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.

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

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.

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
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