Color by Chemistry - This is the default color scheme, and matches the colors used in DNASTAR’s Protean 3D and MegAlign Pro applications. 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.”
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.
Need more help with this?