The Alchemyst is a kaleidoscope of colors. Nicholas Flamel's magical aura is green, and Dr. John Dee's is a sickly yellow. The twins have silver and gold auras. And don't even get us started on the absolutely gorgeous description of Perenelle's multicolored aura (but you should definitely take the time out to read the description of it at 16.27, and then come right back).
What's more, the colors seem to be linked with the characters' symbolic scents. Nicholas Flamel's magic is a green color and smells like peppermint—go figure; Dr. John Dee's gross sulfur-smelling aura is yellow (the color of sulfur itself, as well as the yolk of rotting eggs).
If magic is about using all of your senses on a deeper level, it makes sense that sight and scent would be so closely tied. Magic is a powerful, sensory experience that engages every part of a person. It's gotta look good and smell strong.