So, as I understand it you are saying that molecules are being split across the periodic boundary and ChimeraX is drawing the bonds that cross the boundary all the way through the box and you would like to suppress that. There is no builtin way to do that, but it is a very simple piece of Python code, namely:

too_long = 10.0

from chimerax.atomic import all_atomic_structures

for s in all_atomic_structures(session):

bonds = s.bonds

bonds.displays = bonds.lengths < too_long

The above code would hide bonds longer than 10 angstroms. It you put that code in a file (say, hide_long.py in your home folder), then you could run it every frame with the perframe command, e.g. “perframe “open ~/hide_long..py”. I have attached a file containing the above code for convenience.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab