By default, although the dihedral angles are computed and output, only the pseudodihedral angles are used in the alignment. By entering positive weights for dihedral angles, they will play a role in the alignment.

The contribution of any dihedral or pseudodihedral angle in the alignment will be proportional to its weight divided by the sum of all dihedral/pseudodihedral angles.

The pseudodihedral angle η (ETA) is determined by taking the dot product of the normal vectors to each of the planes stipulated by the atoms C4'(i-1),P(i),C_4'(i) and P(i),C_4'(i),P(i+1). Similarly, the pseudodihedral angle θ (THETA) is determined by taking the dot product of the normal vectors to each of the planes stipulated by the atoms P(i),C4'(i),P(i+1) and C4'(i),P(i+1),C_4'(i+1).