When showing the molecular surface of a subset of atoms (not the entire molecule), then the surface_proximity setting controls whether triangles are shown which are between an included and an excluded atom.
- surface_proximity=on: (default) Show all triangles which have at least one vertex belonging to the atom selection. In this case colors from hidden atoms can leak into the open surface edge.
- surface_proximity=off: Show only triangles where all three vertices belong to the atom selection.
This example demonstrates the color "leaking" from atoms which don't belong to the surface selection.
fetch 5hpr, async=0 color red color yellow, chain B show surface, chain B set surface_proximity, off