package, e.g. RasMol or Jmol and then moving to another package, such a PyMOL or CCP4mg for, say, better renderings of certain features without having to redo all the work of selecting orientations and types of displays. For some uses, the scripting language can be used a block box, much the way we use Postscript for text documents, but, where feasible, SBEVSL is designed to be comprehensible to scientists by using simple menu-click-like commands and reasonable defaults. RasMol, PyMOL and Jmol are being given "native“ SBEVSL support and external translators will allow the approach to be applied with other packages, such as CCP4mg. This work is part of the combined efforts of the SBEVSL groups at Dowling College and Rochester Institute of Technology.. Work supported in part by grant 1R15GM078077-01 from NIGMS. External Support Once the SBEVSL dictionary is complete, we will implement it a as a database with web interface, so that users can input scripts from any script-driven molecular visualization program and output scripts for any related program. We will start with CCP4, Input Script Input ProgramCCP4WebmolMolmolVMDO Output ProgramCCP4Webmol MolmolVMDO Input Script Acknowledgments RIT College of Science and Provost’s Office Dowling College NIH 1R15GM078077-01

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