Michael,

As far as I know, ChimeraX has no dedicated feature for updating bonds while animating a trajectory. I did write a Python script for updating bonds for another project, but I can't find the final version of it. Here's what I did find:

```

from chimerax.atomic import AtomicStructure
from chimerax.core.models import ADD_MODELS

from scipy.spatial import distance
import numpy as np

# tolerance so bonds don't erroneously break
tolerance = 0.4
max_dist_arrays = {}

def check_bonds(trigger_name, changes):
    mdl, diff = changes
    if not diff.structure_reasons():
        return
    # squared distance between atoms
    D = distance.squareform(
        distance.pdist(
            mdl.coordset(mdl.active_coordset_id).xyzs,
            "sqeuclidean"
        )
    )
    try:
        max_connected_dist = max_dist_arrays[mdl]
    except KeyError:
        # make an array for how far atoms can be and still be bonded
        # to each other
        max_connected_dist = np.zeros((mdl.num_atoms, mdl.num_atoms))
        for i, a1 in enumerate(mdl.atoms):
            for j, a2 in enumerate(mdl.atoms[:i]):
                max_connected_dist[i, j] = (
                    a1.element.bond_radius(a1.element.name) +
                    a1.element.bond_radius(a2.element.name) +
                    tolerance
                ) ** 2
        max_dist_arrays[mdl] = max_connected_dist
   
    # these are bonded
    connected = np.tril(D < max_connected_dist).nonzero()
    # these are not
    not_connected = np.tril(D > max_connected_dist).nonzero()
    # add new bonds
    for (ndx1, ndx2) in zip(*connected):
        try:
            b = mdl.new_bond(mdl.atoms[ndx1], mdl.atoms[ndx2])
            # set the bond radius ot 0.16 to match the BSE preset
            b.radius = 0.16
        except TypeError:
            pass

    # delete bonds that are too long
    for (ndx1, ndx2) in zip(*not_connected):
        a1 = mdl.atoms[ndx1]
        a2 = mdl.atoms[ndx2]
        for bond in a1.bonds:
            if a2 in bond.atoms:
                bond.delete()
   

def register_bond_monitor(trigger_name, models):
    for mdl in models:
        if not isinstance(mdl, AtomicStructure):
            continue
        mdl.triggers.add_handler("changes", check_bonds)


session.triggers.add_handler(ADD_MODELS, register_bond_monitor)

```

Save the script to a .py file and open it in ChimeraX, and then open your trajecories. Until you close ChimeraX, the script will update bonds any time the coordinates change. Bonds are only checked for structures opened after the script. Performance will take a noticeable hit when playing trajectories, but there's probably some room for optimization. You do have to restart ChimeraX to disable the bond checking.

I'm pretty sure the final version would show metal coordination bonds correctly, as well as TS pseudobonds once things got a bit longer than normal bonds. If you want that, let me know and I can probably add it quickly.

Best,

Tony