There are a number of different causes of colour, incorporation of traces of other elements is only one. In the case you mention:
"some varieties of quartz - like smoky quartz and amethyst - actually derive their beautiful colors from defects in their crystalline structures".
http://www.webexhibits.org/causesofcolor/12.html
"some varieties of quartz - like smoky quartz and amethyst - actually derive their beautiful colors from defects in their crystalline structures".
http://www.webexhibits.org/causesofcolor/12.html