Hi Steve, Your image is from Chimera (not ChimeraX) so maybe you mean in Chimera? There are two different mailing lists: chimera-users@cgl.ucsf.edu and chimerax-users@cgl.ucsf.edu In Chimera, you can specify the planar cap color in the "Surface Capping" tool opened by clicking "Surface capping..." on the Per-Model Clipping tool, or directly from the menu under Tools... Depiction. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-mode...> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcapper/surfcap...> ChimeraX does not yet have per-model clipping (clipping the surface but not the structure). However, clipped surfaces have a planar cap with many ways to color them, including: select cap with mouse (Ctrl-click), use menu Actions... Color... [choose color] specify directly in command line by model number (use Model Panel to find out number), e.g. command: color #1.2.1 cyan transparency #1.2.1 50 See also ChimeraX command "surface cap" <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#cap> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jun 14, 2020, at 8:11 PM, Steve Chou <stevezchou@gmail.com> wrote:

I mean “the color of the cutting plane in a section view”. Sorry for any confusion. Steve

On Sun, Jun 14, 2020 at 8:44 PM Steve Chou <stevezchou@gmail.com> wrote: Dear ChimeraX developers and users, Is it possible to define the color surface cut-through sessions? Thanks in advance! Steve