Would a simple hack, like renaming all of the atoms in each file to be
'CA' and then using a conventional alignment program work? Maybe I am
caffeine deficient at the moment, but that seems worth trying.
Steve
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
Gerard DVD Kleywegt
Sent: Friday, February 26, 2010 10:50 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] 3D fitting
But it still won't solve Miri's problem. I think what she is asking for
is a
program that detects which atoms should be matched to which,
irrespective of
their names (i.e., not assuming they are called " CA ") and order (i.e.,
not
nicely sequential such as amino-acid residues), and then applies the
operator
that follows from that.
--dvd
On Fri, 26 Feb 2010, Kevin Cowtan wrote:
> SSM is also available in Coot and CCP4MG of course...
>
>
> Eleanor Dodson wrote:
>> would ssm serve your purpose?
>>
>> eleanor
>>
>> ebi or ccp4i
>>
>>
>>
>> Miri Hirshberg wrote:
>>> Sun., Jan. 17th 2010
>>> EBI
>>>
>>> Greetings,
>>>
>>> I am looking for a 3D structure superposition program which takes
>>> two structures and superpose them based only on the coordinates
X,Y,Z
>>> regardless of of residue/atoms name.
>>>
>>> (both files are in PDB format)
>>>
>>> Thanks
>>> Miri
>>>
>>> ------------------------------------
>>> Dr Miri Hirshberg
>>> European Bioinformatics Institute UK
>>> PDBe - EBI -EMBL
>>> http://www.ebi.ac.uk/pdbe
>>>
>>> Phone: +44 (0) 1223 492647
>>> FAX: +44 (0) 1223 494468
>>> ------------------------------------
>
Best wishes,
--Gerard
******************************************************************
Gerard J. Kleywegt
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:[log in to unmask]
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