Hi Mikael, Well, one way is to only specify the sets of atoms for which you want to show hbonds in the hbonds command (or tool). For example, if you want only the h-bonds between ligand and protein, commands: open 2gbp select ligand hbonds selRestrict protein ~select See hbonds command help <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html> Note also that by default, hbonds are not shown unless their endpoint atoms are shown, except backbone-only hbonds can be shown if the ribbon is shown since the ribbon substitutes for backbone-atom display. So one way to hide an existing hbond is to hide the atom it goes to. Another way to hide an existing hbond is to Ctrl-click to select it (will then be highlighted in green outlines), open the Selection Inspector by clicking the green magnifying glass at the bottom right corner of the Chimera window, Inspect: Pseudobond, "displayed" from "if atoms shown" to "false"... also, changing that setting to "true" is how you would allow that hbond to be shown even if its endpoint atom(s) are not. See Selection Inspector help <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.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 Aug 29, 2023, at 3:39 AM, Karjalainen, Mikael via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hi! I am having problems to show certain hydrogen bonds and hide others. For example, I would like to hide some completely. Then others should be shown always. Even when atoms are not shown and only ribbon is.

I couldn’t find how to do this by googling or for example reading how to use hbonds command. I am using Chimera 1.16. I know that there is ChimeraX, but now I need to modify old project. Regards, Mikael