Not so much on the whole atom as much as the electrons themselves (we’re still talking about the atomic scale here lol). Depending on how electrons in the atoms in some specific matter are arranged and move around, they will absorb photons (light) in a specific way, and maybe even reflect some back. The combination of absorbed and reflected photons are perceived by us as different colors.
If all of the photons are absorbed, it would show black. If all of the photons are reflected (depending on the how), it would show white or a reflective surface such as a mirror. Anything in between is every other color in this universe.
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