Re: [Biopython] Conformation assignment

João Rodrigues <[email protected]> Wed, 16 Sep 2020 10:11:20 -0700

Newsgroups	gmane.comp.python.bio.general
Message-ID	<CAB=-b2YVDpOtwmCb+35SvXm61RKU_7i+7ZpoN6j-PCv_SvE9FQ@mail.gmail.com>

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
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