A correction, sorry: this command

color zone #1 near #1 sharpEdges true

...should really be color zone #1.2.1 #1.3.1 #1.4.1 #1.5.1 near protein sharpEdges true ... so as to (1) only apply color zone to the planar caps; you can use the disclosure triangle(s) in the Models panel to see what their model numbers are (2) only use protein atoms for color zone reference, not solvent etc. which might be outside the surface yet still nearby Best, Elaine

On Nov 12, 2025, at 4:31 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi David, Yes, the molecular surface of each chain is another model in addition to the atomic model, so there are situations in which it would not reflect the individual atom coloring. However, you can use the special color name "fromatoms" to make molecular surface patches match the atoms.

For example,

open 4hhb surface

...shows tan surfaces even though the atoms have hetatom coloring. The following command makes the surface patches get colored according to the corresponding atoms:

color #1 fromatoms

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple>

The above covers the un-clipped surface. The cap on a clipped surface is yet another (sub)model. Say I show the Side View and then use the near plane to clip the surface. As you said, the planar cap is all tan. If I want to make it match the atoms I would need to use a color zone command (or the Color Zone GUI tool) because the vertices in the cap are not specifically assigned to one atom or another:

color zone #1 near #1 sharpEdges true

...see docs for explanations of the options, including ones I didn't use in the example... <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone>

In the case of coloring the planar cap by potential (lipophilicity or electrostatic), see the tutorial: <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#ca...>

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Nov 12, 2025, at 3:11 PM, stokes--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

I am having trouble with the surface color and specifically of capped surfaces. To start, surfaces of individual chains are given a single color, despite individual domains having been assigned a variety of colors. I can change the colors of the surface for individual domains subsequently, so that is not so bad. However, the color of the capped surface remains the initial color adopted when the surface was created. When I change colors of the individual chains, or domains, the surface color changes, but not the color of the capped/clipped surface. If I change the color of the entire model, then the surface cap changes. But it does not respond to subsequent changes of individual chains and domains. Hiding/showing the surface does not solve the problem (though I have a dim memory of this working in the past - maybe that was the old chimera). I am only using near/far clipping planes - not front/back. ChimeraX 1.10.1 on Ubuntu and 1.8 on Windows behave the same.

Thanks in advance for any insight, David

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