High pressures and temperatures within the Earth's crust can change rocks from one type to another. Scientists call this process metamorphism, which comes from the Greek words for "after" and "form." At the junctions where the Earth's crustal plates collide, pushing up mountain ranges, or where one plate slides underneath another, the original rocks, or protoliths (from the Greek words meaning "first" and "rock") undergo reactions that change the chemical or crystal structure of the rocks with little or no actual melting. The grains of minerals within many metamorphic rocks are aligned in parallel due to the forces pushing on them. The pressure-temperature combination causes some sedimentary rocks to lose water molecules or become anhydrous.

One of the most striking, yet least diagnostic, features of many minerals is their color. Well-formed mineral crystals span the entire rainbow of tinctures, from red (cinnabar, garnet) to yellow (sulfur), green (malachite), blue (azurite, lazurite), and violet (the amethyst variety of quartz). Minerals containing iron and magnesium are often dark brown or dark green. Impurities, trace amounts of elements that do not normally belong in the mineral, may change the overall color of a crystal. For instance, depending on the trace amounts of impurities it contains, quartz may look colorless (no impurities), light pink (titanium, iron, or manganese), milky white (tiny bubbles of gas or liquid), purple (iron), yellow (iron), or brown (extra silicon). However, multiple minerals may have almost the same color, so scientists must rely on other physical properties to make definite identifications of mineral specimens.