Hello guys, There is too much text in this discussion to respond to every part of it. Apart from “jiggle” in certain software like PHENIX and I believe in X-PLOR derivatives the word “shake” means the same. In the “MAIN” environment I use the word “kick” to randomly distort coordinates. It's first use introduced in the early 90’s was to improve the convergence of model refinement and minimization. I have seen it as a substitute to molecular dynamics under real or reciprocal crystallographic restraints (we call this simulated annealing or slow cooling) as it is computationally much faster. The procedure in MAIN is called "fast cooling” because the atoms move only under the energy potential energy terms with no kinetics energy present. The “fast cooled” the structure is thus frozen - take from a high energy state to the one with the lowest potential energy reachable. In order to reach the lowest possible point in potential energy landscape the kick at the beginning of each cooling cycle is lowered. The initial kick coordinate size is typically from 0.8A and drops down each cycle down to 0. The experience shows values beyond 0.8 may not lead to recovery of chemically reasonable structure in every part of it. Towards the end of refinement the starting kick is typically reduced to 0.05. Apart from coordinates also B-factors can be kicked.
Are the structures after “kick” cooling refinement the same as without the kick? My over two decades long experience shows that by kicking convergence of refinement is improved. The resulting structures can thus be different as the different repeating cooling cycles may shift them to a lower energy point. However, after the structure is refined (has converged), the different refinements will converge to approximately the same coordinates as Ian described. I assume the this is the numerical error of the different procedures. As to the use of different TEST sets we came to a different conclusion (see bellow). As to the claim(s) that kicking/jiggling/shaking does or does not remove the model bias the color of the answer is not black and white, but it is grey. Kicking namely reduces the model bias, but does not eliminate it. We have shown this in our kick map paper by Praznikar J et al (2009) "Averaged kick maps: less noise, more signal... and probably less bias." Acta Crystallogr D Biol Crystallogr. 921-31. As for the use of % or number of reflection for R-FREE and the TEST, my suggestion is not use the TEST set and concept of R-free at all. Namely, - excluding the data from the target changes the target, because in refinement the information present in every missing reflection can not be recovered from the rest of data. (The Fourier series terms are orthogonal to each other, therefore information from each reflection is not present in any other reflection.) The absence of certain data thus contains a bias of their absence. - In addition, in the ML refinement using the cross validation the shape of ML function is calculated from the TEST set of structure factors of chemically reasonable structure, which is regularized by chemical energy terms and thus contains systematic error. Because of this propagation of this effect on the whole model structure under refinement, the cross validation introduces model bias in refinement. For detailed explanation you are invited to read our paper "Free kick instead of cross-validation in maximum-likelihood refinement of macromolecular crystal structures” which just appeared on line in Acta Crys D (2014). best regards, dusan Dr. Dusan Turk, Prof. Head of Structural Biology Group http://bio.ijs.si/sbl/ Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director http://www.cipkebip.org/ Professor of Structural Biology at IPS "Jozef Stefan" e-mail: [email protected] phone: +386 1 477 3857 Dept. of Biochem.& Mol.& Struct. Biol. fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com
