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
  • Propose HCAII mutations that you find scientifically interesting


NOTE: This lab requires you to install PyMOL on your computer.


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 LAB BEGINS make sure you can open PyMOL on your computer!! If you have trouble downloading or installing the software, contact DoIT directly.

It is helpful to use PyMOL with a mouse (rather than a laptop trackpad) if possible.


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Biochemistry 551 (Online Version) Lab Manual Copyright © by Lynne PROST is licensed under a Creative Commons Attribution 4.0 International License, except where otherwise noted.

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