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Table 4 List of default color plugins

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



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


defined by its element

Residue Color

Color based on amino acid or nucleic acid residue


(i.e., glycine, histidine, etc.)


Color atoms matching a specific SMARTS pattern


with a custom color