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Re: [ccp4bb] XDS and overlaps -cumulative intensity distributions, E-test |
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CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 22 February 2008Subject: Re: XDS and overlaps -cumulative intensity distributions, E-test From: Kay Diederichs kay {- dot -} diederichs {- at -} UNI-KONSTANZ {- dot -} DE Date: 2008-02-22 > 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. > I observed the same, in numerous tests. > 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. Sorry, have to disagree. Just look at e.g. MODPIX.pck and you know why the MODULATION correction is needed. The detectors are unfortunately not ideal. > 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 > > >> 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 > > > CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 22 February 2008 |
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