Molecular modeling and visualization software: Difference between revisions
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*[[Jmol]], an open-source java-based program available in stand-alone or applet forms. The applet is used in Proteopedia. | *[[Jmol]], an open-source java-based program available in stand-alone or applet forms. The applet is used in Proteopedia. | ||
*[[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. | |||
*[[RasMol]], an open-source stand-alone program released in 1993, and still popular. | *[[RasMol]], an open-source stand-alone program released in 1993, and still popular. | ||
*[[Chime]], a free browser plugin released in 1996, now superceded by [[Jmol]]. Not open-source. | *[[Chime]], a free browser plugin released in 1996, now superceded by [[Jmol]]. Not open-source. | ||
*[[Protein Explorer]], an extensive and powerful open-source user-interface to [[Chime]]. | *[[Protein Explorer]], an extensive and powerful open-source user-interface to [[Chime]]. | ||
==Free molecular modeling software== | ==Free molecular modeling software== | ||
Revision as of 16:56, 4 November 2008
Visualization vs. ModelingVisualization 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 softwareFree 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.
- FirstGlance in Jmol, an open-source user-interface to Jmol utilized in the 3D View links in papers in the journal Nature that report new macromolecular structures.
- RasMol, an open-source stand-alone program released in 1993, and still popular.
- Chime, a free browser plugin released in 1996, now superceded by Jmol. Not open-source.
- Protein Explorer, an extensive and powerful open-source user-interface to Chime.
Free molecular modeling softwareFree molecular modeling software
Molecular modeling software usually includes visualization capabilities.
- Swiss-PDBViewer = DeepView, a powerful and popular free modeling package (not open-source).
- Coot (Crystallographic Object-Oriented Toolkit) (also at [Google Code, is very popular among crystallographers for building macromolecular models from electron density maps. Open source (GNU GPL).
- O has long been popular with crystallographers for building macromolecular models from electron density maps. Free. (License unclear.)
See AlsoSee Also
- PyMOL, an open-source molecular visualization program that requires a subscription fee.
- World Index of Molecular Visualization Resources, MolVisIndex.Org, which has links to more than one hundred free and commercial molecular visualization software packages.