Re: [Biopython] Conformation assignment

Navid Shervani-Tabar <[email protected]> Wed, 16 Sep 2020 13:12:41 -0400

Newsgroups	gmane.comp.python.bio.general
Message-ID	<CAAaLMm0nA=TuumSMiVpMeovYZe6=v82N=sW3wABdWkovYmycsw@mail.gmail.com>

Thanks João!

Best,
Navid

On Wed, Sep 16, 2020 at 1:11 PM João Rodrigues <
[email protected]> wrote:

> Dear Navid,
>
> Biopython does include parsers for trajectories, nor are our data
> structures appropriate for that type of data. I'd recommend MDanalysis or
> mdtraj for that! You can always dump frames in pdb and then parse with
> Biopython.
>
> Cheers,
>
> João
>
> A quarta, 16/09/2020, 09:35, Navid Shervani-Tabar <[email protected]>
> escreveu:
>
>> Dear biopython experts,
>>
>> I have a trajectory of alanine dipeptide molecule (from
>> https://markovmodel.github.io/mdshare/ALA2/#alanine-dipeptide) and would
>> like to save the conformation label (alpha_L, alpha_R, beta, etc) at each
>> timestep. I was wondering if biopython can do this. I have two files
>> available: 1) .pdb file and 2) .xtc file. Thanks!
>>
>> Best,
>> Navid
>> _______________________________________________
>> Biopython mailing list  -  [email protected]
>> https://mailman.open-bio.org/mailman/listinfo/biopython
>
>

_______________________________________________
Biopython mailing list  -  [email protected]
https://mailman.open-bio.org/mailman/listinfo/biopython