[Chimera-users] chimera, H-bonds

Rio Aquarius rioxel at gmail.com
Fri Nov 19 07:30:15 PST 2021

Dear Elaine,
Now I have installed Chimera as well and used algorithm you sent. I have
got the result I need.
Thank you so much. I appreciate it.

чт, 18 нояб. 2021 г. в 23:20, Elaine Meng <meng at cgl.ucsf.edu>:

> 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
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
> 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
> -----
> 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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