Hi Kelly, Color zone colors a surface to match atoms. However, the hydrophobicity coloring is on the molecular surface of the protein, not the protein atoms. If you want to color the tunnel by the molecular lipophilicity potential (MLP) from the protein, you first have to show a "molecular" surface of the tunnel spheres, and then color that fake molecular surface based on the hydrophobicity of the protein atoms. There is a similar example in this tutorial, except that the tunnel spheres came from MOLEonline instead of Caver: <https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole-channel.html> If the tunnel spheres are open as #2 you would need to show their "molecular" surface, and probably also better to hide the spheres, e.g. as in the last two commands in the "Background and Setup" section of that tutorial: surface #2 hide #2 ...then the last command in the "Lipophilicity Coloring" section of that tutorial colors the tunnel surface by the MLP calculated from the protein atoms: mlp protein surfaces #2 If your protein might have some missing atoms (truncated residues when the density was not clear enough to resolve their positions) you might also want to look at that whole section, including the other commands before the "mlp" coloring step. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On May 16, 2023, at 2:23 AM, Kelly May Frain via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

Previously you were super quick and helping when answering my ‘tunnel’ question, so I thought I could try another question for chimeraX.

I have a protein which via Caver I have found a tunnel which runs through. This tunnel has been exported as a pdb and using your help and python, the tunnel now changes diameter perfectly as it weaves through the structure.

I had this idea to colour the tunnel according its surrounding residues and their hydrophobicity. So in chimeraX I can colour my model ‘hydrophobically’ from cyan to gold. Then I wanted to 'zone’ these colours into my tunnel pdb. But when I use color zone #2 near #1 distance 20 for example, the tunnel is coloured in red and blue patches? Even though the model is cyan and gold. Is there a way to achieve my goal please?

Best wishes, Kelly

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