Many 2D and 3D molecular editors utilize distinctive Jmol color scheme , which can be defined in a legend as such (all colors except for hydrogen are preserved; hydrogen was intentionally made light-gray instead of white):
Although I up-voted your request, because I like the idea of making structures more accessible to the general user base, I would still need some really good convincing that this was necessary, and which cases would actually benefit from it. I personally dislike JSmol and other embedded interactive elements, because from my experience they drastically ...
Atoms in JMol and in molecular modelling kits follow the CPK Coloring Scheme.
As a basic identification, hydrogen is white, carbon is grey, oxygen is red, nitrogen is blue, sulfur is yellow, and phosphorus is orange.