Hi Elaine, That makes sense. The suggested color code works. I surely should pay more attention to color opacity. I am surprised that when I use the following commands the model does not become visible. It appears that the opacity of the previous color was carried on to the next one. color #2 #f17d21cc color #2 red Best, Kai ________________________________ From: Kai Cai via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Tuesday, October 17, 2023 12:58 PM To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] model becomes invisible behind the map when color with hexadecimal color codes EXTERNAL MAIL 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 ________________________________ UT Southwestern Medical Center The future of medicine, today. CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.