[BioPython] Bio.PDB for RMSD structure alignment
Peter
biopython at maubp.freeserve.co.uk
Fri Jan 19 14:01:56 UTC 2007
There is some code in Bio.PDB for superimposing two protein structures
by minimising the RMSD using singular value decomposition.
This seems to use a StructureAlignment object (created using a two
aligned sequences) as input to a Superimposer object, which in turn
calls Bio.SVDSuperimposer.SVDSuperimposer
Does anyone have an example script that puts this all together?
i.e. Starting from two PDB files (or mmCIF files) and a pairwise
sequence alignment, rotate the second structure to overlay the first
(minimizing the RMSD calculated using the residue mapping from the
sequence alignment), and save the rotated structure to a PDB file.
Thanks
Peter
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