[Matias Ekstrand]

As far as I understand, there are two modern versions of CPK coloring of atoms in molecular models. On one hand, there is the Jmol-version, and on the other hand there is the Rasmol/Chime-version.

Is one of these preferred to use over the other? And if so, why?

[Polytriazole]

After a lot of digging in the literature, it seems that there isn't really a preferred standard for the discipline as a whole.  A particular journal or professional society (like the American Chemical Society) may have a standard they hold to, but it looks like a lot of different color schemes are okay as long as you provide a legend.

[Matias Ekstrand]

Thank you for your answer Polytriazole.