One option would be molrep
molrep -m <model1> -mx <model2>
Of course it assumes that your two structures have overall similar
structures and no substantial conformational changes.
As the question posed, I think, it does not have solution (only
approximations). Almost all programs assume either atom labeling or
shape similarity (molrep assumes shape similarity).
If you have connectivity and the number of atoms is small then graph
matching would work fine (at least it would give correspondence
between atoms and then it is just matter of calculating rotation
matrix and applying it)
Garib
On 26 Feb 2010, at 15:11, 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
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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
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