Chem 110L: Macromolecular Visualization Laboratory Exercise: Other Programs
Other Modeling and Visualization Programs
The programs SYBYL and RasMol that you used today are just two examples of many modeling and visualization programs. There are several other programs that have their own strengths and weaknesses. Below you can find a short list of free modeling and visualization programs for PC-Windows, PC-Linux, and Apple MacOS. More complete lists are available at http://www.chem.swin.edu.au/chem_ref.html
- PyMOL
http://pymol.sourceforge.net/
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PyMOL is an excellent free program with strengths in rendering ray-traced, publication quality images and movies. Independent manipulation of many molecules is supported. Based on Python programming language, it combines strong control over the program through the command line with an attractive graphical user interface.
- RasMol/Chime
http://www.umass.edu/microbio/rasmol/
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Rasmol was one of the earliest free visualization programs for that worked on PC's, Mac's and Unix machines. It is still a good choice for visualization of very large, multicomponent systems. The Chime plug-in for web browsers is largely based on the RasMol code.
- SwissPDB Viewer
http://us.expasy.org/spdbv/
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SwissPDB Viewer allows analysis of several proteins at the same time, which facilitates comparison and identification of structural alignments. The program is linked to a homology search tool Swiss-Model.
- MOLEKEL
http://www.cscs.ch/molekel//
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MOLEKEL is a free visualization tool with emphasis on displaying molecular properties as obtained by quantum mechanical calculations. It can render many molecules simultaneously.
- UCSF Chimera
http://www.cgl.ucsf.edu/chimera/
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UCSF Chimera is a powerful visualization tool with emphasis on extensibility to incorporate user-provided analysis tools.
- gOpenMol
http://www.csc.fi/gopenmol/
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gOpenMol is a modern free program for Windows, SGI, and Linux workstations that can be used to read a large variety of molecular structure formats and play back molecular dynamics trajectories.
- MOLDEN
http://www.cmbi.kun.nl/~schaft/molden/molden.html
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MOLDEN, originally developed to visualize results from quantum chemical calculations, has a powerful molecular editor for manipulating structures of both small molecules as well as biological macromolecules. Recent version has added docking capability. The program runs readily on SGI and Linux workstations but you need to have the X-Windows server in order to run it under Windows or MacOS