[phenixbb] Calculation of bond lengths, angles and torsion angle for large number of proteins

Ashraya Ravikumar ashrayar at gmail.com
Wed Jan 11 23:19:08 PST 2017

Hi Pavel,

Thanks a lot for your help. I have one question though. I noticed that all
the measures have been sorted by residual. Is there a way to order them
based on the residue number?


On Thu, Jan 12, 2017 at 12:10 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Ashraya,
> I would like to calculate all the bond lengths, bond angles and main chain
>> torsion angles for a large set of proteins, in PDB format. Could you please
>> let me know which module/command in phenix is suitable for this task?
> phenix.pdb_interpretation model.pdb write_geo_files=true
> this will write a file with full list of bond/angle/plane/torsion/etc
> definitions for the model you provide.
> Let me know if you have any questions.
> Pavel
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