Bi1_2011_PyMOL_Tutorial

Bi1_2011_PyMOL_Tutorial - Bi1 2011 Introduction to Pymol...

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1 Bi1 2011 – Introduction to Pymol Pymol is a powerful open-source molecular graphics and analysis program developed by Warren Delano. The program is available for various platforms (Windows, MacOS, Linux) and is extensible with the programming language Python. Pymol allows a user to examine a molecular structure while creating high quality images and movies for publications and presentations. This tutorial will show the user how to install and navigate Pymol on either Windows or MacOS. Part I: Installation and Setup If Pymol is not already present on your computer you‟ll need to download the educational version from Pymol.org. The instructions to download the software will be provided by the TA separately. Do not use any other versions of Pymol you may find other than the one provided in Bi1. Download and uncompress the educational version of Pymol suitable for your operating system. Decompressing the file can be accomplished with WinZip (PC) or Stuffit Expander (Mac). If you have a recent operating system, extraction tools may be built into your file explorer. Follow the operating system specific directions on the website to install the program. Once installed, open the program. You should see two windows if you are on a Windows OS and a single window if you are using a Mac. Windows Interface
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2 Mac Interface Note: Though commands are given for 2 button systems, it is highly recommended that you use a mouse with a scroll wheel (especially if you are currently using a Mac or other laptop) to navigate a molecular structure without difficulty. Part II: Opening a Molecular Structure Structural data is contained in a world wide database called the Protein Data Bank (PDB). The collection consists largely of structures solved by crystallographic or NMR-based methods. For simplicity, we will focus primarily on the crystal structure of HIV-1 protease in complex with the inhibitor bea403 (PDB ID 1EC0). 1) First, navigate to the PDB: www.pdb.org 2) In the search box, type in the PDB ID code „1EC0.‟ You can also search by the protein name or any other identifier. Make sure you find the structure 1EC0 page, though. 3) Expand “Download Files” on the right toolbar by clicking on it. Save the PDB text file (see red arrow) to a known destination. 4) Open Pymol and expand the File menu. Click on Open and locate the file 1EC0.pdb. 5) If you are connected to the internet, you can go through the same process by opening Pymol and expanding the Plugin menu (if you do not see a Plugin menu, do not worry about this feature). Open the PDB Loader Service and enter the ID code „1EC0.‟ The structure should pop onto the screen. 6) Practice with other molecules until you feel comfortable opening them. Part III: Viewing and Manipulating the Structure
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Bi1_2011_PyMOL_Tutorial - Bi1 2011 Introduction to Pymol...

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