One of our assignments has students making pretty PDB structure diagrams using UCSF Chimera. Some of them are very good at it too. (The picture left is from the Chimera Image Gallery, not a student.)
I am always amazed by some of the figure legends, though, which feature colour descriptions such as "hot pink", "forest green" and "dodger blue". This is not so bad when there is only one pink, green and blue in the diagram - it can just be written off as idiosyncratic and superfluous. When I am asked to contrast "cornflour blue" with just "blue" in the same image, however... well, now we've crossed a line into downright unhelpful. Stick to "light blue" and "dark blue" - and if that's not clear enough, then pick another colour!