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

[Tom Goddard]

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 at 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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