Re: [chimerax-users] [Chimera-users] chimera, H-bonds
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
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Elaine Meng