Dear all,
I've written
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/INTEGRATE
hoping that this will explain how XDS works (the last part focuses on
the overlap question). Caveat: this is written to the best of my knowledge.
I would also like to draw your attention to the article "Quality
Control" in XDSwiki. This would benefit _a_ _lot_ if people who have/had
problems with data from XDS could donate their raw data (to be put on
our FTP server, like the PulG data), with the goal of having a proper
data reduction (pinpointing and solving problems!) and evaluation in the
wiki. I believe that by moving from "anecdotal evidence" and "hearsay"
to an evidence-based evaluation of algorithms (with publicly accessible
data), everybody would benefit.
best,
Kay
Engin Ozkan schrieb:
In this case, XDS-processed data is clearly twinned, if one were to
believe moments and the cumulative intensity distribution calculated by
truncate (and everyone should - channelling Dr. Dodson).
Why I'm worried about XDS separating relatively overlapped spots is the
funny intensity stats that may result from this (as George Sheldrick and
Martin Hallberg has pointed out)? The incomplete HKL2000-processed data
(70%) still has intermediate values for the intensity stats, leaning
towards twinning. This somewhat agrees with twinning, but not
overzealous data integration.
Engin
P.S. If twinning (perfect in this case) is taken into account structure
refines to 20/26% R at 2.8 Ang., unlike in Martin's case. Without
twinning, numbers are 29/33%.
Quoting "George M. Sheldrick" <[EMAIL PROTECTED]>:
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:
<vloeken in de kerk>
or use phenix, which is indifferent to format and asu choice.
</vloeken in de kerk>
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
