Dear Sreetama,
I use an ancient superposition program which rejects all atom pairs deviating
more than 3 sigma and repeats this procedure until convergence. It then reports
the RMSD for all atoms and for the atoms deviating less than 3 sigma. I find
this an excellent method to separate the
I think PISA does this for you - it overlaps structural features and gives
an RMSD on those parts that fit and a useful list of matching residues.
You can run it from CCP4I or at PDBe.
If you ant more than CA RMSD then you will need to select out the spans to
fit and use the LSQKAB overlap
It is probably Gesamt/SSM (Superpose in CCP4), or PDBeFold at EBI rather than
PISA -- Eugene
On 13 Aug 2014, at 12:33, Eleanor Dodson wrote:
I think PISA does this for you - it overlaps structural features and gives an
RMSD on those parts that fit and a useful list of matching residues.
You
Thanks to the mailing list I came across this:
http://www.ncbi.nlm.nih.gov/pubmed/24167157
The C code to compute is available on the link mentioned in the paper.
Best wishes,
George
On Wed, Aug 13, 2014 at 8:01 AM, Eugene Krissinel
eugene.krissi...@stfc.ac.uk wrote:
It is probably
