Colton, I think you're looking for the sample and map keywords of the color​ command. I'm not sure if there's a tool for doing this like the Surface Color tool in Chimera. https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sample For example, I've got an electron isodensity surface in model #1 and the ESP in model #2. I can color the electron density based on the ESP with `color sample #1 map #2 palette -0.024,red:-0.012,yellow:0,green:0.012,cyan:0.024,blue` This will color #1 rainbow colors based on the ESP values between -0.024 to 0.024 from #2. The custom palette specification is the thresholds levels and colors separated by commas, with each of those separated by colons. https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette I used color names, but there are several other ways to specify colors: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html Best, Tony ________________________________ From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Colton Carlson <cdc01@chem.ubc.ca> Sent: Tuesday, March 9, 2021 12:39 PM To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Volumes [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Hello, I am just wondering if ChimeraX has added the ability to colour surfaces based on the values of a different surface? That is, input 2 cube files, then colour one cube file based on the values of the other. It is available in the other version of chimera, but the only information I could find on this was from 2018 and said it was not yet implemented in ChimeraX. Thanks a bunch! Colton _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users

Hi Colton, Yes, you can color a surface (including a map isosurface) by the values in any map model with the "color" command, specifically "color sample": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map> You can access your downloaded copy of the User Guide from the ChimeraX Help menu, or see the copy on our website (e.g. the links above). E.g. if the cube file shown as isosurface that you want to color is #1 and the other cube file with the values you want to use for coloring is #2 and the range of values you want to map to coloring is 0.1-0.5, something like: color sample #1 map #2 palette puor range 0.1,0.5 ... but see the links above for all the options, how to control which colors go with which values, etc. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Mar 9, 2021, at 9:39 AM, Colton Carlson <cdc01@chem.ubc.ca> wrote:

Hello,

I am just wondering if ChimeraX has added the ability to colour surfaces based on the values of a different surface? That is, input 2 cube files, then colour one cube file based on the values of the other. It is available in the other version of chimera, but the only information I could find on this was from 2018 and said it was not yet implemented in ChimeraX.

Thanks a bunch! Colton