SBEVSL Structural Biology Extensible Visualization Scripting Language PyMOL to and from SBEVSL

1. Future plans will allow users to seamlessly replicate viewing information in a variety of molecular modeling programs. Users will no longer have to spend time regenerating a script for different programs to render the same general view, and can use that time for more directed study. Abstract: Structural biologists and molecular scientists in many other disciplines need to communicate effectively about biological macromolecules. The number and complexity of available structures are both increasingly dramatically. There are many free molecular visualization programs that facilitate macromolecular structure analysis and experimental design. Each program has distinct features and limitations, often leading researchers to utilize multiple programs to successfully investigate all qualities of macromolecular structure. To alleviate this problem, we are creating a common ontology called the Structural Biology Extensible Visualization Scripting Language (SBEVSL) that will serve as a central resource for communicating scripts between different visualization programs. As a first step, we have prepared a list of individual commands that are used in PyMOL, as well as groups of commands which we are calling “features” to serve as input to SBEVSL. We have also created a plug-in for PyMOL that can take information from the central ontology by reading files line by line, find the associated commands, and output them to another script file. Future steps will script interchange between PyMOL, Rasmol, Jmol and Chime using the SBEVSL ontology as the intermediary in the communication. The completion of this project will allow researchers to move easily between these programs and quickly reproduce the same view in each program, giving them more time to spend on analysis of the macromolecular structure instead of manipulation. SBEVSLStructural Biology Extensible Visualization ScriptingLanguagePyMOL to and from SBEVSL • Introduction: • Initial efforts directed at identification of similar and differing abilities of various molecular modeling programs to enable more precise translation between programs. • PyMOL and Rasmol were the first programs addressed. • PyMOL and Rasmol have different methods of identifying hydrogen bond schemes. • A script was created to enable PyMOL to replicate Rasmol’s hydrogen bond schemes as accurately as possible • Efforts were next directed towards creating plugin programs for PyMOL to allow PyMOL to directly read Rasmol scripts and to convert PyMOL scripts into Rasmol readable scripts. • Once the SBEVSL language is complete, these programs will be adapted for use with PyMOL, allowing PyMOL to read SBEVSL scripts and to output to the SBEVSL language. #Define the translate-out Function def translate_out(Event): import tkFileDialog #Open the script write a blank line Q = tkFileDialog.askopenfilename(initialdir=('./startup')) f = open(Q, 'a') f.write('\n') f.close() f = open(Q, 'r') Y = tkFileDialog.askopenfilename(initialdir=('./startup')) r = open(Y, 'w') #Make a loop running = True while running: #Read each line and see if line contains these variables p = f.readline() if p == "cmd.zoom\n": r.write('move\n') #Define the translate Function def translate(Event): import tkFileDialog #Open the script write a blank line Q = tkFileDialog.askopenfilename(initialdir=('./startup')) f = open(Q, 'a') f.write('\n') f.close() f = open(Q, 'r') #Make a loop running = True while running: #Read each line and see if line contains these variables p = f.readline() if p == ‘move’: cmd.zoom • Methods: • Processes going to or from PyMOL require the use of plugins. • Plugins were written in the Python programming language. • Hydrogen bonding schemes are based on specific donor and acceptor atoms, bonding restrictions, and bonding lengths. • PyMOL’s selection algebra was used to provide hydrogen bonding specificity. • Translation from SBEVSL to PyMOL requires an SBEVSL script that the PyMOL plugin reads line by line, executing each recognized function. • Translation from PyMOL to SBEVSL requires creation of a PyMOL script which is then scanned by the plugin for supported commands and converted to a SBEVSL script. • Testing of the SBEVSL to PyMOL translating plugin was performed by creating a plugin allowing PyMOL to directly read Rasmol scripts. After a script has been generated in PyMOL the resulting Python based file can be converted into the common SBEVSL ontology. Above is a sample from the translation function. Because PyMOL and Rasmol have differing hydrogen bond schemes, a script was generated to calculate bonds in PyMOL comparable to those found in Rasmol. After generating a script from within another molecular modeling program, the translate plugin takes the SBEVSL script file and enables PyMOL to read it directly. • Future Plans: • Completion of the SBEVSL language and dictionary • Full support for PyMOL and Rasmol command interchange via SBEVSL • Implementation of SBEVSL support for Jmol, Chime, and Chimera. • Investigation of higher level functions and how to implement them in other molecular modeling programs to make SBEVSL output equivalent scripts. • Acknowledgements: • NIH 1R15GM078077-01 • NSF DUE 0402408 • Rochester Institute of Technology • Dowling College • Brookhaven National Laboratory