Hi Sergio,
I wouldn't call it a bug, just that the assumption for a trajectory or other ensemble (e.g. from NMR) is that it has the same atoms and bonds at each frame.  However, you can destroy and re-guess bonds at each frame, with some possible hit on live playback speed, as described in this recent chimerax-users post:

<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fpipermail%2Fchimerax-users%2F2023-April%2F005164.html&data=05%7C01%7Chassan%40mail.nih.gov%7C1b4ea0b92345462253f208db5571c60c%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638197719374440268%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=E4P6A3V8R6Myc0fGybd9jzR92ERH0%2BVkzjlWANn8eTk%3D&reserved=0>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 13, 2023, at 9:24 AM, Hassan, Sergio (NIH/NIAID) [E] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hi, I am not sure whether this is a bug or something not yet implemented or else.
>
> I performed QM/MM simulations of a proton translocating along a water chain. This involves the breaking of a bond and the making of a new bond. The visualization of the trajectory does not show this process; instead, the original definition of bond is retained, without being updated at each timeframe.
>
> Is there a way to tell ChimeraX to automatically check covalent bonds at each snapshot and update the bond accordingly? A simple distance criterion will do. This is only for rendering purpose.
>
> In case further clarifications are needed: D—H.......A (with -- indicating the covalent bond between proton and domor and .... indicating the proximal acceptor) must be transformed to D.......H—A. Instead, it is rendered as D-------H..A (with an artificially elongated DH bond and no new HA bond)
>
> thanks
> s

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