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

On Fri, Nov 3, 2023 at 4:21 PM Michael Patzschke via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Dear colleagues,

I have a trajectory from an ab initio MD run. The output is in the form of concatenated .xyz information. I can open and visualise this in ChimeraX, but the bond topology is determined from the first step. As the simulation progresses, bonds are stretched and the broken bond in my example just gets drawn, although the distance of the involved atoms gets larger then 7 Å by the end of the simulation. Is there a way to use dynamic bonds in ChimeraX? By this I mean that the bonds are only drawn when the distance of the involved atoms is below a certain threshold.

I would appreciate any help in the matter.

Kind regards, Michael Patzschke _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

I forgot about perframe, but it's not ideal for viewing trajectories interactively. Lately I've been doing some AIMD myself, so I figured it would be worth it to expand on my previous script and eventually add it to seqcrow. The updated script is here: https://gist.github.com/ajs99778/640ccd2c7e15a8bbb39d5f650de00111 (note: this requires AaronTools, which is included with seqcrow).

Opening the script will add a command called "monitorBonds" to ChimeraX. Run the command and give either an atom or model selection (e.g. `monitorBonds #1` or `monitorBonds sel`). As before, any time the coordinates change, it will add or delete bonds as appropriate. It will also now draw metal coordinate bonds, and draw TS bonds when atoms are a bit too far to be bonded. You can also add `guess true` to the command, and it will limit the atoms it checks to those that have a different connectivity at the first and last frames of the trajectory. Limiting the atoms reduces lag.

There's also `tolerance` and `tsTolerance` options for adjusting when different bond types are drawn. These tolerances get added to the atoms' covalent radii, and help prevent connectivity from changing too frequently. I might tweak these parameters some more later.

Tony

On Fri, Nov 3, 2023 at 4:21 PM Michael Patzschke via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Dear colleagues,

I have a trajectory from an ab initio MD run. The output is in the form of concatenated .xyz information. I can open and visualise this in ChimeraX, but the bond topology is determined from the first step. As the simulation progresses, bonds are stretched and the broken bond in my example just gets drawn, although the distance of the involved atoms gets larger then 7 Å by the end of the simulation. Is there a way to use dynamic bonds in ChimeraX? By this I mean that the bonds are only drawn when the distance of the involved atoms is below a certain threshold.

I would appreciate any help in the matter.

Kind regards, Michael Patzschke _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

Ooooh, fancy! This will be very helpful for people doing MD of transition states for sure.

—Eric

On Nov 5, 2023, at 11:08 PM, Tony Schaefer via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

I forgot about perframe, but it's not ideal for viewing trajectories interactively. Lately I've been doing some AIMD myself, so I figured it would be worth it to expand on my previous script and eventually add it to seqcrow. The updated script is here: https://gist.github.com/ajs99778/640ccd2c7e15a8bbb39d5f650de00111 (note: this requires AaronTools, which is included with seqcrow).

Opening the script will add a command called "monitorBonds" to ChimeraX. Run the command and give either an atom or model selection (e.g. `monitorBonds #1` or `monitorBonds sel`). As before, any time the coordinates change, it will add or delete bonds as appropriate. It will also now draw metal coordinate bonds, and draw TS bonds when atoms are a bit too far to be bonded. You can also add `guess true` to the command, and it will limit the atoms it checks to those that have a different connectivity at the first and last frames of the trajectory. Limiting the atoms reduces lag.

There's also `tolerance` and `tsTolerance` options for adjusting when different bond types are drawn. These tolerances get added to the atoms' covalent radii, and help prevent connectivity from changing too frequently. I might tweak these parameters some more later.

Tony

On Fri, Nov 3, 2023 at 4:21 PM Michael Patzschke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:

...

Dear colleagues,

I have a trajectory from an ab initio MD run. The output is in the form of concatenated .xyz information. I can open and visualise this in ChimeraX, but the bond topology is determined from the first step. As the simulation progresses, bonds are stretched and the broken bond in my example just gets drawn, although the distance of the involved atoms gets larger then 7 Å by the end of the simulation. Is there a way to use dynamic bonds in ChimeraX? By this I mean that the bonds are only drawn when the distance of the involved atoms is below a certain threshold.

I would appreciate any help in the matter.

Kind regards, Michael Patzschke _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu mailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

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