Dear Kay, thank you ver much for the (as always) detailed and nicely
explained answer.
However this brings up some questions for me:
1. Could you please tell me how the "correct high-resolution cutoff"
will effect the data processing in the INTEGRATE CORRECT step.
In other words what will be the difference if I leave
INCLUDE_RESOLUTION_RANGE=50.0 0.0
2. Additionally if I leave FRIEDEL'S_LAW= TRUE in XDS.INP and choose
FRIEDEL'S_LAW= FALSE in XDSCONV.INP will the results be different?
3. With all the optimizations done in the last years are these tips and
tricks still valid?
FRIEDEL'S_LAW=FALSE ! This acts only on the CORRECT step ! If the anom
signal turns out to be, or is known to be, very low or absent, ! use
FRIEDEL'S_LAW=TRUE instead (or comment out the line); re-run CORRECT !
remove the "!" in the following line: !
STRICT_ABSORPTION_CORRECTION=TRUE ! if the anomalous signal is strong:
in that case, in CORRECT.LP the three ! "CHI^2-VALUE OF FIT OF
CORRECTION FACTORS" values are significantly> 1, e.g. 1.5 (from
https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/2QVO.xds)
Many thanks in advance, best regards, Georg.
Am 23.01.2018 um 21:16 schrieb Kay Diederichs:
Dear Oliver,
sorry for the trouble!
A default should be correct in the majority of situations, but it's impossible
to have it work for _all_ situations. The XDS default for REFINE(IDXREF) was
changed (i.e. POSITION was removed) to improve the indexing for weak and lousy
data, _and_ because the distance values from the header are nowadays almost
always accurate. For data with very high resolution such as yours, and
significantly wrong distance, this means that at high resolution in particular
this default will lead to worse data. generate_XDS.INP (in XDSwiki) and (I
think) autoPROC and xia2 explicitly include POSITION in the REFINE(IDXREF),
i.e. override the default. Where did you get XDS.INP from?
Some comments:
a) this is why I recommend, for data sets that may be important, to always do one cycle of
optimization, i.e. after CORRECT, "mv GXPARM.XDS XPARM.XDS", change XDS.INP to have the
correct high-resolution cutoff (cutting after the last shell which still has a "*" in the
CC1/2 column), adjust the FRIEDEL'S_LAW= setting, and run JOB=INTEGRATE CORRECT. In your case this
would make the refined distance available to INTEGRATE, and should result in very good data.
b) at which beamline did you collect the data? Such a high difference between
refined distance and distance from header is unusual, and should be reported to
(and fixed by) the beamline staff.
c) for this beamline at least, one should use REFINE(IDXREF)=CELL BEAM
ORIENTATION AXIS POSITION . I understand that you tried this and it didn't
work? Maybe there is something else wrong then, e.g. another line later in
XDS.INP resetting REFINE(IDXREF) to something else.
If you cannot find the reason why including POSITiON into REFINE(IDXREF) does
not help, pls send me enough data to reproduce the problem.
best wishes,
Kay
On Tue, 23 Jan 2018 14:31:09 +0000, "Weiergräber, Oliver H."
<o.h.weiergrae...@fz-juelich.de> wrote:
Dear all,
After upgrading XDS from build date 20170601 to 20171218, I am experiencing
severe degradation of apparent data quality reported by CORRECT for certain
data sets. Following first indications of issues with a slightly problematic
candidate, I went back to a previously very well-behaved test case with
diffraction extending beyond 1.1 A. Using the same input with both program
versions, statistics are not too different out to approx. 1.6 A, but become
more and more divergent in outer shells. These are the values for the
highest-resolution shell (1.10--1.16 A):
20170601: I/sigI = 1.80; Rmeas = 59.9 %; CC(1/2) = 82.0 %
20171218: I/sigI = 0.14; Rmeas = 506.4 %; CC(1/2) = 5.8 %
The refined cell constants are unreasonably different as well. Obviously,
something is going awfully wrong here, presumably related to errors in geometry
parameters (which are expected to become increasingly detrimental with
decreasing dmin). As it turns out, geometry refinement behaves differently in
the latest version of XDS: most notably, IDXREF no longer refines the detector
distance by default. This is significant in this case, as in version 20170601
the distance would shift by as much as 1.3 mm, resulting in successful
integration and scaling. Unfortunately, re-adding POSITION refinement into
REFINE(IDXREF) does not help, and even having it in all refinement scopes
(IDXREF, INTEGRATE, CORRECT) only yields a limited improvement of CORRECT
statistics.
It is worth noting that examination of a dataset from an unrelated crystal
(dmin = 1.4 A) did not reveal such enormous differences -- in this case,
however, the shift in detector distance applied in the old version of XDS was
quite small (0.2 mm), which, together with the lower resolution, explains the
absence of large discrepancies.
To sum up, I suspect that, due to recent changes to the XDS code, the
refinement of geometry parameters is now overly restrained, resulting in
drastic problems in cases where the detector distance is not as precise as
desirable (and even more so at very high resolution). For such datasets, the
new version appears to be essentially unusable (at least within the parameter
space I have tested), and even in modest cases may often be inferior to the
previous one. Is there an option to revert to the former behaviour?
Best regards
Oliver
================================================
PD Dr. Oliver H. Weiergr�ber
Institute of Complex Systems
ICS-6: Structural Biochemistry
Tel.: +49 2461 61-2028
Fax: +49 2461 61-9540
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