Hi Gabriele,
It would be useful to give more detail on what exactly you tried and what you want. I don't know if you were using the menu, or the "color" command, or the "transparency" command and whether you mean the atomic representation (sticks, balls, ...), ribbons, and/or molecular surface.

However, here is an example of changing the transparency of the atomic representation of selected atoms only, using the transparency command and a value of 70%.  Example commands:

open 2gbp
select ligand
transparency sel 70 target a

You can use command "help transparency" to show the help page for the command:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html>

In commands, you use "sel" to mean the selected atoms.  See:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>

The Actions menu automatically applies to the selected parts, but it does not have an option for changing transparency of atomic representations.

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

> On Nov 20, 2020, at 4:02 PM, Gabriele Cerutti <gc2695@columbia.edu> wrote:
>
> Hello,
> I am trying to display transparency only for selected residues in my protein model but I am having a hard time trying to restrict the transparency only to the selected set of atoms (it sets the transparency to all residues).
> Do you have any suggestions and/or examples about this?
> Thanks,
> Gabriele