From: Thomas E. <te...@mb...> - 2009-11-01 22:41:20
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No it doesn't, both in Fedora 11 and Ubuntu 9.04. I get: NameError: global name 'cealign' is not defined Thomas > 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 >> >> > ----- End message from jas...@gm... ----- |