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


8hju_fade.png
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> wrote:

On Oct 19, 2023, at 4:21 AM, Carl Johan Hagstromer <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 (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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