Re: [PyMOL] how to get RMSD from CEalign command

[Thomas E. <te...@mb...>]

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  
> <te...@mb...> 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
>>
>>
>> ------------------------------------------------------------------------------
>> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
>> is the only developer event you need to attend this year. Jumpstart your
>> developing skills, take BlackBerry mobile applications to market and stay
>> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
>> http://p.sf.net/sfu/devconference
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>


----- End message from doc...@gm... -----