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
- Since PyMol is in rapid development, we prefer not to maintain a local copy. Check out pymol.sourceforge.net
instead! There are currently binaries for Linux, Windows and and OSX.
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.
- You can download a copy of VMD at the UIUC Theoretical Biophysics Group webpage. It works on Windows, Linux, and OSX. It is free, but in order to get a copy you need to give them your email address so they can give you a password and username. VMD is a bit easier to pick up than Pymol which is good for a beginner, but it is worth learning both VMD and Pymol so you can take advantage of the relative strengths of each.
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
- Author: Stefan Larson
is a simple Perl script which is designed to read in PDB files and then
output their sequence in one letter code FASTA format files. Simply
type in "./PdbToSql.pl" at the prompt on a Unix machine, and it will
ask for the name of the pdb file, outputting the sequence. Users of Mac
OS 9 and below may need to visit MacPerl.com to use this, or simply install it in your home
directory on any unix machine (like the Stanford servers).
Although this may be useful for scripting purposes, it is worth mentioning that each of the above listed molecular graphics packages can display the pdb as a linear amino acid sequence.
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