The user now has the choice of carrying out either distance geometry, ab initio simulated annealing starting from the template coordinates, or simulated annealing starting from random coordinates. The substructure distance geometry protocol, in combination with simulated annealing regularization, is usually more efficient than the pure simulated annealing protcols for well-determined systems. However, if there is any doubt about the uniqueness of the solution, ab initio simulated annealing or full-structure distance geometry should also be tried.