[Chimera-users] Adding rotamers programmatically
pett at cgl.ucsf.edu
Wed Jun 27 14:34:01 PDT 2018
I don’t know how familiar you are with Chimera programming, but I’m going to assume you have a residue you want to add the rotamers to in a Python variable named r. If so, the code to add all its rotamers as altlocs is:
from Rotamers import useRotamer, getRotamers
useRotamer(r, getRotamers(r), retain=[‘’])
The retain=[‘’] argument will cause the original sidechain position to be retained (assuming it itself is not an altloc). If you need help finding the residues you want to work on in Python, let me know.
UCSF Computer Graphics Lab
> On Jun 27, 2018, at 10:42 AM, Ahir Pushpanath <ahir29 at gmail.com> wrote:
> Dear Chimera Team/Users,
> I wanted to write a python script within chimera that aims to essentially print out a contact map of a selected chunk of residues on an open structure. However, before doing so, I wondered if there is any programmatic way to generate the rotamer library at every position (i.e when you open up the rotamer tool, you get an option of 5-6 conformations you can pick for a residue), I wanted to generate that for every residue in the protein programmatically (and save every rotamer possibility) (as an altlocation?) in the crystal structure. Only after that do I want to calculate the contact map, in essence, I am trying to be as expansive as possible for each residue's "possible" contacts with any other, taking into account the full rotamer ensemble. Any tips on how to manage this programmatically?
> Dr. Ahir Pushpanath PhD.
> Senior Biologist,
> Johnson Matthey.
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