On Wed, 19 Jun 2013 11:01:22 -0400, Ed Pozharski <[log in to unmask]> 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
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