Welcome to the PyMOL Tutorial!
Written by Jae Woo Choi, Wayne Gui, Trevor Halle, Mohamed Khattab, Priya Malhotra, Dmitriy
Migdalovich, Cina Sasannejad, Seung Youn Shin, Rob Tirrell, and Jerry Feigenson
part of the biochemistry course will give you the power to examine the structure
of many thousands of molecules-- large polymers such as HIV protease, DNA, and RNA, and small
molecules such as estradiol, iboprofen, and ATP.
is a software program used to display and examine 3-D representations of biomolecules. Why the
name PyMOL? It was written in the Python programming language.
Though not required for this class, you
can learn more about PyMOL at the website, http://PyMOL.sourceforge.net/newman/user/toc.html
Table of Contents:
1. Set-Up (Inserting PyMOL CD, Unzipping Files)
2. Introduction to Menus (Interface)
3. Menu Buttons
4. Reading Directions in PyMOL, Help, and Wiki
5. Using the Mouse (Windows, Mac)
6. Building Polypeptides
2. Ebola Virus
3. Antibody Fragment Binding to a piece of HIV-Protease
Insert the PyMOL CD.
Unzip the file WindowsPyMOL.zip, then double click on SETUP.exe, then to open the
application, click on "PyMOL + Tcl-Tk GUI" wherever it has been installed.
Note that older
versions of WinZip might not work easily. If the program does not seem to start, restarting your
computer may fix the problem.
Double click on MacPyMOL.tar.gz. The MacPyMOL application icon will be created on your desktop.
Drag this icon to your applications folder
In order to get a simple screen to start this tutorial: From the menu at the very top of the screen,
choose Build > Residue > Alanine
Be sure to modify as per
modified LG Tutorial!