You could save all the hydrogen bonds to per-frame files with:

perframe "coordset #1 $1 ; save /path/to/savedir/hbonds-$1.pbonds" range 1,number-of-frames

Then you would have to use some scripting/editing magic to create a combined non-redundant .pbonds file, which could then be opened to show all the hydrogen bonds.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Oct 18, 2023, at 10:50 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

No.  The only way to show multiple frames of a trajectory in ChimeraX is to open them as separate models.

Tom

On Oct 18, 2023, at 9:37 AM, Alexander Hung Lee <Alexander.Lee@uga.edu> wrote:

Oh, and I forgot to ask… Is there an option in command line to show all the hbonds in a trajectory concurrently, even if the bond shows up at a different point in time but not current frame?



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