On Wed, 19 Jun 2013 11:01:22 -0400, Ed Pozharski <epozh...@umaryland.edu> wrote:
>Dear Kay and Jeff, > >frankly, I do not see much justification for any rejection based on >h-cutoff. I agree > >French&Wilson only talk about I/sigI cutoff, which also warrants further >scrutiny. It probably could be argued that reflections with I/sigI<-4 >are still more likely to be weak than strong so F~0 seems to make more >sense than rejection. The nature of these outliers should probably be >resolved at the integration stage, but these really aren't that >numerous. > >As for h>-4 requirement, I don't see French&Wilson even arguing for that >anywhere in the paper. h variable does not reflect any physical >quantity that would come with prior expectation of being non-negative >and while the posterior of the true intensity (for acentric reflections) >is distributed according to the truncated normal distribution N(sigma*h, >sigma^2), I don't really see why h<-4 is "bad". > >From what I understand, Kay has removed h-cutoff from XDSCONV (or never >included it in the first place). Perhaps ctruncate/phenix should change there was a h<-4 cutoff in previous versions of XDSCONV which has been removed. Concerning removal of negative observations/reflections, it may be justified to refer to a very recent paper - see http://journals.iucr.org/d/issues/2013/07/00/ba5192/index.html best, Kay >too? Or am I misunderstanding something and there is some rationale for >h<-4 cutoff? > >Cheers, > >Ed. > > >On Wed, 2013-06-19 at 06:47 +0100, Kay Diederichs wrote: >> Hi Jeff, >> >> what I did in XDSCONV is to mitigate the numerical difficulties associated >> with low h (called "Score" in XDSCONV output) values, and I removed the h < >> -4 cutoff. The more negative h becomes, the closer to zero is the resulting >> amplitude, so not applying a h cutoff makes sense (to me, anyway). >> XDSCONV still applies the I < -3*sigma cutoff, by default. >> >> thanks, >> >> Kay > >-- >I don't know why the sacrifice thing didn't work. >Science behind it seemed so solid. > Julian, King of Lemurs
