[Chimera-users] chimera, H-bonds

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 18 12:20:47 PST 2021

Dear Rio,
Sorry I accidentally told you to send the message to chimera-users but now I see it is a ChimeraX question, not Chimera.  Below is the answer for Chimera (not ChimeraX), so you may want to ignore it.  I will send a separate message about ChimeraX on the chimerax-users at cgl.ucsf.edu list.

The H-bond displays are lines (pseudobonds) drawn between atoms.  When you hide those atoms, by default 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:

You can set pseudobond display to be "on" regardless of whether their atoms are displayed, e.g. with the command:

setattr p display 1


That would do it for ALL pseudobonds including missing segments, metal coordination bonds, etc.

To limit it to the H-bonds only, you would need to open the Pseudobond Panel (under Tools... General Controls in the menu) and then in that panel, click "hydrogen bonds" on the left to choose that row, then click "select bonded" in the right side.

...then when all the H-bonded atoms are still selected, use command:

setattr p display 1 sel

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> 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?

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