From: Jason V. <jas...@gm...> - 2009-11-01 04:23:25
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Thomas, The command cmd.do(".../cealign.py") runs cealign.py, which runs cmd.extend. So you should have the cealign command in your namespace after the cmd.do. Have you tried running cmd.do("your/path/to/cealign") cealign(protA, protB)? I just tried this on my system and it worked for me. Let me know if it works for you. -- J Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org 2009/10/31 Thomas Evangelidis <te...@mb...>: > >> Thomas, >> >> The PyMOL UI runs asynchronously. I think you are deleting your PDB >> files before they can be aligned. I made a couple changes in your >> script. Instead of calling cmd.do just call cealign directly. See >> below, >> >> query_template_chains = { >> "1ebh" : ["1ebg", "1els", "1one", "2one", >> "5enl", "6enl", "7enl"] >> } >> >> for query in query_template_chains.keys(): >> for template in query_template_chains[query]: >> cmd.fetch(query, async=0) >> cmd.fetch(template, async=0) >> print "Superimposing ", query, " onto ", template >> cealign( query+" and c. A", template+" and c. A") >> cmd.delete(query) >> cmd.delete(template) >> >> Hope this helps, >> >> -- Jason >> >> Jason Vertrees, PhD > > Jason, > > I can't run cealign() from a script: > > NameError: global name 'cealign' is not defined > > I installed pymol from Fedora repositories and can't find .pymolrc, > therefore I load CEalig in my script like this: > > cmd.do("run /home/thomas/Documents/cealign-0.9/cealign.py") # load CEalign > plugin > cmd.do("run /home/thomas/Documents/cealign-0.9/qkabsch.py") > > The only way to run CEalign is using cmd.do(). > > Thomas > > And of > > |