Hi Yishai,
(I changed the subject line).  Sorry, you can't show another transparent thing behind a transparent thing in ChimeraX.  This is a limitation, see the section at the bottom of this page:
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html*transparency-limitations__;Iw!!IKRxdwAv5BmarQ!a0EHrzgLGQVo-hBPZEX48sjEl-dM1uacCi0tUZWAdXLSU6BNWXp7uXTHQn-kfh4TmjVQPykbyqDUgUsN3el0$ >

As mentioned in the section linked above, you might  instead try showing the surface as mesh, but not transparent.  E.g. command

transparency 0 surface
surface style mesh

See surface style help
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html*style__;Iw!!IKRxdwAv5BmarQ!a0EHrzgLGQVo-hBPZEX48sjEl-dM1uacCi0tUZWAdXLSU6BNWXp7uXTHQn-kfh4TmjVQPykbyqDUgXzymFnh$ >

Or, you could keep the surface as transparent solid surface but make the ribbon thinner so it doesn't block as much, e.g.

surface style solid
transparency 50 surface
cartoon style width 1.0

See cartoon style help
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html*style__;Iw!!IKRxdwAv5BmarQ!a0EHrzgLGQVo-hBPZEX48sjEl-dM1uacCi0tUZWAdXLSU6BNWXp7uXTHQn-kfh4TmjVQPykbyqDUgbq_uWP5$  <mhttps://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style><

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 Aug 20, 2024, at 10:36 AM, Yishai Gilron via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> HI Elaine,
> Thank you for your timely answer.
>
> Any chance you can help me with getting across this graphic point in a different way?
> Is there a way to see both a surface and cartoon as transparent, with a non transparent ligand showing through?
>
> I tried with different colors for cartoon and surface, but I can only see the outline of the surface and the cartoon is invisible even when I do:
>      transparency   30  c
>      transparency   70  s
> Yet when I do this the cartoon becomes invisible, unless I hide the surface.
> Best,
> Yishai