Hi, * Michael George Lerner <mler...@umich.edu> [2005-07-06 09:28] wrote: > <with my editing to put the original e-mail in the correct location>
> On Wed, 6 Jul 2005, Sebastien Gerega wrote: > > >Is there a way to list the residues that are in a selection? For example > >if I use the command "select near, sel01 around 6" how can I obtain a list > >of the residues in the "near" selection? > > I asked a similar question a while ago, and Kristan Rother archived the > answer at <http://www.rubor.de/bioinf/tips_python.html#insel>. Here it > is: > > Using PyMOL commands: > > list=[] > iterate (name ca),list.append((resi,resn)) > print list > > [('ASP', '1'), ('CYS', '2'), ('ALA', '3'), ('TRP', '4'), ('HIS', '5'), > ('LEU', > '6'), ('GLY', '7'), ('GLU', '8'), ('LEU', '9'), ('VAL', '10'), ('TRP', > '11'), > ('CYS', '12'), ('THR', '13')] > > or using a Python script (in PyMOL): > > from pymol import cmd,stored > stored.list=[] > cmd.iterate("(name ca)","stored.list.append((resi,resn))") > print stored.list > > [('1', 'ASP'), ('2', 'CYS'), ('3', 'ALA'), ('4', 'TRP'), ('5', 'HIS'), > ('6', ' > LEU'), ('7', 'GLY'), ('8', 'GLU'), ('9', 'LEU'), ('10', 'VAL'), ('11', > 'TRP'), > ('12', 'CYS'), ('13', 'THR')] Or as a variation on the first method, you don't need to make the list, just do (using the original questions selection "near": iterate near, print resi,resn,name (to get all atoms) or iterate near & n. ca, print resi,resn (for just the alpha-carbons, though if the "near" selection wasn't created with the "byres" option, then some residues in the selection may not have a CA included) Cheers, Rob -- Robert L. Campbell, Ph.D. <r...@post.queensu.ca> Senior Research Associate phone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
