[chimerax-users] specify pseudobonds

[Elaine Meng]

Hi Ruchika,
If you want to hide only some specific contacts pseudobonds, there are several ways.

(A) One way is to select them (Ctrl-click, Shift-Ctrl-click on them in the graphics window so that they have a green outline) and then use command

hide sel pseudobonds

(B) Another way is to hide the atom on at least one end of the pseudobond, which will also automatically hide the pseudobond.

(C) Another approach is to use the Contacts options to limit the calculation to only selected atoms so you don't get the extra ones you didn't want in the first place.  See the "Limit by selection" options:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html>

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

> On Apr 15, 2021, at 4:10 AM, Ruchika Bajaj <phd.ruchika at gmail.com> wrote:
> 
> Hi Elaine
> 
> I am using the contact tool from the structure analysis tool. It is giving me a few pseudobonds and I want to delete a few of them for the picture I am working on. I also tried checking the pseudobond command. So, could you please help me in specifying pseudo bonds and how to delete or hide specified pseudobonds in the figure, instead of all of them. 
> 
> Thanks a lot !!
> Regards
> Ruchika