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:ccp...@jiscmail.ac.uk] On Behalf Of
Gerard DVD Kleywegt
Sent: Friday, February 26, 2010 10:50 AM
To: CCP4BB@JISCMAIL.AC.UK
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:ger...@xray.bmc.uu.se
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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:ger...@xray.bmc.uu.se
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