Hi Noé, To get the rotamer list specifically for residue :3.a, the code would be: from chimera.specifier import evalSpec from Rotamers import getRotamers for r in evalSpec(":3.a").residues(): rots = getRotamers(r) # do whatever you were going to do with the rotamer list However, you can use any string you like as the argument to evalSpec(). For instance you could use "#0 & protein" to go through all the protein residues of model #0. In that case r.oslIdent() would return the atom specifier for the residue which you could then use in other commands. --Eric
On Jan 7, 2023, at 7:07 AM, Noe Robert via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, I would like to come back to this answer from M. Pettersen : "To answer the Python side of this, chimera.Rotamers.getRotamers(residue) gets a list of rotamers (really Molecule instances) for that residue (Dunbrack library by default). Each of those Molecule instances has a 'rotamerProb' attribute, which is the value you see in the graphical user interface." As I'm not used to this scale of Chimera use, I don't know how to run getRotamers on the specific residue I want and I'm having quite a hard time exploring python scripts refering to getRotamers. I would just need to run this function to get the 'rotamerProb' attribute of each rotamer, the rest would be performed using commands. So I would like to know what would be the code line to have getRotamers returning "mols" on a specific residue, for instance ":3.a" Thank you a lot and have a great weekend ! De : Eric Pettersen <pett@cgl.ucsf.edu> Envoyé : mardi 3 janvier 2023 18:26 À : Noe Robert <noe.robert@etu.univ-cotedazur.fr> Cc : chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Objet : Re: [Chimera-users] Question concerning rotamer choosing
To answer the Python side of this, chimera.Rotamers.getRotamers(residue) gets a list of rotamers (really Molecule instances) for that residue (Dunbrack library by default). Each of those Molecule instances has a 'rotamerProb' attribute, which is the value you see in the graphical user interface. You apply the rotamer you want by calling chimera.Rotamers.useRotamer(residue, rotamers) where rotamers is a list of rotamers to apply, probably just one (at a time) in your case because if you supply multiple rotamers then they will all be used by putting each one in a different alternate location.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 2, 2023, at 6:26 AM, Noe Robert via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:
Hi, I'm currently trying to write a python script which automatizes mutageneses on Chimera 1.16, and calculates clashes inducted by the change of amino acid through a local minimization (which explains why I'm using Chimera instead of ChimeraX). I would like to choose which rotamer to use depending on their probability from the rotamer library Dunbrack (for instance, when probability is >0.1), which is visible on the "Rotamers graphical user interface". Is there a way to extract these probability values using a script, in order to run it on a certain number of rotamers ? That way it would be quite automated. On Jul 1, 2015, Eric Pettersen advised to modify the "Python script that uses the functions in the Rotamers module" (here <https://www.cgl.ucsf.edu/pipermail/chimera-users/2015-July/011193.html>), but I don't which one it is.
Thank you,
Noé Robert, Fifth-year student in bioengineering, minor in Bioinformatics and Modelling, at engineering school Polytech Nice Sophia, France Phone : +33 7 81 00 52 02 "let's limit the use of our resources and lighten our mails"
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