Molecular modeling and visualization software
From Proteopedia
(Difference between revisions)
(created page) |
(→Free molecular modeling software - polishing) |
||
| Line 15: | Line 15: | ||
Molecular modeling software usually includes visualization capabilities. | Molecular modeling software usually includes visualization capabilities. | ||
| - | *[[Swiss-PDBViewer = DeepView]], | + | *[[Swiss-PDBViewer = DeepView]], a powerful and popular free modeling package (not open-source). |
* [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). | * [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). | ||
| + | * [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.) | ||
==See Also== | ==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. | *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. | ||
Revision as of 21:21, 3 November 2008
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.
- 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.
- 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.
Free 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 Also
- World Index of Molecular Visualization Resources, MolVisIndex.Org, which has links to more than one hundred free and commercial molecular visualization software packages.
