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
> Hey Thomas,
>
> if you want to use align anyway, make sure to use the quite=0 option.
> The "quiet" option (if present) is set to zero by default for parsed
> PyMOL commands, but is not set for Python API calls.
>
> align
> is nearly equal to
> cmd.align(quiet=0)
>
> Thus, if you want to get rmsd output, include quiet=0 and run your
> script with output redirection.
>
>
> Andreas
>
>
>
> On Thu, Oct 29, 2009 at 2:48 AM, Thomas Evangelidis
> <te8...@mbg.duth.gr> wrote:
>> Simple question, it must have been answered before but couldn't find
>> it so far:
>>
>> how can I get the RMSD value from the align command in a python
>> script? cmd.align() returnes a tuple of 8 numbers and none of them is
>> the actual RMSD value I get when I align these 2 structures manually.
>>
>> thanks,Tom
>>
>>
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