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DireX - Tutorial
Refinement of the Ribose-binding Protein, a rather simple 2-domain protein
This example is described in detail in the following paper:

G.F.Schröder, A.T.Brunger, and M.Levitt 'Combining Efficient Conformational Sampling with a Deformable Elastic Network Model Facilitates Structure Refinement at Low Resolution' Structure, Vol 15, 1630-1641 (2007) [PDF]