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

[João Rodrigues]

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>).

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.

Cheers,

João


2014-01-16 13:18 GMT+01:00 Jurgens de Bruin <debruinjj at gmail.com>:

> Hi João Rodrigues,
>
> Thanks for the reply much appreciated, this does make sense but I would
> greatly appreciate examples with some code.
>
> Thanks
>
>
> On 16 January 2014 13:59, João Rodrigues <anaryin at gmail.com> wrote:
>
>> Hi Jurgens,
>>
>> When you pass the two sequences to the Superimposer I guess you can trim
>> the sequence to that which you want (pass a list of residues that is sliced
>> to those that you want to include). The only requirement would be that both
>> have the same number of atoms.
>>
>> If this doesn't make much sense I can give an example with code.
>>
>> Cheers,
>>
>> João
>>
>>
>>  2014/1/16 Jurgens de Bruin <debruinjj at gmail.com>
>>
>>>  Hi,
>>>
>>> I am trying to calculate the RMS for two pdb files but the proteins
>>> differ
>>> in length. Currently I want to exclude the leading/trailing parts of the
>>> longer sequence but I am having difficulty figuring out how I will be
>>> able
>>> to do this.
>>>
>>> Any help would be appreciated.
>>>
>>>
>>> --
>>> Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
>>> distinti saluti/siong/duì yú/привет
>>>
>>> Jurgens de Bruin
>>>
>>> _______________________________________________
>>> Biopython mailing list  -  Biopython at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biopython
>>>
>>
>>
>
>
> --
> Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
> distinti saluti/siong/duì yú/привет
>
> Jurgens de Bruin
>