[Biopython] PBD SuperImpose

[Eric Talevich]

>
> 2009/8/28 Carlos R?os Vera <crosvera at gmail.com>:
> > Hello people,
> >
> > I'm trying to use the superimpose() method from the Bio.PBD module, but
> when
> > I use the set_atoms() method with two atoms list, I got this:
> >
> > "Bio.PDB.PDBExceptions.PDBException: Fixed and moving atom lists differ
> in
> > size"
> >
> > So, my question is: How can I superimpose to structures with different
> size
> > ??


Peter <biopython at maubp.freeserve.co.uk>:

>
> This sounds more like a methodology question than a Python
> question.
>
> You must decide how to map between the atoms of one chain and
> the atoms of the other. If they are different lengths, you will need
> to exclude some residues (e.g. peptide GHIL versus EGHILD, you
> would probably ignore the extra trailing/leading residues on the
> longer sequence).
>
> If in addition the residues are (at least in some cases) different
> amino acids, then you will probably only want to calculate the
> superposition using the backbone (or even just the C alpha
> atoms).
>
> One approach to this is to base the atomic mapping on a
> pairwise protein sequence alignment.
>
> Peter
>
>
If you're trying to align the structures of two different proteins, or two
different structures of the same protein, you might want to try MultiProt:

http://bioinfo3d.cs.tau.ac.il/MultiProt/

It can handle more than two proteins at a time, too. (If that's overkill,
then +1 for Peter's approach.)

Eric