On Nov 18, 2021, at 11:37 AM, Rio Aquarius via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Dear Developer, I have a specific task for ChimeraX. I want to show H-bonds and hide all amino acid residues. But when I hide amino acid residues, all H-bonds I need disappear. Is there a way to do what I want?

Dear Rio, The H-bond displays are lines (pseudobonds) drawn between atoms. When you hide those atoms, the H-bonds are also hidden. I don't understand why you would want to display a bunch of lines in space without any atoms, as you won't be able to see most of the valuable information from the calculation. However, I will explain how to do it: In ChimeraX, there is no pseudobond option to display even when its atoms are hidden. The only way to make it look like the H-bond lines are shown when you can't see the atoms (and/or ribbons) is to make the atoms (and/or ribbons) 100% transparent with the "transparency" command. Example commands: open 2gbp hbonds reveal true transparency 100 target ar <https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco