The RasMol amino colour scheme colours amino acids according to traditional amino acid properties. The purpose of colouring is to identify amino acids in an unusual or surprising environment. The outer parts of a protein that are polar are visible (bright) colours and non-polar residues darker. Most colours are hallowed by tradition. This colour scheme is similar to the shapely scheme.
ASP,GLU bright red [230,10,10] CYS,MET yellow [230,230,0] LYS,ARG blue [20,90,255] SER,THR orange [250,150,0] PHE,TYR mid blue [50,50,170] ASN,GLN cyan [0,220,220] GLY light grey [235,235,235] LEU,VAL,ILE green [15,130,15] ALA dark grey [200,200,200] TRP pink [180,90,180] HIS pale blue [130,130,210] PRO flesh [220,150,130]