[BioPython] Alternate Conformations in PDB

[thamelry at binf.ku.dk]

> How does the PDB module deal with alternate conformations?  It appears
> to me that it is completely ignoring them, at least in the polypeptide
> builder.

Bio.PDB's representation of alternate conformation is actually quite
sophisticated IMO (it can even deal with point mutations, ie. for
example a Ser and a Pro residue in the same position).

OTOH CaPPBuilder indeed breaks the chain if it finds a disordered
CA atom, which is a bit questionable, especially since
PPBuilder does take disorder into account. So I'll submit a more
sophisticated version of CaPPBuilder to CVS today.

Best regards,

-Thomas