Lab 1: Structural Analysis of HCAII using PyMOL
Lab 1 Objectives
This week you will use the molecular graphics program PyMOL to:
- Explore crystal structures downloaded from the Protein Data Bank (PDB)
- Examine the structure of the HCAII protein
- Determine which mutations you are interested in analyzing in lab this semester
Some of the mutations you choose this week will actually be made and tested this semester! Due to time and financial constraints, teaching team will generate a total of six mutant clones based upon the requests from the sections. Once the six mutants have been generated, you will be given one of the mutant clones to express, purify, and analyze. Each pod will work on one mutation so that each lab section analyzes all six.
The full version of PyMOL is available to UW students as a free download from this link (opens in a new tab): Campus Software Library
It is important that you download the full version through the provided link; DO NOT download the “Education Version” directly from PyMOL, which is available for free to everyone but does not include all the required functionality.
Be sure to download the appropriate version of PyMOL. For Mac users, there is only one option. For Windows users, you want PyMOL, not AxPyMOL, and 32-bit vs 64-bit depends on the version of Windows you have installed on your computer. Info from Windows can be found at this link (opens in a new tab): 32-bit and 64-bit Windows: FAQ
If downloading PyMOL v2.0 or later, you must also download the PyMOL License File (available from the same Campus Software Library website).
BEFORE COMING TO LAB make sure you can open PyMOL on your computer!! If you have trouble downloading or installing the software, contact DoIT directly.
Please bring a charger and, if possible, a mouse with you to lab as well.