Colouring of atoms in O is controlled by the Paint commands.
Some commands affect an object that has already been created.
This implies that some colour has already been used in the object creation creation. The other Paint commands modify a datablock that is an atomic property associated with a particular molecule. If it does not exist, it will be created by the program with default colours. This datablock contains integer colouring codes, the RGB triplets are packed into a byte each. Skeleton atoms are in practise treated a bit differently.