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 <te8...@mbg.duth.gr>:
>
>> 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
>
>
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