Hi Carl, I've seen figures of atomic models (ribbons and atoms) where most of it is faded with just one part in bright colors, which focuses the viewers attention on the bright part without being too distracted by the surrounding parts. That can be done in ChimeraX by using transparency, making all the non-selected parts transparent. Here's an example open 8hju select /C transparency ~sel 80 atoms,ribbon The last command says make all the atoms and ribbon that are not selected 80% transparent. Image below. Tom 
On Oct 19, 2023, at 10:57 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Also not sure because I haven’t used PyMOL in years, but maybe the crossfade command does what you want? I like using it for smooth transition between graphics settings in movies.
Guillaume
On 19 Oct 2023, at 18:47, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
On Oct 19, 2023, at 4:21 AM, Carl Johan Hagstromer <carl.johan.hagstromer@ki.se <mailto:carl.johan.hagstromer@ki.se>> wrote:
Would love fading options, like in PyMOL
Hi Carl, We aren't Pymol users so we don't know exactly what you are referring to, but it may well be possible in ChimeraX if you could give more detail. We can put this discussion on chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (CC'd here) so that more folks can weigh in.
ChimeraX can do: depth cueing (fading front->back), gradual fading in/out of structures and/or 2D labels by increasing or decreasing transparency over a number of image frames, and/or color modification (e.g. increasing whiteness of all current colors).
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
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