For traditional protein dynamics, or for traditional storage of protein structures, what they do is they take the numerically computed (or experimentally observed) protein structure, and define a map $\pi$. The map $\pi(n)$ roughly gives the (relative) spatial position of the $n$th amino acid in the chain. Separately there is also a map $\nu(n)$ which gives the orientation of the amino acid, and what is hanging off the backbone there.