Figure 1.

(a) The sphere represents the SO(3)×ℜ³ manifold and the plane represents the tangent space at the identity. The dots on the tangent space correspond to optimization steps and the position of each dot corresponds to the first two coordinates of the exponential map parametrization at the identity. The position produced by the local optimization algorithm on the tangent space after every ten steps is shown by a color dot. Colors correspond to the energy value at that step of the optimization. Red represents high energy and blue represents low energy. Each step of the optimization is connected by a line to the next step. (b) Each sphere represents the center of mass of the ligand at every ten step of the optimization of the 1AY7 complex. The color codes are the same as in (a). The axes connected to each sphere show the rotational axes of the ligand at that step of the optimization.