[Biopython] clustering pdb

[Christian Schaefer]

On 07/19/2010 12:07 PM, Peter wrote:
> 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...

Thanks Peter for that. I didn't know that Biopython provides 
superimpositioning of two pdb structures. I'd need that badly for my 
current project, and I used ProFit [1] so far. A native python 
implementation is of course very convenient in my case.

Chris

[1] http://www.bioinf.org.uk/

-- 
Dipl.-Bioinf. Christian Schaefer
Technical University Munich
Department for Bioinformatics
Faculty of Computer Science/I12
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http://www.rostlab.org/~schaefer