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RasMol
Original authorRoger A. Sayle
DeveloperHerbert J. Bernstein
Initial release1992; 34 years ago (1992)
Stable release
2.7.5.1 / July 17, 2009; 16 years ago (2009-07-17)
Written inC
Operating systemUnix, Windows
PlatformIA-32, x86-64
Available inEnglish
TypeMolecular graphics
LicenseGPL
Websitewww.rasmol.org
Repository

RasMol is a computer program written for molecular graphics visualization intended and used mainly to depict and explore biological macromolecule structures, such as those found in the Protein Data Bank (PDB).

History

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It was originally developed by Roger Sayle in the early 1990s.[1]

Historically, it was an important tool for molecular biologists since the extremely optimized program allowed the software to run on (then) modestly powerful personal computers. Before RasMol, visualization software ran on graphics workstations that, due to their cost, were less accessible to scholars. RasMol continues to be important for research in structural biology, and has become important in education.

RasMol has a complex licensing version history. Starting with the version 2.7 series,[2] RasMol source code is dual-licensed under a GNU General Public License (GPL), or custom license RASLIC.[3] Starting with version 2.7.5, a GPL is the only license valid for binary distributions.

RasMol includes a scripting language, to perform many functions such as selecting certain protein chains, changing colors, etc. Jmol and Sirius software have incorporated this language into their commands.

Protein Data Bank (PDB) files can be downloaded for visualization from members of the Worldwide Protein Data Bank (wwPDB). These have been uploaded by researchers who have characterized the structure of molecules usually by X-ray crystallography, protein NMR spectroscopy, or cryogenic electron microscopy.

Interprocess communication

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Rasmol can communicate with other programs via Tcl/Tk on Unix platforms, and via Dynamic Data Exchange (DDE) on Microsoft Windows.

With a multiple sequence alignment program, the responsible Java class can be freely used in other applications.[4]

See also

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References

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  1. ^ 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
  2. ^ Herbert J. Bernstein, "Recent changes to RasMol, recombining the variants, Trends in Biochemical Sciences (TIBS), September 2000, Vol. 25, No. 9, pp. 453-455
  3. ^ RASLIC license
  4. ^ Multiple alignment program
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📚 Artikel Terkait di Wikipedia

CPK coloring

scheme used by the molecular visualizer Jmol. Column R is the scheme used by Rasmol; when two colors are shown, the second one is valid for versions 2.7.3 and

Simplified Molecular Input Line Entry System

Designer Avogadro BALL Biskit Gabedit Ghemical Jmol Molekel PyMOL QuteMol RasMol Proprietary Abalone ACD/ChemSketch Atomistix ToolKit ChemDraw ChemWindow

MDL Chime

display the three-dimensional structures of molecules. and was based on the RasMol code. Chime was used by a wide range of biochemistry web sites for the visualization

List of free and open-source software packages

Folding@home Jmol MODELLER Molecular Modelling Toolkit Molekel NUPACK QuteMol RasMol ShelXle Chimera VMD VOTCA Avogadro Biskit Chemistry Development Kit Gabedit

Sirius visualization software

Command line interpreter and scripting support fully compatible with extant RasMol scripts Full support for molecular dynamics trajectory visualizing BLAST

Glide (docking)

Designer Avogadro BALL Biskit Gabedit Ghemical Jmol Molekel PyMOL QuteMol RasMol Proprietary Abalone ACD/ChemSketch Atomistix ToolKit ChemDraw ChemWindow

List of molecular graphics systems

Retrieved 24 September 2009. Sayle RA, Milner-White EJ (September 1995). "RASMOL: biomolecular graphics for all". Trends in Biochemical Sciences. 20 (9):

Anthony Nicholls (physicist)

OpenEye has employed several notable people in cheminformatics, including RasMol developer Roger Sayle. OpenEye was acquired by Cadence Design Systems in