On Apr 30, 2024, at 10:41 AM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Ute,

This seems to be a problem in the interaction between the "perframe" and "coordset" commands.  When the hydrogen bonds are evaluated, the coordinate set hasn't been advanced yet, so when the coordinate set later gets advanced the hydrogen bonds are gone.  I will open a ticket in our bug-tracking database for this with you cc'ed.  You can get close to what you were trying to get with the following two commands (though not 100% the same):

hide solvent; hb :LIG reveal true coordsets true makePseudobonds true

perframe view; coordset #1 1,20 holdsteady :LIG; wait 20; ~perframe

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

On Apr 30, 2024, at 5:51 AM, Ute Roehrig via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I'm trying to visualize the hydrogen bonds of a small molecule in water over the trajectory of a molecular dynamics simulation, using the following commands:

alias evalhb hide solvent; hb :LIG reveal true coordsets false makePseudobonds true ; view

perframe evalhb; coordset #1 1,20 holdsteady :LIG; wait 20; ~perframe

However, this does not work as expected. Could you please help me with this issue?

Thank you,

Ute

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