Hi Roger, You are correct, that *conceptually* the contribution to the target function is sum(w (|d|-|dcurrent|)^2)… however this is not actually applied to the target function. The target function remains unchanged. Only the 2nd derivative is affected by the jelly-body restraints.
Also, note that the refmac5 ccp4i interface quotes: "use jelly body refinement with sigma 0.02". You mention that "bigger w, more rigid jellyfish". This is correct. However, note that w is inversely related to sigma, thus it should be acknowledged that "smaller sigma, more rigid jellyfish"… Also, note that the utility of such regularisers is greater when the effective observation-to-parameter ratio is worse, i.e. at lower resolutions. At this stage, it is not certain exactly what the resolution threshold is such that jelly-body restraints are useful. I can envisage that it not only depends on the resolution, but also on the quality (or noisiness) of the data. I am sure that there are 2.9A datasets out there that would benefit from such regularisers. Cheers Rob On 23 Aug 2012, at 19:31, Roger Rowlett wrote: > 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: [email protected] > > 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
