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Table 4 List of default color plugins

From: Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

Name Description
Atom Index Color Color based on atom ID (from atom 1, 2, etc.)
Charge Color Color based on predicted electrostatic partial charge
Custom Color Color all atoms a specific, custom color
Distance Color Color based on distance from one end of the
Element Color Standard color scheme, giving each atom a color
(Default) defined by its element
Residue Color Color based on amino acid or nucleic acid residue
  (i.e., glycine, histidine, etc.)
SMARTS Color Color atoms matching a specific SMARTS pattern
  with a custom color