> Message: 6
> Date: Thu, 29 Oct 2009 13:40:56 +0200
> From: Thomas Evangelidis <te8...@mbg.duth.gr>
> Subject: Re: [PyMOL] how to get RMSD from CEalign command
> To: Andreas Forster <docandr...@gmail.com>
> Cc: pymol-users@lists.sourceforge.net
> Message-ID: <20091029134056.136077awqo817...@webmail.duth.gr>
> 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
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