[Chimera-users] Question concerning rotamer choosing

[Elaine Meng]

Hi Noé Robert,
If I understand your question, it is exactly as I said in the previous reply, use option "criteria p" in the "swapaa" (which omits the other measures entirely).  

> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html#options>
> So even though you may still want to use python for various reasons like looping, you should consider carefully how you choose the rotamer, and possibly use the default settings of the "swapaa" command.  Even if you decide you only want to use probability, then you can still use the "swapaa" command option with "criteria p" as explained in the help link above.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 3, 2023, at 3:23 AM, Noe Robert via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine, 
> Thank you a lot for this clarification, my group and I will reconsider the parameters to use for the rotamers selection, because they are indeed really interesting. 
> One thing though, and it's just a semantic question out of curiosity, but how would you write the option to run swapaa on the first rotamer depending on the probability only ? It would be something comprising "criteria", "1" for the rank and "p" for the parameter concerned, but I don't know how to take the 2 last into account at the same time.
> Thank you again for your time, and best wishes for 2023 !
> Robert Noé
> De : Elaine Meng <meng at cgl.ucsf.edu>
> Envoyé : lundi 2 janvier 2023 18:48
> 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
>  
> Hi Noé Robert,
> I can't answer the python part, but wanted to make sure that you understand the meaning of the probability: it is the probability based on backbone conformation only.  It is NOT the total probability for the specific position, because it does not look at sidechain interactions.  So the one with the highest probability might be a very poor choice for the specific position (might have high clashes, low H-bonds).  
> 
> It is a common misconception that the highest probability is the best one to choose.
> 
> Rotamers mutagenesis is implemented as the "swapaa" command where the default is to take account first clashes, then H-bonds, the probability (again because that value is only based on the backbone conformation).   See the "swapaa" command "criteria" option:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html#options>
> 
> So even though you may still want to use python for various reasons like looping, you should consider carefully how you choose the rotamer, and possibly use the default settings of the "swapaa" command.  Even if you decide you only want to use probability, then you can still use the "swapaa" command option with "criteria p" as explained in the help link above.
> 
> I hope this clarifies the situation,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Jan 2, 2023, at 6:26 AM, Noe Robert via Chimera-users <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), 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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