You can try doing

"transparency #1 50 target abs"

So it makes the atoms, bonds, and surface of #1 50% transparent. You can also do multiple models at the same time like

"transparency #1-50" or "transparency #1,3,5" etc

From: Ioannis Skalidis via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Sent: Tuesday, October 22, 2024 5:41 AM
To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: [chimerax-users] Set transparency of multiple models

Dear ChimeraX mailing list,

I was wondering if there is a command to set the alpha (transparency) of multiple models (not maps). So far, I know that this is possible for maps through the transparency command, but the only way I know of to make a model transparent is to set each model alpha value individually in its color panel.

Thanks for your help!

Cheers,

Dr. Ioannis Skalidis | Structural Biochemist | Twitter: @imjohnskal | johnskalidis@gmail.com