Robert, Great point! My original script had selections from protein A to a ligand in any other protein B. I just left it in there.
I agree that creating a named selection for each object is unnecessary. If he really wanted a clean namespace, he could dump all of those into a group(s) or a multi-state object. Nice attention to detail, -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Sun, Nov 29, 2009 at 9:50 PM, Robert Campbell <robert.campb...@queensu.ca> wrote: > Hi Jason, > > On Sun, 29 Nov 2009 12:29:08 -0500, Jason Vertrees <jason.vertr...@gmail.com> > wrote: > >> You can automate the task. Load your 100 proteins. Use a wildcard >> from the command line or a script like loadDir >> (http://pymolwiki.org/index.php/LoadDir). Align them. Then, run: >> >> python >> for n in cmd.get_names("objects"): >> selName = "s" + n >> cmd.select(selName, n) >> cmd.distance("dist"+n, selName, selName + " and (organic and " + n + ")", >> 3.2, mode=2) >> python end > > I'm just curious, but why do you go to the trouble to create a selection that > is just the whole object? Especially if Chimed has 100s of objects, he > doesn't need to add a named selection for each. Why not do the following? > > python > for n in cmd.get_names("objects"): > cmd.distance("dist"+n,n,n + " and organic",3.2, mode=2) > python end > > The latter worked for me. If you wanted to eliminate waters from > the selection for the protein, you could change it to: > > python > for n in cmd.get_names("objects"): > cmd.distance("dist"+n,n + " and not solvent",n + " and organic",3.2,mode=2) > python end > > Or to make it more readable: > > python > for n in cmd.get_names("objects"): > protein_sele = n + " and not solvent" > organic_sele = n + " and organic" > cmd.distance("dist"+n, protein_sele, organic_sele, 3.2, mode=2) > python end > > Cheers, > Rob > -- > Robert L. Campbell, Ph.D. > Senior Research Associate/Adjunct Assistant Professor > Botterell Hall Rm 644 > Department of Biochemistry, Queen's University, > Kingston, ON K7L 3N6 Canada > Tel: 613-533-6821 Fax: 613-533-2497 > <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
