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Surface proximity

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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

Surface proximity.png

See Also