[Chimera-users] Question concerning rotamer choosing

[Noe Robert]

Thank you a lot for answering this, I understand the need to save computing time. Knowing this we'll be able to adjust our script more easily.
I appreciate the time you took to answer all of this !
Regards,
Noé Robert

________________________________
De : Eric Pettersen <pett at cgl.ucsf.edu>
Envoyé : mardi 3 janvier 2023 à 21:11
À : Noe Robert <noe.robert at etu.univ-cotedazur.fr>
Cc : Chimera <chimera-users at cgl.ucsf.edu>
Objet : Re: [Chimera-users] Question concerning rotamer choosing

Hi Noé,
The numeric criteria cannot be mixed with any of the other criteria and simply picks the Nth most probable rotamer (based on its prevalence in all proteins).  It cannot be used to pick the 3rd-least clashes, etc.  If you really want to do that you would have to resort to using Python.
The rotamers you get from chimera.Rotamers.getRotamers() only have their probability attribute (rotamerProb) assigned, since the clashes and H-bonds take time to compute and may not be needed, depending on what the user requested.  To assign clash score and number-of-H-bonds attributes (clashScore and numHbonds respectively) you would need to call chimera.Rotamers.processClashes()/processHbonds().  You should look at the part of the chimera.Rotamers.useBestRotamers() function that calls those routines to see what you need to do.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Jan 3, 2023, at 10:08 AM, Noe Robert via Chimera-users <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>> wrote:

Thank you for answering this side of my question, I now have a small deviation to take in my approach thanks to Elaine C. Meng who clarified to me the value on the probability parameter.
Have a great day,
Robert Noé
________________________________
De : Eric Pettersen <pett at cgl.ucsf.edu<mailto:pett at cgl.ucsf.edu>>
Envoyé : mardi 3 janvier 2023 18:26
À : Noe Robert <noe.robert at etu.univ-cotedazur.fr<mailto:noe.robert at etu.univ-cotedazur.fr>>
Cc : chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> <chimera-users at cgl.ucsf.edu<mailto: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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