id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
9008	rendering of bond making/breaking along a trajectory	hassan@…	Eric Pettersen	"{{{
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

_____________________________________
Sergio A. Hassan
https://bioinformatics.niaid.nih.gov/cmm/
BCBB/NIAID/NIH/DHHS
301 761 7221 (office) 301 741 5579 (mobile)


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"	defect	closed	normal		MD/Ensemble Analysis		not a bug						all	ChimeraX