From: Jason V. <jas...@gm...> - 2009-10-30 21:50:57
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> Message: 6 > Date: Thu, 29 Oct 2009 13:40:56 +0200 > From: Thomas Evangelidis <te...@mb...> > Subject: Re: [PyMOL] how to get RMSD from CEalign command > To: Andreas Forster <doc...@gm...> > Cc: pym...@li... > Message-ID: <200...@we...> > Content-Type: text/plain; charset=ISO-8859-7; DelSp="Yes"; > format="flowed" > > Thank you Adnreas. > > I'm straggling with cealign now. When I run it in batch mode I get > "Selector-Error: Invalid selection name" for certain structures, which > in fact are very close homologs, whereas the number of RMSD values I > get varies (sometimes 3, 5, etc). Here's the code: > > 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) > cmd.fetch(template) > print "Superimposing ", query, " onto ", template > cmd.do("cealign "+query+" and c. A, "+template+" and c. A") > cmd.delete(query) > cmd.delete(template) > > Do you know what's wrong? > > Thomas 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 PyMOLWiki -- http://www.pymolwiki.org |
From: Thomas E. <te...@mb...> - 2009-10-31 14:11:48
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> 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 |
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 > > |
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... ----- |