[Biopython-dev] superimposition question

[Peter]

On Tue, Dec 7, 2010 at 5:27 PM, George Devaniranjan  wrote:
> Hello everyone,
>
> Suppose I wan to see the conformational variation in protein loops and
> extracted say 2 loops of same length and want to superimpose the 1st and
> last resiude (say like clamp them together like pivots) how will I go about
> doing that? I can use the superimposer and superimpose based on either the
> 1st/last residue calculate the rot/tran then apply to the entire molecule
> but don't know how I could do it for say the 1st and last while the
> intermediate loops are not superimposed but are free moving?
>
> Thanks for your help and sorry if its written in a slightly confusing
> manner.

Hello George,

This kind of end user query would be better off asked on the main
Biopython mailing list, rather than the Biopython development list
(which is for discussing changes to Biopython itself).
http://lists.open-bio.org/mailman/listinfo/biopython

Could re-ask the question there? If you can give an actual
example (e.g. two PDB identifiers, and which residues you
are trying to align) it would probably be clearer.

Thanks,

Peter

P.S. Have you looked at this example?
http://www.warwick.ac.uk/go/peter_cock/python/protein_superposition/