RasMol
From Proteopedia
RasMol[1] is a very popular, open-source macromolecular visualization stand-alone program, first released in 1993. From its release until 1999, nearly all of RasMol was written by Roger A. Sayle, initially while a student. Beginning in 2000, development continued by volunteers under an open-source license.
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Public Domain RasMol (1993 - 2000)
Sayle released RasMol and its C source code into the public domain. From 1995-2000, the RasMol Classic Site, RasMol.MolviZ.Org (called the RasMol Home Page at that time), provided downloads, extensive documentation, tutorials, and RasMol Movie Scripts. This site supported public domain RasMol through its last release, version 2.6-beta-2a.
About 16,000 lines of the public domain source code of RasMol were adapted by MDL Information Systems to construct the web browser plugin Chime.
Sayle also created a proprietary version of RasMol capable of outputting stereolithograpy data which enables 3D printers to create solid physical molecular models (see 3DMolecularDesigns.Com).
The molecular visualization command scripting language developed by Sayle for RasMol was implemented and extended in Chime and Jmol.
Open Source RasMol (2000-present)
In 1999, after Sayle had largely stopped developing RasMol, and with Sayle's blessing, Herbert J. Bernstein[2][3] assumed development and support for RasMol, but under a strict GNU GPL (or similar) license. Subsequent releases of RasMol (versions 2.7.x) incorporate many substantial enhancements contributed by numerous programmers.
Downloads
Downloads and documentation for open-source RasMol are available from RasMol.Org.
Limitations of RasMol
Effective use of RasMol requires typing commands from RasMol's extensive command language. People who use RasMol infrequently are generally unable to remember the commands, severely limiting what they can see. Even if you know the command language well, certain complex visualization tasks require so many commands that few if any users would ever accomplish them. An example of such a task is visualization of all the non-covalent interactions with a designated moiety. Molecular visualization software that does not require learning a complex command language has been developed to make powerful visualization accessible to a wider range of users. Examples include FirstGlance in Jmol and Protein Explorer, which have extensive automatically-displayed context sensitive help, built-in color keys, and also include routines to accomplish complex visualization tasks (such as visualization of non-covalent bonds to a designated moiety, including protein cation-pi orbital interactions) with just a few clicks of the mouse.
Other software packages offer visualization capabilities not available in RasMol. Jmol, for example, has a higher-quality rendering mode, translucent rendering, automated animation of multiple models, surface, molecular orbital and cavity visualization, biological units, crystal symmetry operations (including visualization of crystal contacts and the unit cell), arbitrary objects such as arrows and planes, and true slabbing with slab rotation.
See Also
- RasMol.Org, open-source RasMol latest version and documentation.
- RasMol.MolviZ.Org, RasMol Classic (public domain version) site with extensive documentation for beginners, and reference documents on the command language that remain largely applicable to open-source RasMol.
- Roger Sayle's personal history of RasMol written in 1995 (at RasMol.MolviZ.Org).
- RasMol at Wikipedia.
- RasTop another clone of RasMol.
- Molecular modeling and visualization software
- History of Visualization of Biological Macromolecules
References
- ↑ RasMol: Biomolecular graphics for all, by Roger A. Sayle and E. James Milner-White, Trends in Biochemical Sciences 20(Sept):374-376, 1995. This is the primary citation for public-domain RasMol. Publications on RasMol for the prior and subsequent few years are listed at RasMol.MolviZ.Org.
- ↑ Bernstein + Sons.
- ↑ Herbert J. Bernstein, Professor of Computer Science, Dowling College, Oakdale NY.
