Mario Valle Web

Color usage in chemistry visualization

Color in chemistry visualization is used for two distinct purposes:

  1. To represent discrete nominal quantities, like element types, residue names, chain identifies, etc.
  2. To color code continuous quantitative variables, like charge, hidrophobicity, etc.

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.

Color schemas for discrete 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.

Color for quantitative data

The points to be covered are:

  1. Goal: show quantitative data, contrast, highlight. Example of the first: show charge. Of the second: show positive, zero, negative areas. Of the third: show high field areas where a probable docking can happen.
  2. Data type: continuous in one interval; continuous with a separator point (as negative-zero-positive); discrete (as coordination number)
  3. Perception issues: rainbow is bad, perceptive color scales: gamma corrected, non linear

Color on final media

A quick recap of issues related to color:

  1. Color gamut
  2. Color management for printing. Why reproduced colors does not match the one on the screen
  3. Color and file formats: file size considerations, banding

Here is a small interesting suggestion for colors for ball-and-stick from the MOLMOL pages.