RasMol: Difference between revisions

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Eric Martz, Alexey Nikitin

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-RasMol<ref name='ras1995'>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 [http://rasmol.molviz.org/rasbib.htm RasMol.MolviZ.Org].</ref> is a very popular, open-source [[Molecular modeling and visualization software|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.
+RasMol<ref name='ras1995'>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 [http://rasmol.molviz.org/rasbib.htm RasMol.MolviZ.Org].</ref> is a very popular, open-source [[Molecular modeling and visualization software|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.
 ==Public Domain RasMol (1993 - 2000)==
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 ==Downloads==
 Downloads and documentation for open-source RasMol are available from [http://rasmol.org 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 interactions|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==
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 *[http://rasmol.molviz.org 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.
 *[http://rasmol.molviz.org/pershist.txt Roger Sayle's personal history of RasMol] written in 1995 (at [http://rasmol.molviz.org RasMol.MolviZ.Org]).
+*[http://en.wikipedia.org/wiki/Rasmol RasMol at Wikipedia].
+*[http://www.geneinfinity.org/rastop/ RasTop] another clone of RasMol.
 *[[Molecular modeling and visualization software]]
 *[http://history.molviz.org History of Visualization of Biological Macromolecules]