Hi Kai,
If you're using the "pbond" command, you can specify option "name model-name" and each different model name creates a separate model.  (This command also has a "showDist" option to label with the distance.)
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/pbond.html__;!!MznTZTSvDXGV0Co!D78ZFOjFAsKUMKacnGO-0p01XdhlaPkVb9wvRe6x5Wk9pYFB_2VTmRduepIU2O6Chbglu-EuznHQzW6MMuN8zJRa$>

If you're opening a pbond file, each file will create a separate model.
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html*pbfiles__;Iw!!MznTZTSvDXGV0Co!D78ZFOjFAsKUMKacnGO-0p01XdhlaPkVb9wvRe6x5Wk9pYFB_2VTmRduepIU2O6Chbglu-EuznHQzW6MMoE_IIEG$>

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 Jun 8, 2026, at 8:40 AM, Kai Cai via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
> 
> Hi ChimeraX Community,
> When I create pseudobonds or distance measurements between atoms in ChimeraX, all of the pseudobonds/distances are grouped together. Is there a way to organize them into separate groups or subgroups so that I can modify their properties (e.g., color, radius, labels) independently?
> Thanks for your help.
> Best,
> Kai
> UT Southwestern
> Medical Center
> The future of medicine, today._