Calculation of bond lengths, angles and torsion angle for large number of proteins
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Hi All, 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? Regards, Ashraya
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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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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?
Regards,
Ashraya
On Thu, Jan 12, 2017 at 12:10 PM, Pavel Afonine
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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No.
On Jan 11, 2017 11:19 PM, "Ashraya Ravikumar"
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?
Regards, Ashraya
On Thu, Jan 12, 2017 at 12:10 PM, Pavel Afonine
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
participants (2)
-
Ashraya Ravikumar
-
Pavel Afonine