On 30 Dec, Dean Madden wrote: > It's also a good point that NCS can help improve the quality of > structures in a lot of other ways. If properly accounted for, its > benefits clearly outweigh any drawbacks.
Yes, in fact excluding NCS-related reflections is undesirable ideally, because of the benefits of NCS-symmetry averaging, and because their amplitude is likely to be high. Excluding such reflections in a sphere is also likely to lead to systematic errors, although such errors might be small. It is important to note that coupling is not a problem if _all_ of the NCS-related reflections are included in the phase calculations. In that case the R-free set would obviously be independent of the coupled set. NCS-related reflections pile up in narrow slabs of reciprocal space that are not coincident to the reciprocal space axes. A better way to account for the coupling problem would be to choose a random R-free set, which excludes these slabs, so that _all_ of the NCS-related data can be included in the phase calculation. The random selection of the R-free set would then be unbiased with respect to the working set including _all_ of the NCS-related reflections, and the full benefit of NCS would be realized while solving the problem of coupling. If one insists on excluding some NCS-related reflections, then intersections between the slabs and thin resolution spheres could be used. This intersection could be included in the R-free set, since these reflections obviously have some degree of coupling, and if they are excluded from the calculation, they should be excluded together. I am troubled by the possibility however that there may be additional coupling between reflections within these NCS-symmetry related reciprocal space slabs which are not restricted to the same resolution sphere. Moreover a spherical intersection is not a random intersection of the set of NCS-related reflections. It seems to me that none of them should be included in the R-free set ideally. Now, one of us needs to figure out the width of the slab and write some code ;-}. Regards, Michael L. Love Ph.D Department of Biophysics and Biophysical Chemistry School of Medicine Johns Hopkins University 725 N. Wolfe Street Room 608B WBSB Baltimore MD 21205-2185 Interoffice Mail: 608B WBSB, SoM office: 410-614-2267 lab: 410-614-3179 fax: 410-502-6910 cell: 443-824-3451 http://www.gnu-darwin.org/ -- Visit proclus realm! http://proclus.tripod.com/ -----BEGIN GEEK CODE BLOCK----- Version: 3.1 GMU/S d+@ s: a+ C++++ UBULI++++$ P+ L+++(++++) E--- W++ N- !o K- w--- !O M++@ V-- PS+++ PE Y+ PGP-- t+++(+) 5+++ X+ R tv-(--)@ b !DI D- G e++++ h--- r+++ y++++ ------END GEEK CODE BLOCK------
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