[Biopython] PBD SuperImpose

[Peter]

2009/8/28 Carlos Ríos 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
> ??

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