Molecular visualization

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* '''[[Jmol]]''' ([http://jmol.org jmol.org]) - a free, open-source java-based program available in stand-alone or applet forms. It uses a superset of the RasMol/Chime command language. It is widely accepted as a replacement for Chime. The Jmol applet is used in the [http://proteopedia.org Proteopedia.Org wiki]. Jmol is extremely powerful both for small molecules (e.g. molecular orbitals) and macromolecules (e.g. symmetry operations, unit cells, crystal contacts, translucent surfaces and cavities, arbitrary objects, animations, etc. etc.).
* '''[[Jmol]]''' ([http://jmol.org jmol.org]) - a free, open-source java-based program available in stand-alone or applet forms. It uses a superset of the RasMol/Chime command language. It is widely accepted as a replacement for Chime. The Jmol applet is used in the [http://proteopedia.org Proteopedia.Org wiki]. Jmol is extremely powerful both for small molecules (e.g. molecular orbitals) and macromolecules (e.g. symmetry operations, unit cells, crystal contacts, translucent surfaces and cavities, arbitrary objects, animations, etc. etc.).
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* '''[[BALLView]]''' ([http://www.ballview.org]) - a powerful open-source molecular modeling and visualization tool. It is available for Windows, MacOS X and Windows. BALLView provides powerful visualization capabilities for proteins, nucleic acids and small molecules. The modeling functionality includes various molecular mechanics methods (molecular dynamics, geometry optimization) using
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various force fields (AMBER, CHARMM, MMFF94). The functionality of BALLView can be extended and scripted through a convenient Python interface.
* '''[[PyMol]]''' - a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. PyMOL is extremely powerful and is very popular with crystallographers. A large percentage of macromolecular structure figures in scientific journal articles are made with PyMOL. Although it is open source, use of PyMOL requires a modest subscription fee, except for educational use.
* '''[[PyMol]]''' - a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. PyMOL is extremely powerful and is very popular with crystallographers. A large percentage of macromolecular structure figures in scientific journal articles are made with PyMOL. Although it is open source, use of PyMOL requires a modest subscription fee, except for educational use.

Latest revision as of 09:41, 5 March 2010

Contents

Software

Easy to use

The following visualization packages have extensive built-in help, and do not require that you learn any command language. All of these work in web browsers online.

More powerful, more complicated to use

Effective use of these packages requires learning some more complicated controls and/or command language. In return, they have considerably more power.

various force fields (AMBER, CHARMM, MMFF94). The functionality of BALLView can be extended and scripted through a convenient Python interface.

Additional

See also

Notes

  1. 1.0 1.1 1.2 Opinion of Eric Martz, who authored FirstGlance in Jmol and Protein Explorer, and is a member of the Proteopedia.Org development team.

External links

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