[chimerax-users] [Chimera-users] chimera, H-bonds

[Elaine Meng]

> On Nov 18, 2021, at 11:37 AM, Rio Aquarius via Chimera-users <chimera-users at 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
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco