Hi Matt,
The address for ChimeraX questions is chimerax-users@cgl.ucsf.edu CC'd here, as mentioned in the "contact us" page:
<https://www.rbvi.ucsf.edu/chimerax/docs/contact.html>

Yes, of course you can make some of the atoms transparent and others not.  I say "atoms" because at least in your image, you are displaying the atoms in the sphere style. You just need to specify that set of atoms in the transparency command, for example, for atoms of B chain only to be 70% transparent:

transparency /B 70 target a

...or you could use menu: Select... Chains... [choose the one that you want]

...and then use command:

transparency sel 70 target a

The "target a" part means atoms.  The default is to change transparency of only molecular surface (target s), so if you omit "target a" nothing happens to the atoms.  Of course you can use a different % value than 70.

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


From: Matthew Bubak <Matthew-Bubak@omrf.org>
Subject: ChimeraX Chain Transparency
Date: April 18, 2024 at 12:48:22 PM PDT

Hello,

I am trying to make specific chains of mitochondrial complexes more or less transparent. I am able to make the entier complex transparent, but not individual chains.  For example in the figure below (mitochondrial complex I), I would like to make the purple chains approximately 50% transparent, and the blue chain 90% transperent, and leave the rest untouched. Is this possible? 


Thank you for your help, 

Matt Bubak, PhD.
Post-Doctoral Fellow
Aging and Metabolism Program
The Oklahoma Medical Research Foundation