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

[Willis, Jordan R]

This will calculate an all_atom_RMSD, c-alpha and backbone atom rmd. I took out all the extra stuff specific to the Rosetta community that will actually score the file too. But this is generalized

scoreimposer_align.py -n native.pdb -m *.pdbs

-m is the multiprocess flag (requires python2.7)

https://gist.github.com/jwillis0720/9097426

Jordan

On Feb 19, 2014, at 11:07 AM, João Rodrigues <anaryin at gmail.com<mailto:anaryin at gmail.com>> wrote:

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<mailto: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<mailto:p.j.a.cock at googlemail.com>> wrote:

> On Wed, Feb 19, 2014 at 4:42 PM, João Rodrigues <anaryin at gmail.com<mailto: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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