Have you ever wondered how the same type of mineral can look so different from one specimen to another? A deep purple Amethyst crystal, a golden yellow Citrine, a dark and dreamy Smoky Quartz, all different colors, yet all belonging to the same mineral family, Quartz!
With the same Silicon Dioxide chemistry (SiO2), how is it that these "crystal chameleons" ended up with such drastically different colors?
It isn't magic, it's a result of subtle variations in their chemical composition, atomic structure, and the growing conditions under which they formed. So let's dive into the key factors that contribute to these amazing crystal formations.
How We Perceive Colors in the Mineral World
When light, specifically white light, hits a mineral specimen it can be transmitted through the specimen, reflected, refracted, scattered or absorbed. If the light does not get absorbed at all, the mineral appears colorless in reflected and transmitted light, such as clear Quartz.
When we perceive a mineral with color, we are viewing certain wavelengths being absorbed by the mineral (and therefore removed from the spectrum), causing the excitation and sometimes movement of electrons between orbitals. For example, if red, orange, yellow, blue and violet wavelengths are being absorbed, we would perceive a mineral as being green.. Those wavelengths that do not get absorbed combine and reach our eye as a specific color. So how do minerals get their colors?
A World of Color: Trace Elements / Transition Metals
A mineral is any naturally occurring, inorganic solid with a definite chemical composition and an organized internal structure. While the definite chemical formula of a mineral helps to define it, the presence of tiny impurities, known as trace elements, can dramatically alter its color.
If you were to add food coloring to a glass of clear water, even a single drop would create a significant change in the color of the water. In this analogy, we can think of trace elements and transition metals as the drop of coloring in our mineral water.

Quartz
Quartz for example, is naturally clear or colorless. While different varieties of Quartz are classified by different names given their color (i.e. Amethyst is purple), they all have the same basic chemistry, Silicon Dioxide (SiO2). So let's take a look at some trace elements / transition metals that alter the color of Quartz.

Amethyst
The purple variety of Quartz, Amethyst exhibits a vibrant purple hue due to trace amounts of the element Iron (Fe) that have been naturally irradiated within the Earth. This irradiation causes electrons within the Iron atoms to become excited, leading to the absorption of certain wavelengths of light, resulting in the transmission of purple light to our eyes.
Even if a minerals known base chemistry, in this case SiO2, does not seem to contain any light absorbing elements, tiny concentrations of a trace element / transition metal can alter the color of the mineral.

Certain transition metals including Iron, Manganese, Chromium, Copper, Nickel, and Cobalt that are present in minerals have electrons which can be excited by energy from light and often produce very vibrant crystal colors.
The chemical formula for Emerald (Beryl) is Be₃Al₂Si₆O₁₈. You'll notice Chromium (Cr) is not listed in its formula. However, a tiny concentration of a Chromium (Cr₃), ion, replaces a tiny amount of Aluminum (Al) in the formula, allowing for the absorption of the other colors, causing the transmitted light to our eyes to be green.
As you can see, even a minuscule replacement or addition of an element or ion can effect the color of a mineral!
How Can the Same Mineral Form Into Different Colors?
Fluorite is a fairly common mineral that can form into a variety of different colors and shapes. But how can a mineral with the same basic chemistry, Calcium Fluoride (CaF2) look so different from specimen to specimen?

Internal Geometry and Crystal Structure
Atomic structural defects inside a mineral can cause changes in coloration. On an atomic level, an excess electron that is unattached to any single atom, or a "hole" from an absence of an electron can have the same effect.
In Fluorite, formula CaF₂, a purple color is scene when there is a defect in the structure. An F- ion is missing from its usual site in the Fluorite structure. This can be caused by a variety of factors, such as the Fluorite forming in an environment with excess Calcium, or perhaps from radiation within the Earth displacing the F- from its usual position.
This causes it to occupy an excited state, similar to the transition metals we described earlier. This movement can cause not just variations in perceived color but also optical fluorescence!
A World of Shapes: Growth Conditions and Crystal Habits
While color is often the first thing that catches our eye, the shape, or crystal habit of a mineral is equally intriguing. The same mineral can crystallize into vastly different forms due to changes in temperature, pressure, impurities within the growing medium, and constraints within the growth cavities / crystal pockets of the host rock in which the minerals are forming. For example, a crystal growing in a tightly confined space may end up with a more tabular appearance than if it had adequate space to develop.
The atomic structure of a mineral dictates its potential growing shapes, but the surrounding environmental conditions will ultimately influence how the final crystal shape actually develops.
Conclusion
The color and shape of a crystal are often a result of the interplay between its chemical composition, the presence of trace elements, and the specific environmental conditions it underwent during its formation. These factors determine the stunning and seemingly endless array of colors and shapes we see in the mineral world.