using_Chimera

using_Chimera - Using UCSF Chimera D. Belnap UCSF Chimera...

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October 8, 2009 1 Using UCSF Chimera D. Belnap UCSF Chimera (Chimera, www.cgl.ucsf.edu/chimera) is a freely available program for viewing, manipulating, and analyzing molecular coordinates and densities. Below are instructions for basic operations. See "Help" (below) if you want to use other features. 1. Options for opening a coordinate file a. download a PDB file (.pdb) from the Protein Data Bank, open with "File", "Open" b. "File", "Fetch by ID", enter PDB identification number and Chimera will retrieve 2. To select a molecule or macromolecular complex a. "Select", "Chain" to select a specific polypeptide chain b. "Select", "Select All" to select all parts of all molecules c. Select a small region with Ctrl + mouse button 1 (drag mouse) d. "Select", "Residue", "HOH" to select water molecules, if present (note: some versions of Chimera or some structures may allow selection via "Select", "Chain") e. To select from sequence, see "View Sequence" below f. See other selection options under "Select" menu g. "Select", "Clear Selection" will deselect the current selection h. "Select", "Undo" will set selection to previous selection 3. Form of molecular display , select molecule or part of molecule then, a. "Actions", "Atoms/Bonds", see various options, (e.g. "backbone only", "chain trace" gives C α atoms only and a connecting line between them)
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This note was uploaded on 03/08/2012 for the course CHEM 391 taught by Professor Vollmer-snarr,h during the Winter '08 term at BYU.

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using_Chimera - Using UCSF Chimera D. Belnap UCSF Chimera...

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