ChimeraX Recipes

Flip Atom Z Coordinates

Here is Python code defining a command flip that changes atom z coordinates z -> -z. This changes the hand of the atomic structure, for instance changing all L amino acids to D amino acids. Open flip.py in ChimeraX 1.0 to define the flip command

open flip.py

then use the command on the atomic model.

flip #1

Here is the flip.py code:

# Create command to change atom coordiates z -> -z.
# Opening this file in ChimeraX 1.0 defines the flip command.
#
#  flip #1

def flip(session, atoms):
    xyz = atoms.coords
    xyz[:,2] *= -1
    atoms.coords = xyz

def register_command(session):
    from chimerax.core.commands import CmdDesc, register
    from chimerax.atomic import AtomsArg
    desc = CmdDesc(required=[('atoms', AtomsArg)],
                   synopsis='flip atom z coordinates')
    register('flip', desc, flip, logger=session.logger)

register_command(session)

Tom Goddard, September 3, 2020