RasMol

2013-07-16T09:20:35Z

Alexey Nikitin: /* See Also */

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)==
Sayle released RasMol and its C source code into the public domain. From 1995-2000, the ''RasMol Classic Site'', [http://rasmol.molviz.org 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 [http://3dmoleculardesigns.com 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<ref>[http://www.bernstein-plus-sons.com/ Bernstein + Sons].</ref><ref>[http://arcib.dowling.edu/~BernsteH/ Herbert J. Bernstein, Professor of Computer Science, Dowling College, Oakdale NY].</ref> assumed development and support for RasMol, but under a strict [http://www.gnu.org/copyleft/gpl.html 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 [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==

*[http://rasmol.org RasMol.Org], open-source RasMol latest version and documentation.
*[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]

==References==
<references />

Molecular modeling and visualization software

2013-07-16T09:15:47Z

Alexey Nikitin: /* Free molecular modeling software */

==Visualization vs. Modeling==

Software for visualizing the three-dimensional structures of molecules, ''molecular visualization software'', can be distinguished from molecular modeling software. Strictly speaking, ''Visualization'' software displays a pre-existing molecular model without changing it, while ''modeling'' software can create the model, or modify it by adding or removing moieties, changing covalent bonds, bond angles, conformation, or non-covalent interactions.

==Free molecular visualization software==

Examples of popular free molecular visualization software packages include:

*[[Jmol]], an open-source java-based program available in stand-alone or applet forms. The applet is used in Proteopedia, and in the free educational software [[Molecular Workbench]]. Effective use of Jmol requires learning a command scripting language.
*[[FirstGlance in Jmol]], an open-source user-interface to [[Jmol]] utilized in the ''3D View'' links in papers in the journal [http://www.nature.com/nature Nature] that report new macromolecular structures. Proteopedia's automatically seeded pages (pages titled with a [[PDB code]]) have links for further exploration of the structure in'' FirstGlance in Jmol''. Although ''FirstGlance in Jmol'' by no means exploits all the power in Jmol, it does show the main structural features of a macromolecule '''without learning any command scripting language'''. [[FirstGlance in Jmol|More ...]]
*[[Kinemages, Mage and KiNG]] (KiNG = Kinemage, Next Generation) are designed to present the author's viewpoint of a molecular structure. They excel in specialized areas, but are not optimal for general purpose visualization. KiNG can be used in Proteopedia; an example may be seen at [[Hemoglobin#Hemoglobin_subunit_binding_O2]].
*[[RasMol]], an open-source stand-alone program released in 1993, and still popular. Effective use of RasMol requires learning a command scripting language.
*[[Protein Explorer]], an extensive and powerful open-source user-interface to [[Chime]]. Although there is nothing else available in 2009 that combines the power and ease of use of Protein Explorer, it is falling into disuse because of difficulties related to installation and operation of the [[Chime]] browser plugin. Because Jmol is now much more powerful and easier to get working, especially on OS X, maintenance of Protein Explorer ceased in 2007. A start has been made at implementing [http://chemapps.stolaf.edu/pe/protexpl/htm/index.htm Protein Explorer with Jmol], but this project is in its infancy. (Volunteers are needed!)
*[[Chime]], a free browser plugin released in 1996, now superceded by [[Jmol]]. Not open-source.
*[http://www.molsoft.com/icm_browser.html ICM-Browser] and [http://www.molsoft.com/activeicm.html the free plugi-in ActiveICM both by Molsoft] are now used to view enhanced content in [http://mcponline.org/content/current Molecular and Cellular Proteomics Journal] and [http://www.plos.org/ PLoS (Public Library of Science)] series of journals, such as [http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0011905 an example is enhanced version that is viewable in a browser] and [http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000426 this example article with separate Datapack]. Requires a download and/or plugin. Not open-source.
*[http://hollow.sourceforge.net/ HOLLOW] is not a stand-alone molecular visualization program; however, it facilitates the production of surface images of proteins. You input a PDB file and get out a PDB file of dummy water atoms that forms a "cast" of the voids and channels of a protein.
* [http://rinalyzer.de/ RINalyzer] enables analyzing and visualizing residue interaction networks (RINs) constructed from the three-dimensional structure of a protein as stored in PDB files from the Protein Data Bank. RINalyzer allows simultaneous, interactive 2D visualization and exploration of a RIN in [http://www.cytoscape.org/ Cytoscape], in conjunction with the molecular 3D structure visualized in the [http://www.cgl.ucsf.edu/chimera/ UCSF Chimera] visulization/modelling system. [http://www.cytoscape.org/ Cytoscape] is a free, open-source software platform for the analysis and visualization of molecular interaction networks. RIN Data for any PDB entry can be downloaded [http://rinalyzer.de/rindata.php here] using the [[PDB code]], alternatively the [http://protein.cribi.unipd.it/ring/ RING web server] can be used to generate RINs.
* [http://qutemol.sourceforge.net/ Qutemol] is an open source (GPL), interactive, high quality molecular visualization system. QuteMol produces images in real time by running algorithms that rely on modern graphic card features, including programmable fragment & vertex shaders, and frame and vertex buffer objects. Other molecular visualization software has also been developed to take advantage of the current generation of high powered video graphic cards or graphic processing units (GPUs), see [http://www.ncbi.nlm.nih.gov/pubmed/21310717 Chavent et al. 2011. GPU-powered tools boost molecular visualization.].

==Free molecular modeling software==

Molecular modeling software usually includes visualization capabilities.

*[[Swiss-PDBViewer = DeepView]], a powerful and popular free modeling package (not open-source). Although menu-driven, there is a significant learning curve.
*[http://www.ysbl.york.ac.uk/~emsley/coot/ Coot] (Crystallographic Object-Oriented Toolkit -- also at [http://code.google.com/p/coot/ Google Code]), is very popular among crystallographers for building macromolecular models from electron density maps. Open source (GNU GPL).
*[[CCP4]] (Collaborative Computational Project No. 4: Software for Macromolecular X-Ray Crystallography) is very popular with crystallographers. Free for non-commercial use.
*[http://xray.bmc.uu.se/~alwyn/index.html O] has long been popular with crystallographers for building macromolecular models from electron density maps. Free. (License unclear.)
*[http://salilab.org/modeller/ Modeller]
*[http://www.cgl.ucsf.edu/chimera/ UCSF Chimera]
*[http://dasher.wustl.edu/ffe/ TINKER] a free molecular modeling package for molecular mechanics and dynamics, with some special features for biopolymers.
*[http://www.biomolecular-modeling.com/Abalone/ Abalone] a program focused on molecular dynamics of biopolymers.

==See Also==
*World Index of Molecular Visualization Resources, [http://molvisindex.org MolVisIndex.Org], which has links to more than one hundred free and commercial molecular visualization software packages.
*[[Homology model]]
*[[PyMOL]], an open-source molecular visualization program, extremely popular with crystallographers, that requires a subscription fee. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language.
*[http://www.weizmann.ac.il/ISPC/eMovie.html eMovie] is a plugin for PyMOL that facilitates creation of [[Morphs#True_Movies|true movies]] using a storyboard approach.

Proteopedia - User contributions [en]

RasMol

Molecular modeling and visualization software