The Sequence section allows you to select color schemes for sequences in the Sequences view. Each available color scheme is described below:

Color by Chemistry - This is the default color scheme, and matches the colors used in DNASTAR’s Protean 3D application. Amino acids are colored according to their side chain chemistry:

Shapely - This color scheme matches the RasMol amino acid and RasMol nucleotide color schemes, which are, in turn, based on Robert Fletterick’s “Shapely models.”

Taylor - This color scheme is taken from Taylor and is also used in JalView (Waterhouse et al., 2009).

Zappo - This scheme colors residues according to their physico-chemical properties, and is also used in JalView (Waterhouse et al., 2009):

Solid – These scheme colors residues with the color shown. After selecting Solid, you can specify the color by clicking on the colored box to the right of the menu.

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