Hi Kai, This happens when you have multiple transparent models or layers, and (I believe) is not related to whether you specified the transparency with hexadecimal code or in some other way: only the topmost transparent layer will be shown. If you want the other (underneath) model to show, it should not be transparent. Or, if you require the underneath model to be transparent, then the surface over it should not be transparent, although you can show it as mesh to make it possible to see both models at the same time. From your commands, the surface is 50% transparent, and the ribbon color #f17d21cc is 80% opaque (20% transparent). I agree that it can be surprising that recoloring the ribbon without specifying a transparency (say "orange") does not change the 20% transparency back to 0%, but you can do it explicitly, e.g. color #2 #17d21ff See "transparency and its limitations" at the bottom of this page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html#transparen...> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Oct 17, 2023, at 10:58 AM, Kai Cai via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi, I've got this weird bug that hope you can help me with. When I try to color a selected protein model with nonmajor hexadecimal color codes (e.g. #f17d21cc), the selected model will become invisible behind the map it was fit with. The map is set as transparent surface. Once it becomes invisible, it won't come back no matter how I change the color.

This appears to be a recent issue. Not sure if it's a bug caused by recent macOS update. I am running the most recent ChimeraX daily update on a macOS 14.0.

Here is an example if you would like to test it:

open 25428 fromDatabase emdb open 7sth transparency 50 select #2 color sel #f17d21cc

Thanks, Kai