ChimeraX Recipes

Show a binding pocket surface

Here are commands that show the surface of a protein binding pocket. This uses a fancy ChimeraX command measure contactArea which shows the protein surface where it is within 3 Angstroms of the ligand surface. This creates a fairly nice pocket surface without too many jagged edges. The commands also make the surface have a small thickness and makes two copies of it so the inside and outside of the surface can be given different colors. The example uses Protein Databank model PDB 2zcp.

open 2zcp
delete /b
surface :fps sharp false
surface protein sharp false
measure contactArea #1.3 with #1.2 distance 3 slab -.1,0 color tan
measure contactArea #1.3 with #1.2 distance 2.99 slab -.11,-.01 color cornflowerblue
surface close #1
surface dust #2,3 size 1 metric "size rank"
hide atoms,ribbon
show #1:fps,mg
color C white
set bgcolor gray
graphics silhouettes true

Tom Goddard, April 3, 2024