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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 Introduction: This molecular graphics 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. PyMOL 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: Basic Features: 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 Tutorial Exercises: 1. Myoglobin 2. Ebola Virus 3. Antibody Fragment Binding to a piece of HIV-Protease Tutorial: 1. Insert the PyMOL CD. To open: Windows : 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. Macs : Double click on MacPyMOL.tar.gz. The MacPyMOL application icon will be created on your desktop. Drag this icon to your applications folder . 2. 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 1 Be sure to modify as per modified LG Tutorial!
Menus There are two menus: 1) The ones at the very top of your screen are the main program menus. These can be used to open and close structure files, and perform general commands. 2) The other important menus are located at the right of the PyMOL program in the long rectangle. 3. We will now examine how to use the menus on the right: There are six buttons in a row; one long rectangular button followed by five small square buttons labeled • The first one is a label naming what you want to manipulate. For example, when it says “all”, that means you will manipulate every part of the molecule that is open. When it says “<sele>”, you will manipulate only what is selected (more about 'selecting' below). • The next five buttons allow you to manipulate the protein or parts of the protein depending on which menu button you choose: A ≡ Actions. With this menu, you can perform general actions such as adding or removing hydrogens, or
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