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

[João Rodrigues]

Hey Jordan,

Mind pasting that somewhere? I spent a few hours coding something like that
recently so it would be nice to compare !

Cheers,

João


2014-02-19 18:05 GMT+01:00 Willis, Jordan R <jordan.r.willis at vanderbilt.edu>
:

> I also have an example where I have one native and several models that
> needs an RMSD.
>
> It performs a multiple sequence alignment one at a time and iterates
> through the alignment file to do a one-to-one array of atoms in the
> sequence alignment before calculating a superposition. If the atoms do not
> match, they are thrown out of the alignment. Let me know if  you want to
> see this, it’s a bit complex.
>
> Jordan
>
>
>
>
> On Feb 19, 2014, at 10:47 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>
> > 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
> >
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>
>
>