Hi Miao, You would need to use "color zone" *after* using the clipping plane to slice the surface. Then the surface cap where the slicing occurs will also be colored by zone. If you use "color zone" before slicing, the cap does not yet exist, so it does not get colored. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Nov 13, 2020, at 7:30 AM, Gui, Miao <Miao_Gui@hms.harvard.edu> wrote:

Dear chimeraX team, I have some issues when coloring a cryo-EM map.

I firstly colored a map gray, then fitted the models in the map and colored the map by zone. I'd like to generate a cross-section slice, but the slice color is always white. Please see the attached image for example, the green surface color is good, but the slice is white. Is there a feature I could use to cap the slices with colors? Thanks.

Best wishes, Miao <test.png>