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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: Ulrich Baumann ulrich {- dot -} baumann {- at -} IBC {- dot -} UNIBE {- dot -} CH Date: 2008-02-22 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. 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 > 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 CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 22 February 2008 |
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