[Biopython] clustering pdb

[Peter]

On Mon, Jul 19, 2010 at 10:59 AM, Bala subramanian
<bala.biophysics at gmail.com> wrote:
> Hello peter,
> Sorry for the incomplete information. I want to cluster the structures say
> for example using rmsd between the pdb.
>
> Thanks,
> Bala

Provided you can specify the atomic mapping between the structures,
you can calculate RMSD using Bio.PDB, see for example:
http://www.warwick.ac.uk/go/peter_cock/python/protein_superposition/
One way to do this would be pairwise sequence alignments. There
are probably specialised tools out there for this sort of clustering...

Peter

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