The modeling software to be used in this class is called PyMOL. It uses a file of atomic coordinates to generate an interactive model on your computer screen. The raw files are in the "Protein Data Bank" format and have a suffix *.pdb. In this class, you will generally be given a file that has been manipulated for easy viewing - and they will have the suffix *.pse.

Installation

PyMOL software is available as a free download to students. There are versions for Mac, PC and Linux. For Mac users, I recommend the "MacPyMOL" version. Also, if you are a Mac user, I strongly recommend getting a three-button mouse or a two-button mouse with a scroll wheel.

Note for people without computers: PyMOL is installed in the Chemistry Computer Lab (room 205).

Resources

Hopefully each assignment will provide you with the necessary information to complete it. However, PyMOL is a very powerful package, and there's much more thaat you can do with it than we'll cover this semester. If you're the type of person who likes clicking buttons to see what happens, take a look at the following sources of information:

PyMOLWiki: User-maintained encyclopedia of commands and tricks

Users Manual: Pretty out of date, but a good source of basic information.