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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.