PyMol
PyMol is a powerful open source molecule viewer program that looks quite promising. You can make avanced selections both through menus and a scripting language, you can generate beautiful raytraced images, and even build molecules. It is available for all Unix platforms, Windows and OS X.
- 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 IRIX. For OS X you can either download a binary program, or install it from source using fink and the Apple version of X11 (see the Pymol site for details).
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
RasMol
RasMol is a small, fast, and simple program that has become the standard for molecular visualization in many branches of science. It is the
easiest program to use when you just want to open up a PDB file and play around with the protein. However, to access many of it's more powerful
features you need to use the command line (see the manuals!), so many people prefer something else for more serious work.
Here we have included links to Rasmol version 2.6. To download the latest version (2.7.2.1) see the Rasmol Home Page.
SwissPDBViewer
SwissPDBViewer is a very nice and full featured molecular visualization tool, that has extensive menus and can be much more intuitive to use
than RasMol for complicated operations. However, it also suffers from the fact that when using rendering (ie making things look pretty), it can
become quite slow.
Parsing the PDB
- PdbToSql.pl
- Author: Stefan Larson
- This 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).
Problems? Questions about the Page or the Class? Contact us