Hi Elaine,

thank you for your response! Unfortunately, this is a thing I have already tried. And atoms are even selected and highlighted after hbonds calculation.  I wonder if hydrogen atoms need to be added? Or the problem lies in the fact that user-defined assembly is loaded and only intra-submodel hbonds are displayed?

Once again, thank you for your time!

Best,

Maciek
Od: Elaine Meng <meng@cgl.ucsf.edu>
Wysłane: czwartek, 7 października 2021 18:24
Do: Maciej Basczok <mmaciej.basczok@amu.edu.pl>
DW: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Temat: Re: [chimerax-users] hbonds display problem
 
Hi Maciek,
Glad you like ChimeraX!

I'm guessing that you are displaying the RNA as simplified objects like tubes and slabs instead of atoms.  If you show the atoms, then all of the H-bonds will be shown.

You can do this by clicking the all-atom icon in the Nucleotides tab of the toolbar across the top, or command:

nuc atoms

If you only want to show all atoms for part of the molecule you can select that part before clicking the icon.  You can also make the command apply to selection, for example:

nuc sel atoms

See "nucleotides" command (I was using "nuc" above for short):
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fnucleotides.html&amp;data=04%7C01%7Cmmaciej.basczok%40amu.edu.pl%7C851e235d140043e077ba08d989aefa22%7C73689ee1b42f4e25a5f666d1f29bc092%7C0%7C0%7C637692207413181946%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&amp;sdata=02yyckn52a%2Fe0tRdK29QYpHOf5yAOI9TX9to7FmoUqU%3D&amp;reserved=0>

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


> On Oct 7, 2021, at 1:13 AM, Maciej Basczok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear Expert,
> at the beginning would like to thank you for developing such a wonderful tool as ChimeraX is! I have one problem, namely, when hbonds calculation is run on an RNA molecule with an option to display as pseudobonds, there are many hbonds detected, but displayed are only two of them. Do I keep doing something wrong? I would be very grateful for your help.
> Kind regards,
> Maciek