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
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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