ChimeraX Recipes

ChimeraX copy selected atoms recipe

A utility to create new models containing only selected atoms while preserving original structures.

Features

• Creates copies of selected regions as new models

Installation

1. Save the following code as copysel.py
2. Place the file in your ChimeraX scripts folder:
   • ~/ChimeraX/scripts/ (Linux/Mac)
   • C:\Users\<you>\AppData\Roaming\ChimeraX\scripts\ (Windows)

Usage

1. Copy defined selection:

     copy #1/A:100-200
   

2. Copy selected region:

     copy sel
   

Code Implementation

print("")
print("Copy subset of model")
print("Command: copy atom-spec")
print("e.g.copy sel")

def copy_sel(session, atoms):

    from chimerax.core.commands import run
    for s, s_atoms in atoms.by_structure:
        copied = run(session, f"combine {s.atomspec}")
        copied.atoms[~s.atoms.mask(atoms)].delete()

def register_copy(session):

    from chimerax.core.commands import CmdDesc, register
    from chimerax.atomic import AtomsArg
    desc = CmdDesc(
        required=[('atoms', AtomsArg)],
        synopsis='Copy selected atoms into new models, delete unselected regions, and combine original models.'
    )
    register('copy', desc, copy_sel, logger=session.logger)

register_copy(session)

Alternative implementation using only commands

Here is an alternative implementation of this command Copy.py that uses just ChimeraX commands Python functions. ⚠️ Important: Temporary models use ID 1000 - ensure this ID is available

 print("Copy subset of model")
 print("Command: copy model-spec")
 print("e.g. copy sel")
 
 from chimerax.core.commands import CmdDesc, register, run
 from chimerax.atomic import AtomsArg
 
 def copy_sel(session, atoms):
     structures = atoms.unique_structures
     run(session, f"sel {atoms.spec}")
     
     for s in structures:
         placeholder_id = 1000
         original_ID = s.id_string
         original_name = s.name 
         
         run(session, f"rename #{s.id_string} id #{placeholder_id} name 'copy of {s.name}'")
         run(session, f"combine #{placeholder_id} model {original_ID} name '{original_name}'")
         run(session, f"select ~sel & ##selected")
         run(session, f"del sel")
         run(session, f"combine #{placeholder_id} name '{s.name}'")
         run(session, f"del #{placeholder_id}")
 
 def register_copy(session):
     desc = CmdDesc(
         required=[('atoms', AtomsArg)],
         synopsis='Create new models from selected atoms'
     )
     register('copy', desc, copy_sel, logger=session.logger)
 
 register_copy(session)

Jackie NG, May 2025