The short answer is no, they cannot both be transparent if you want to see them both. ChimeraX only shows the topmost transparent layer, so if there are two transparent things on top of each other, you will only see the one in front. This is discussed in previous posts: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> If you require the ribbon to be transparent, you could try making the surface as (nontransparent) mesh instead: transparency 0 targ s surf style mesh However, in my experience this does not look very good. Instead it looks better to have transparent surface and nontransparent cartoon. If you want the cartoon to be less "obvious" you could try making it thinner (see cartoon style) and/or a darker color instead of transparent. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 8, 2024, at 6:54 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users,
I am trying to add transparency on the cartoon representation of the protein that have additionally transparent surface in the same session.
hide protein target a surface protein rainbow protein target c palette paired-12 rainbow protein target s palette paired-12 transparency 90 transparency protein 10 target c
The last command hides all cartoons. I've also tried adding the transparency option directly to the rainbow command:
rainbow protein target c palette paired-12 transparency 20
But it had the same effect as the total disappearance of the cartoons.
Is it possible to have two different levels of the transparency on both cartoon and surface representation ?
Thank you in advance !
Enrico