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RasMol to PyMOL Scripting Language Conversions

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Citations DeLano, W.L. The PyMOL Molecular Graphics System (2002) on World Wide Web http://www.pymol.org

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Citations

DeLano, W.L. The PyMOL Molecular Graphics System (2002) on World Wide Web http://www.pymol.org

Roger Sayle and E. James Milner-White. "RasMol: Biomolecular graphics for all", Trends in Biochemical Sciences (TIBS), September 1995, Vol. 20, No. 9, p. 374.Herbert J. Bernstein, "Recent changes to RasMol, recombining the variants, Trends in Biochemical Sciences (TIBS), September 2000, Vol. 25, No. 9, pp. 453-455.

C. Westin, B. Hanson, H.J. Bernstein, I. Awuah Asiamah, D. Boycheva, G. Darakev, J. Jemilawon, N. Jia, P. Kamburov, G. Todorov, P.A. Craig, S. Mottarella, "SBEVSL: Communicating Scripts Between Molecular Visualization Programs", poster presentation TP172 at the 2007 Meeting of the American Crystallographic Association (ACA 2007), 21-26 July 2007, Salt Lake City, UT, abstract E0003.

PDB ID: 1d66

Marmorstein, R., Carey, M., Ptashne, M., Harrison, S.C. (1992) DNA recognition by GAL4: structure of a protein-DNA complex. Nature 356: 408-414

  • Acknowledgements
  • NIGMS grant #1R15GM078077
  • Dowling College
  • H. J. Bernstein, I. Awuah Asiamah, G. Darakev, N. Darakev, J. Ihm, J. Jemilawon, G. McQuillan, G. Todorov, E. Zlateva
  • RIT College of Science

RasMol to PyMOL Scripting Language Conversions

Scott Mottarella, Brett Hanson, Charles Westin, Paul Craig, Herbert Bernstein, Rochester Institute of Technology, Rochester, NY, and Dowling College, Oakdale, NY.

Abstract (W0085-5121)

The aim of the Structural Biology Extensible Visualization Structure Language project is to develop a tool that allows the use of multiple molecular visualization programs without requiring the user to learn a new scripting language. ConSCRIPT is the first such tool. There are many software programs available ranging from the difficult to understand yet mathematically versatile and graphically stunning PyMOL to the user-friendly and familiar RasMol. Each program comes with its own scripting language essential to its functionality. Coordination between these programs is often necessary across projects and sometimes even among them. Valuable time can be lost learning a new visualization program and its scripting language. ConSCRIPT, as the first such iteration of the SBEVSL project, is a plug-in for PyMOL that understands commands entered in the RasMol scripting language as either a premade script or singly from PyMOL’s own command line. Future work will include other molecular visualization programs including scripting into RasMol, Jmol and Chime. ConScript is can be downloaded from the SBEVSL Sourceforge site, https://sourceforge.net/projects/sbevsl/. The project is funded in part by NIGMS grant #1R15GM078077.

VSL Commands

ConSCRIPT now supports running RasMol commands directly from the command line. Support for this new feature is initiated by opening ConSCRIPT and clicking the corresponding “Enable VSL” button. Doing so allows the user to type RasMol commands preceded by the “VSL” prefix in the style “VSL spacefill” and the command will be translated through ConSCRIPT’s script converter and the corresponding PyMOL command will be executed. Current work on this allows the ability to use these commands without opening ConSCRIPT in versions of PyMOL we have been able to compile from the source code.

Map Support for RasMol map commands

With the release to RasMol v.2.7.4, there is now support for maps in CCP4. PyMOL supports the creation of a map object using the map_new command, followed by giving the map a texture by using the isodot or isomesh commands. RasMol generates each map based on the desired texture by requiring the texture in the map generate command. A third possible texture is available in RasMol called surface that generates the Connolly surface of the macromolecule. While PyMOL does not support creation of the Connolly surface as a map feature, it does allow it using the “show surface” command. This allows ConSCRIPT to translate RasMol map commands into PyMOL’s scripting language with few limitations. Shown here is an example of ConSCRIPT’s support for map features. One image is the RasMol map, another the corresponding PyMOL map and the last is the same map generated using ConSCRIPT.

A map generated using RasMol’s native scripting language

A map generated using PyMOL’s native scripting language

rotate x 180

background white

rotate z 90

color cyan

select :a

map generate mesh

map color blue

VSL background white

VSL rotate z 90

VSL select all

VSL color red

VSL select :a

VSL map generate mesh

VSL map color blue

bg_color white

rotate z, -90

color red

map_new map, gaussian, 1, chain a

isomesh mesh, map

color blue, mesh

zoom all

A map generated using ConSCRIPT’s script translator

Continued Work in Command Support

The latest version of ConSCRIPT has coded for almost all of the commands possible in RasMol. While support for some remains minimal, included some that only return incompatibility errors, most commands, including most of those that directly manipulate the image, are supported. Here are some of the commands that have recently been added.

Conclusions

With the latest release of ConSCRIPT, a major piece in the SBEVSL project nears completion. While it may never be possible to create a seamless overlap between two distinctly different molecular visualization programs such as RasMol and PyMOL, ConSCRIPT does allow someone with no experience to get in and begin working with PyMOL immediately. There is no need to learn the more complex scripting language of PyMOL for its basic function. From ConSCRIPT, it is only a short step to incorporate other scripting languages that will bring more people together in a common viewing tool.

http://sourceforge.net/projects/sbevsl/