Hi Mohyeddine, You have to also open the second cube file, and then specify coloring the isosurface of #1 using the values of #2. This coloring can be done with the Surface Color tool or the command "color sample" -- see the help links below for details. Surface Color tool (in menu under Tools... Volume Data): <https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html> Or, command "color sample" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map> color sample #1 map #2 [...other options, see help link above...] 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 Jul 8, 2025, at 12:22 AM, mohyeddine.taleb via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi, I would like to ask how to color a given isosurface (built with the commands open cube1.cube and volume #1 level 0.02 style surface) using the values from a second property stored in another cube file, cube2.cube. Please note that the two cube files describe exactly the same grid. I have also attached an example showing the interaction between two water molecules. Best regards,

Mohyeddine Taleb <test01.tbz2>