Hi Tom! 

Thank you so much for your help, especially with the command allowing a residue range that's perfect =D

Best regards,
Thibault.

De: "Tom Goddard" <goddard@sonic.net>
À: "Thibault TUBIANA" <thibault.tubiana@i2bc.paris-saclay.fr>
Cc: "chimerax-users" <ChimeraX-users@cgl.ucsf.edu>
Envoyé: Lundi 31 Octobre 2022 18:29:27
Objet: Re: [chimerax-users] Get atom from selection string in script

Hi Thibault,

  I suggest you make your command syntax like this

copyTorsion #1:78 to #2

This will be a more familiar way of specifying command arguments in ChimeraX.  Also it is easy to get the torsion angle and set it using the residue "psi" angle.  Here is a modified version of your code.  It allows specifying multiple residues also ("copytor #1:55-65 to #2").

  Tom


def copy_torsion(session, residues, to_structure):
    for residue in residues:
        res_num = residue.number
        cmd = f"torsion {to_structure.atomspec}:{res_num}@n,ca,c:{res_num+1}@n {residue.psi}"
        from chimerax.core.commands import run
        run(session, cmd)
    
def register_command(logger):
    from chimerax.core.commands import CmdDesc, register
    from chimerax.atomic import ResiduesArg, AtomicStructureArg
    desc = CmdDesc(required = [ ('residues', ResiduesArg) ],
                   keyword = [ ('to_structure', AtomicStructureArg) ],
                   required_arguments = ['to_structure'],
                   synopsis='Copy torsion angle')
    register('copytorsion', desc, copy_torsion, logger=logger)

register_command(session.logger)



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/ 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
Institute for integrative biology of the cell (I2BC) - CNRS UMR 9198
CEA Saclay, 91191 Gif sur Yvette - Bât 532 pce 34

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