Perhaps supcomb could do this:
http://www.embl-hamburg.de/ExternalInfo/Research/Sax/supcomb.html
Quoting Gerard DVD Kleywegt <[log in to unmask]>:
> 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]
> ******************************************************************
> The opinions in this message are fictional. Any similarity
> to actual opinions, living or dead, is purely coincidental.
> ******************************************************************
>
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