Figure 6.

Mapping principal components back onto structures. (a) Illustration showing PC1. The first eigenvector is projected back onto a cartoon representation of the average structure from all 24 simulations. Rhodopsin is shown as a rainbow, with blue indicating the N-terminus. Black sticks project from the c_α position in the direction of the first principal component, with a length proportional to their contribution to the motion. Transparent overlays show the Meta-II (78) (dark red) and dark-state (72) (marine) crystal structures. The top view shows rhodopsin in the plane of the membrane, the bottom view is normal to the membrane from the cytoplasmic side. (b) As in (a), except with sticks representing the second principal component of motion. To see this figure in color, go online.