Hi, 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 <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/perframe.html> 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 
On Mar 24, 2024, at 12:52 PM, qz.chen--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I want to use ChimeraX to visualize the protein slab simulation in the condensed phase as the link below. Unlike typical protein simulations, simulations of the condensed phase slab often need to keep the atoms inside the box for more accurate visualization. This means that particles between proteins may be jumping, leading to unreasonable lines appearing in the visualization. I have not found a way to adjust this in ChimeraX.
https://www.biorxiv.org/content/10.1101/2020.08.05.237008v1.full
Is there a way to limit the maximum distance between carbon and bond among particles?
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