Dimitry, cmd.align returns a list of numbers, the first of which is the final RMS value for atoms in the final cycle of alignment. You can of course use that result in a script.
Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -----Original Message----- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of DimitryASuplatov Sent: Wednesday, September 03, 2008 1:13 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Script for iterated `align`ment Hello, with your help I was able to write the following script to automatically load 21 structure and align 20 of them to the remaining one. ************************************************* import os import re from os.path import join, getsize cmd.delete(all) p = re.compile('[A-Za-z\.]*pdb') w = re.compile('nowater') for root, dirs, files in os.walk('./'): for file in files: <------>if p.search(file) and w.search(file): <------> cmd.load(file) cmd.delete('1gk9*') cmd.fetch('1gk9') for file1 in files: <------>if p.search(file1) and w.search(file1): <------> if re.search('1gk9', file1): <------><------>continue <------> pdb = re.search('(.+)\.pdb', file1) <------> print pdb.group(1), ' and 1gk9' <------> cmd.align(pdb.group(1) , '1gk9') ************************************************* The problem is that I see only the result - aligned structures. But I want to see the RMSD values and apply them to scrip variables. Is that possible? Thank you. ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
