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Hi Rex, > I would like to specify a target atom in a pdb file and then isolate all > atoms within a given distance of the target. The selected atoms are then to > be placed in a new pdb file. > Any suggestions please. This is simple to do in PyMOL. After loading your structure just use the mouse to select your target atom. After that, on the PyMOL command line type, select all within 5 of (sele) That will quickly identify those atoms within 5 Angstroms of your selection. For more help check out the PyMOLWiki (http://pymolwiki.org) especially selections (http://www.pymolwiki.org/index.php/Selection_Algebra). Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) [log in to unmask] (o) +1 (603) 374-7120