[Biopython] Bio.PDB.PDBParser() Superimposer()

[Peter Cock]

On Wed, Feb 19, 2014 at 4:42 PM, João Rodrigues <anaryin at gmail.com> wrote:
> Hi Jurgens,
>
> Sorry for the delay.. hope it still goes on time.
>
> If the numbering of the two proteins is the same (equivalent residues have
> equivalent residue numbers), usually the case if you compare different
> models generated by simulation, then it is straightforward to trim them (check
> this gist <https://gist.github.com/JoaoRodrigues/9095892>).

Here's a slightly more complex example picking out a stable core
for the alignment (ignoring variable loops):
http://www.warwick.ac.uk/go/peter_cock/python/protein_superposition/

> Otherwise you have to perform a sequence alignment and parse the alignment
> to extract the equivalent atoms and do the same logic as before (this is
> quite tricky..). I have a script that does this but it's not trivial at all
> and might be extremely specific for your application.

Yes. Fiddly.

Peter