BMB170a_2011_Pymol_Manual

BMB170a_2011_Pymol_Manual - BMB170A Introduction to Pymol...

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1 BMB170A – 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 it from the course website: http://saf.bio.caltech.edu/bi170a/ Alternatively, you can obtain it from http://pymol.org/ep . The login name is ‘dec2010’ and the password is ‘mol2View.’ If for any reason you cannot access this website or the login process does not work, register to download pymol using a valid email address from http://pymol.org/educational/ . Download the version of Pymol suitable for your operating system. You may have to decompressing the file using WinZip (PC) or Stuffit Expander (Mac). If you have a recent operating system, extraction tools may be built into your file explorer. Installation should be straightforward on either a Windows or Mac. 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 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.
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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, not the 1ECO page. 3) Expand “Display Files” on the right side of the page 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 and are using Windows, you can open files faster 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. You can also used the fetch command (i.e. ‘fetch 1EC0’). 6) Practice with other molecules until you feel comfortable opening them.
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BMB170a_2011_Pymol_Manual - BMB170A Introduction to Pymol...

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