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Technically, it's possible. In the dark, color actually DOESN't exist! It's not that you can't see it, it's just GONE. If you had infrared goggles, everything would be an eerie weird color. That's what happens when you get a wavelength longer than red, but still visible. Color is just what happens when a particular object absorbs all of the colors but one. If there is a red stop sign, the stop sign is reflecting only red, after a prism in the pigments of the paint used to pain the sign breaks the light wave into a spectrum.

To answer your question, It's very likely and highly possible that atoms could have color if we could observe them. But here's one thing for sure. it's NOT THE ATOMS THAT MAKE THE COLOR! just because a pencil is yellow, doesn't mean the atoms of the paint are yellow. It means that there are atoms that form to make something called a pigment, which breaks the light wave into the spectrum, and reflects the one color that you see (yellow).

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