Rigid body refinement via Nelder-Mead Simplex minimization is available in Coot. Simplex refinement has a larger radius of convergence and thus is useful in a position where simple rigid body refinement finds the wrong minimum. However the Simplex algorithm is much slower. Simplex refinement for a residue range start-resno to end-resno (inclusive) in chain chain-id can be accessed as follows:
(fit-residue-range-to-map-by-simplex start-resno end-resno alt-loc
chain-id imol imol-for-map)
There is currently no GUI interface to Simplex refinement.