Re: [chimerax-users] Get atom from selection string in script

31 Oct 2022


      Hi Thibault,
    It seems to me that what your copy_torsion() function really wants is just two residues.  I'd have your command register just a ResiduesArg (from chimerax.atomic) and have your function take just 'session' and 'residues' args.  The function could check if len(residues) == 2 if you wanted.  You would copy the psi angle from the second residue to the first with residues[0].psi = residues[1].psi.  Phi/omega would work the same way.  What you would then type to your command would be something like "copyTorsion #1:231 #2:231".
--Eric
Eric Pettersen
    UCSF Computer Graphics Lab
...
On Oct 31, 2022, at 6:52 AM, Thibault TUBIANA via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi!
I would like to create a function to copy the torsion angle from a model to another one.
The function would take in argument the model ID of the reference and target model (<int>) and the residue id (<int>).
I looked a bit at the scripts available in https://rbvi.github.io/chimerax-recipes/ https://rbvi.github.io/chimerax-recipes/ to have an idea of how to add function in ChimeraX, but I'm currently stuck at "how to get the list of atoms from a selection string ?".
Here's my current script 
from chimerax.core.commands import run
def copy_torsion(session, model1, model2, residue):
    selection = f"torsion #{model2}:{residue}@n,ca,c:{residue+1}@n"
    from chimerax.atomic import AtomsArg
atoms = AtomsArg(selection)   

from chimerax.geometry import dihedral    
cur_torsion = dihedral([*a.scene_coord for a in atoms])

torsion=run(session, f"torsion #{model1}:{residue}@n,ca,c:{residue+1}@n {cur_torsion}")


def register_command(logger):
    from chimerax.core.commands import CmdDesc, register, FloatArg, IntArg, BoolArg, Color8Arg, StringArg
    from chimerax.atomic import AtomsArg
    desc = CmdDesc(required = [
                                ('model1', IntArg),
                                ('model2', IntArg),
                                ('residue', IntArg),
                                ],
                   synopsis='Copy torsion angle')
    register('copyTorsion', desc, copy_torsion, logger=logger)
register_command(session)
Thank you for your help :)
Best regards,
Thibault.
--
Thibault Tubiana, PhD
Postdoctoral Fellow @IMAPP https://www.i2bc.paris-saclay.fr/equipe-interactions-and-assembly-mechanisms-of-proteins-and-peptides/
Institute for integrative biology of the cell (I2BC https://www.i2bc.paris-saclay.fr/) - CNRS UMR 9198
CEA Saclay, 91191 Gif sur Yvette - Bât 532 pce 34
Web Site: http://www.tubiana.me/ http://www.tubiana.me/

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