The atom colouring system in coot is unsophisticated. Typically, atoms are coloured by element: carbons are yellow, oxygens red, nitrogens blue, hydrogens white and everything else green (see Section Display Manager for colour by chain). However, it is useful to be able to distinguish different molecules by colour, so by default coot rotates the colour map of the atoms (i.e. changes the H value in the HSV 1 colour system). The amount of the rotation depends on the molecule number and a user-settable parameter:
(set-colour-map-rotation-on-read-pdb 30).
The default value is 31^\circ.
Also one is able to select only the Carbon atoms to change colour in
this manner: (set-colour-map-rotation-on-read-pdb-c-only-flag
1).
The colour map rotation can be set individually for each molecule by
using the GUI: Edit -> Bond Colours....