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/ <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...> 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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