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Re: [ccp4bb] XDS and overlaps -cumulative intensity distributions, E-test
 

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CCP4bb <-- 2008 <-- February 2008 <-- 22 February 2008
Previous message:
Subject: Re: XDS and overlaps -cumulative intensity distributions, E-test
From: Kay Diederichs kay {- dot -} diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2008-02-22 		Next message:
Subject: Re: XDS and overlaps -cumulative intensity distributions, E-test
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2008-02-22


Subject: Re: XDS and overlaps -cumulative intensity distributions, E-test
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2008-02-22
Hi Uli,

On Fri, Feb 22, 2008 at 09:53:36AM +0100, Ulrich Baumann wrote:
> It is a known feature that data sets integrated with previous XDS versions
> had frequently cumulative intensity distributions that could be
> interpreted as twinning, i.e. the number of weak reflections was too small
> and the curves for the acentric reflections had a sigmoidal shape. This
> phenomenon also occured in my experience with data sets that had no
> overlapping reflections as judged by integration with HKL2000 or MOSFLM
> (where the intensity distributions then looked perfectly normal). From a
> preliminary test, the December 2007 release of XDS appears to have changed
> in this repect. When integrating the same data sets with a previous
> version (I think August 2007) and this newest version, the intensity
> dsitribution obtained by the latter looks now as expected. Unfortunately
> there is no hint in the release notes.
> As said, this is just my first impression and I would be curios if
> otherpeople obeserve the same.

Absolutely: pre-December2007 releases had the tendency to give
significant intensities for high resolution ranges where visual
inspection of images didn't show any spots. This lead to sometimes
over-optimisitic high-resolution data - the various statistics like
Rmerge/Rmeas and I/sig(I) showed a kind of plateu towards high
resolution.

With the December2007 release this is gone and the statistics nicely
explode towards high resolution and non-existent data - which is a
very good thing, since structures are solved with real data and not
through good I/sig(I) statistics. This also means that the intensity
statistics are now clean and as expected.

At least that's my impression.

Clemens

> By the way, I think a part of the problem may also arise that CORRECT or
> XSCALE apply too many correction factors -- try CORRECTIONS=DECAY only.
> Gives worse R-factors and worse I/sig(I) but sometimes nicer intesity
> distributions.
> Or use pointless on the INTEGRATE.HKL file (not XDS_ASCII.HKL) and then
> SCALA -- we had one SAD case where this aided structure solution
> significantly, just beware that the unit cell is not postrefined by the
> CORRECT step then.
>
>
> Ulrich
>
>
>
>
> On Thu, 21 Feb 2008 19:24:32 +0100, George M. Sheldrick
> wrote:
>
> >All SHELX programs and XPREP are also indifferent to the asu choice
> >and to whether the data have been merged or not (even SHELX-76). It
> >is CCP4 historical baggage and high time it was eliminated.
> >
> >On the official thread of this discussion, my impression is that 3D
> >integration programs (like XDS) are able to handle overlapping
> >reflections better than 2D integration programs, as one would expect.
> >One simple test is the mean value of
E^2-1
; if is is too small,
> >you either have twinning or reflection overlap. Unfortunately and
> >surprisingly XDS often fails this test (especially if the data have
> >been flattened with XSCALE),
> >
> >George
> >
> >On Thu, 21 Feb 2008, Peter Zwart wrote:
> >
> >>
> >>or use phenix, which is indifferent to format and asu choice.
> >>
> >>
> >>P
> >>
> >
> >Prof. George M. Sheldrick FRS
> >Dept. Structural Chemistry,
> >University of Goettingen,
> >Tammannstr. 4,
> >D37077 Goettingen, Germany
> >Tel. +49-551-39-3021 or -3068
> >Fax. +49-551-39-2582
>
>
>
> --
> Prof Ulrich Baumann
> Departement für Chemie und Biochemie
> Freiestrasse 3
> Ch-3012 Bern, Switzerland
> phone + 41 (0)31 631 4320/4343
> fax + 41 (0) 31 631 4887
>

--

***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park
* Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group (http://www.globalphasing.com)
***************************************************************

CCP4bb navigation

CCP4bb <-- 2008 <-- February 2008 <-- 22 February 2008
Previous message:
Subject: Re: XDS and overlaps -cumulative intensity distributions, E-test
From: Kay Diederichs kay {- dot -} diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2008-02-22 		Next message:
Subject: Re: XDS and overlaps -cumulative intensity distributions, E-test
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2008-02-22


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