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://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-April/005164.html> 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