The goal of the SBEVSL project is to create a new extensible scripting language for molecular graphics, as used in structural biology, by combining the intiutive expressive power of the widely used scripting language created by Roger Sayle for RasMol with the general object-oriented extensibility of the Python scripting of PyMOL. Major existing open source molecular graphics programs, including RasMol, Jmol and PyMol will be adapted to accept scripts written in the new scripting language. While it is fashionable and easy to work with GUI interfaces in controlling molecular graphics programs and to minimize the use of command line control, the saving of text files of commands from one program as scripts from which one can later reproduce images with a different program is an essential capability for scientific communication. In addition, use of command languages for visualization in structural biology yields precise control and reproducibility not obtainable by users with an ordinary pointing device such as a mouse or a dial box. There are many molecular graphics programs, most with their own command language and internal approach to storage of a database of structural elements, but for structural biology the conceptual framework to be supported is unified by the practical demands of structural biology. To be successful a molecular graphics program must provide a mechanism to select atoms, residues and chains and must be able to render wireframe, CPK, ball and stick, cartoon and other standard presentations. Rather than impose a language on any program, the SBEVSL project will extract all the concepts used in the command languages of major molecular graphics programs and gather them in one master ontology, using this essential dictionary as a relational database with GIF. Defining SBEVSL in terms of the dictionary and UML will allow expression of scripts in multiple formats so that SBEVSL can be widely used. ? ? This unification of an essential component of the infrastructure used in understanding and communicating the structure and function of biologically significant molecules will help to increase the efficiency of many activities in structural biology, such as drug design. Time now being lost in the struggle to move descriptions of molecular renderings among such programs as RasMol, Jmol, PyMOL, Molscript and Raster3D will become available for more productive activities. ? ? ? ?
| Craig, Paul A (2018) Lessons from my undergraduate research students. J Biol Chem 293:10447-10452 |
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