[Biopython-dev] superimposition question

[George Devaniranjan]

Sorry guys, I will repost in the correct one with 2 examples.
Thanks
George

On Tue, Dec 7, 2010 at 2:59 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> 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/
>