ChimeraX Recipes

Copy coordinate between conformers

Here is Python code defining a command copycrds that copies coordinates from one conformer to another. The conformers must have the same atom and residue names. Open in ChimeraX to define the copycrds command


then use the command to copy coordinates from (e.g.) model #1 to model #2

copycrds #1 to #2

Here is the code:

# Create command to copy all atom coordiates from one conformer to another.
# Opening this file in ChimeraX defines the copycrds command.
#  copycrds #1 to #2

def copycrds(session, from_struct, to=None):
	from chimerax.core.errors import UserError
	if from_struct.num_atoms != to.num_atoms:
		raise UserError("Both structures must have the same number of atoms")
	from_atoms = from_struct.atoms
	to_atoms = to.atoms

	from_info = [a.string(style="command", omit_structure=True) for a in from_atoms]
	to_info = [a.string(style="command", omit_structure=True) for a in to_atoms]
	if from_info == to_info:
		# safe to just copy coordinates directly
		to_atoms.coords = from_atoms.coords

	fi_set = set(from_info)
	ti_set = set(to_info)
	if fi_set != ti_set:
		# different atoms and/or residues
		differences = fi_set ^ ti_set
		raise UserError("The two structures have different atoms (e.g. %s)" % differences.pop())

	# have the same atoms but in a different order -- assign coordinates "by hand"
	to_atom_lookup = {}
	for to_string, to_atom in zip(to_info, to_atoms):
		to_atom_lookup[to_string] = to_atom
	for from_string, from_atom in zip(from_info, from_atoms):
		to_atom_lookup[from_string].coord = from_atom.coord

def register_command(session):
	from chimerax.core.commands import CmdDesc, register
	from chimerax.atomic import StructureArg
	desc = CmdDesc(
		   required = [('from_struct', StructureArg)],
		   required_arguments = ['to'],
		   keyword = [('to', StructureArg)],
		   synopsis = 'copy atom coordinates between structures')
	register('copycrds', desc, copycrds, logger=session.logger)


Eric Pettersen, February 24, 2023