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

[Thibault TUBIANA]

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 at sonic.net> 
À: "Thibault TUBIANA" <thibault.tubiana at i2bc.paris-saclay.fr> 
Cc: "chimerax-users" <ChimeraX-users at 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 < [ mailto:chimerax-users at cgl.ucsf.edu | 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 @ [ https://www.i2bc.paris-saclay.fr/equipe-interactions-and-assembly-mechanisms-of-proteins-and-peptides/ | IMAPP ] 
Institute for integrative biology of the cell ( [ https://www.i2bc.paris-saclay.fr/ | I2BC ] ) - 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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