Color in chemistry visualization is used for two distinct purposes:
For the first purpose there are various traditional schema proposed. Instead the second one is already well studied in the more general scientific visualization area, but can benefit from some fine tuning that consider the specificities of chemistry data.
There are various proposals of color schemas for ball-and-stick representation, here are some of them:
An historical note: The CPK color scheme was first used in Rasmol, and is based upon the colors of the popular plastic space filling models which were developed by Corey, Pauling and later improved by Kultun. This color scheme colors atom objects by the atom (element) type, and is the scheme conventionally used by chemists.
The assignment of element type to colors for this model is:
carbon = light-grey,
chlorine = green,
oxygen = red,
bromine and zinc = brown,
hydrogen = white,
sodium = blue,
nitrogen = light-blue,
iron = purple,
sulfur = yellow,
calcium and other metals = dark-grey,
phosphorus = orange,
unknown = deep-pink.
The points to be covered are:
A quick recap of issues related to color: