ChimeraX Recipes

Show CAVER tunnels

Here is how to show CAVER tunnels in biomolecular structures in ChimeraX. We’ll look at example data that comes with CAVER 3.0 for potassium channel PDB 1bl8. CAVER produces a PDB file for each tunnel in the directory


with names


We can open all those in ChimeraX, then change the atoms to sphere style.

open 1bl8
open ~/Downloads/caver_1bl8/results/data/clusters_timeless/tun*.pdb
style #2-36 sphere

The tunnel radius for each atom is given as the bfactor. ChimeraX does not have a command to set the radius to the b-factor value right now, but we can do it with some Python. First select all the tunnels

select #2-36

Then open this Python file to set the radii of all the selected atoms to the b-factor

 open ~/Downloads/

Alternatively you can type the following Python code into the ChimeraX Python shell, menu Tools / General / Shell

from chimerax.atomic import selected_atoms
for a in selected_atoms(session):
  a.radius = a.bfactor

You can color each tunnel differently with

rainbow #2-36 structures

You can flip through them showing each individually with

mseries slider #2-36

The tunnels also look nicer as surfaces instead of atoms

surface #2-36
hide #2-36 atoms

If you hover your mouse over the central channel tunnel you see it is model #23. I can show just that one and color it by electrostatic potential of the protein as in Elaine’s MOLE tutorial (

hide #!2-36 models
show #23 model

coulombic protein surfaces #23 offset -1

Also to see the side-chains that come close to the central tunnel I can use the clashes command

clashes #23 restrict #1 overlapCutoff -1 reveal true

That reshows the tunnel atoms so hide them again

hide #23 atoms

Elaine’s ChimeraX MOLE tutorial also shows electrostatic surfaces on the protein, and she gave a journal-club review of tunnel programs.

Tom Goddard, October 3, 2023