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
