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Garib gave a nice description of jelly-body refinement at the ACA meeting. IIRC from his talk, conceptually jelly-body refinment is the equivalent of adding "springs" between atoms within a certain radius of each other that restrain their movement during refinement. The restraints contribute to the target function curvature. The weight factor describes the contribution of the restraints to the overall target function. If w=1 and and the radius of atoms considered was infinity, you would have rigid body refinment. If w=0 you have normal uncontrained refinment. The REFMAC defaults are 4.2 A for the constraints radius, and 0.02 for the weighting factor. If I understand it correctly, it's basically like a slightly flexible rigid body refinement. Bigger w, more rigid jellyfish. (Someone will correct me if I have this wrong.) Mathematically, the contribution to the target function is sum(w (|d|-|dcurrent|)^2) where is d is a measure of the distances between atom pairs within a certain radius. The value d is the new distances and dcurrent is the old distances. The value w is the weighting factor. I have a recently obtained 2.9A dataset for which this approach might be interesting to try and see how it works compared to the usual unrestrained refinement and/or TLS, etc. Cheers, _______________________________________ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [log in to unmask] On 8/23/2012 1:27 PM, Nathan Pollock wrote: > Dear experts, > > Could someone explain what it is exactly that jelly body refinement > does? I think that I understand it intuitively but want to make sure. > In the same vein, what does jelly body refinement sigma parameter > control? I.e., in comparison to the default sigma = 0.02, does sigma = > 0.1 make body more or less like a jelly fish? > > Thanks! > > - Nate