Why IPA is rotation-invariant
Two residues each generate a point from their own local frame — a query point and a key point — and the model measures the distance between them. On the right, the entire protein is rotated 35 degrees: every frame rotates the same amount, so the query and key points end up rotated together too, and the distance between them stays exactly the same.
Original orientation
Rotated 35°
res 1
res 4
Q
K
d
res 1
res 4
Q
K
d
|Q − K| ≈ 58
|Q − K| ≈ 58