We “observe” an atom by observing energy or matter that has already bumped into that atom. We observe it by lighting it, warming it, or pinching it in some way. The real problem is trying to study one lonely atom, floating in cold space in the dark, without changing its speed or direction or temperature, since small particles are even changed by simple light. It’s like a police officer who pulls you out of traffic, asks for your license, and shines a flashlight in your face. You’re no longer going your original speed and direction, and you’re blushing red. You have been “observed”, and it’s the method of observing you that changes you because you are sensitive to those things. We don’t have a way to hide from atoms and observe them with anything they don’t react to because they react to just everything.
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