[Chimera-users] Question concerning rotamer choosing

[Eric Pettersen]

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 at 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 at cgl.ucsf.edu>
> Envoyé : mardi 3 janvier 2023 18:26
> À : Noe Robert <noe.robert at etu.univ-cotedazur.fr>
> Cc : chimera-users at cgl.ucsf.edu <chimera-users at 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 at cgl.ucsf.edu <mailto:chimera-users at 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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