The colours of the background to the plot, and of various symbols, plotted on the LIGPLOT diagram, can be defined as follows:-
COLOURS ------- CREAM <- Background colour of page PURPLE <- Ligand bonds [or ATOM - see Note] BLACK <- Non-ligand bonds [or ATOM - see Note] SKY BLUE <- Hydrogen bonds BRICK RED <- Hydrophobic interactions ORANGE <- Accessibility shading: Buried atoms YELLOW <- Accessibility shading: Accessible atoms BLUE <- Nitrogen atoms RED <- Oxygen atoms BLACK <- Carbon atoms YELLOW <- Sulphur atoms TURQUOISE <- Water atoms PURPLE <- Phosphorus atoms PINK <- Iron atoms LIME GREEN <- All other atoms BLACK <- Atom edges BLACK <- Circles in simple-residue representation
Note that, if "ATOM" is entered as the colour of the ligand- or non-ligand bonds, the bonds will be coloured such that each half is of the colour of the atom bonded at that end.