Hi Vincent,
The "pbond" command is only in version 1.8 or newer, according to the Change Log.  Maybe what you have is too old, so get a newer ChimeraX.
<https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog>

What you said should work if those atoms actually exist and the model is not hidden.  Similar commands work just fine for me, e.g.

open 2gbp
pbond #1/A:13@O #1/A:153@O reveal true color magenta dashes 1
cartoon suppress false 

("cartoon suppress false" allows showing backbone atoms at same time as cartoon)

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

On Dec 10, 2024, at 6:38 AM, Vincent CHAPTAL via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi, 

I've been playing a lot with the commands but I can't seem to get it right. 
I'd like to display a line between 2 atoms in a model. 

I tried: pbond #2.1:940@O #2.1:472@O reveal true color blue dashes 1  (and variations around it) but I got an error that pbond or pseudobond are unknown commands. 

I also played around with distance:
distance #2.1:940@O #2.1:472@O 
hide #4.1
color #4 blue
distance style #4 dashes 0

but the distance does not appear on my screen. 

Could you help me work this out? 
Thank you
Vincent


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Vincent Chaptal, PhD
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Drug Resistance and Membrane Proteins Lab

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