UW-Madison BIOCHEM 660 - Desktop Molecular Graphics PyMol 1 (42 pages)

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Desktop Molecular Graphics PyMol 1



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Desktop Molecular Graphics PyMol 1

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Pages:
42
School:
University of Wisconsin, Madison
Course:
Biochem 660 - Biochemical Techniques

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Biochem 660 2008 L01 Desktop Molecular Graphics PyMol 1 From the preface of the User s guide PyMOL was created in an efficient but highly pragmatic manner with heavy emphasis on delivering powerful features to end users Expediency has almost always taken precedence over elegance and adherence to established software development practices is inconsistent PyMOL is about getting the job done now as fast as possible by whatever means were available PyMol is a multiplatform molecular graphics software with many advanced features such as rendered cartoon ribbons and surfaces internal ray tracing and movie tools and is fast becoming the new standard in molecular graphics The PyMol web site is located at http pymol sourceforge net Biochemistry students can download the latest PyMol version from a campus network at http www biochem wisc edu it resources aspx Note within the exercises Bold text shows what actions are taken by the user typing text or clicking the mouse Whenever possible a call for action icon or will be shown e 1 PyMol Exercise A Download a PDB from the repository Reminder Structures have a PDB ID code made of 4 letters and numbers PDB files contain coordinates pertinent to the crystallographic arrangement of the molecules within the crystal The biological functional entity can be either a multimer of the deposited structure or just one of multiple copies within the file In the following example we will download one functional biological subunit in this case a monomer TASK Open a web browser such as Safari or Firefox Point your web browser to www rcsb org In the Search box enter the following ID 2biw and click SEARCH button PyMol 1 39 On the left column click Download Files to show submenus Click the first option Biological UnitCoordinates 2 Note DO NOT USE Biological Unit Coordinates 1 The file is saved on the desktop as 2BIW pdb2 Note The file might be delivered as a gunzipped gz file However the browser should decode it automatically You can now close your



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