No, there would still be an order involved. I think she wants to superimpose
two small molecules with arbitrary atom names. So she needs a subgraph
isomorphism detector without constraints on the labels and ordering of the
vertices (atoms), but which is not scale-free (as we want low RMSDs as opposed
to mere topological equivalence). But I'm just guessing.
--Gerard
On Fri, 26 Feb 2010, Soisson, Stephen M wrote:
> 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]
> ******************************************************************
> The opinions in this message are fictional. Any similarity
> to actual opinions, living or dead, is purely coincidental.
> ******************************************************************
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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.
******************************************************************
