Just a quick comment on low resolution refinement: The concept of Deformable Elastic Network (DEN) refinement is quite similar to jelly-body refinement in the special case of gamma=0, for which the network is not deformable. In contrast to jelly-body refinement, the DEN restraints are however actually applied to the target function (and the first derivative).
For gamma>0 the minimum of the elastic network potential is allowed to move and, thus, to deform the restraints (which changes their equilibrium distances). Some individual distances can deform more than others depending on the force they feel from the target function. This automatically discriminates between those regions in the structure that need to move far (and are allowed to do so) and those regions that are happy where they are (and remain restrained). DEN refinement is implemented in CNS (1.3) and now also in Phenix (>=1.7.3). Cheers, Gunnar
