SB228 Programs


PyMol is a powerful open source molecule viewer program that looks quite promising. You can make advanced selections both through menus and a scripting language, you can generate beautiful raytraced images, and even build molecules. The learning curve for pymol is initially pretty steep, but once you get the hang of it you will find it is easy to use and very powerful. Pymol's best feature is it's ability to create very high-quality ray-traced graphics. It is available for all Unix platforms, Windows and OS X. Do search for pymol tutorials on the web. When you are exporting pictures to use with your web pages we recommend using a white background.
Check out the pymol wiki, or some suggested settings: pymol tips (Mike Syke's Page).


VMD stands for Visual Molecular Dynamics. As such it is a molecular graphics program designed specifically for people who do simulations. Although VMD's graphics are sub-par compared to Pymol's you can look at trajectories and do various analyses (RMSD plots, Multiple Sequence Alignments, Pair Correlation Functions, etc.) from right in the software.

We have made a VMD Tutorial for this class. It is basically an updated version of the tutorial that can be found at the VMD website. Also, searching the VMD website will reveal other useful tutorials on advanced topics with VMD.


SwissPDBViewer (also known as Deepview) is another Molecular Graphics program that you may want to consider. Although the graphics are inferior to both VMD and Pymol, SwissPDB does include some features that can be useful. In particular, SwissPDB has a number of tools for molecular modelling. It can easily mutate residues, join and break protein chains, and even minimize structures. Also, SwissPDB viewer includes an interface that connects directly to the SWISS Model web serfer for homology modelling.

SwissPDV runs on Windows, Mac, and Linux although not all of the binaries are still actively developed.

Parsing the PDB

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