Hi
I'd agree with Kay here - I would think that the original indexing is
incorrect.
One thing I notice on the original image as posted - there's a red
cross on it - if that's supposed to mark the beam position, I think
it's about 4mm or so away from the true position.
So -
(1) check the beam position carefully (it may be wrong in the image
header)
(2) after indexing, make sure that the predictions match the spot
positions
(3) if the predictions don't match the spot positions, don't try to
integrate - find out what's wrong (wrong wavelength, beam position,
distance???). If you can't work it out, ask one of the experts to look
at a sample of your original images (iMosflm ask Andrew or me, XDS ask
Kay, HKL Wladek or ZO...).
(4) If the predictions do match the spot positions, integrate the
dataset in P1 (i.e. triclinic) and see what Pointless suggests as the
symmetry. You may just be trying to impose too much symmetry. If you
can't work out what the issue is, ask an expert to help directly -
we're all happy to help out!
(5) Worry about the ice rings after you've sorted out the above
problems, not before.
HTH
On 15 Oct 2011, at 12:09, Kay Diederichs wrote:
Hi ChenTiantian,
the R-factors and I/sigma are bad even at low resolution where the
first icering does not influence the results.
Thus, the problem with your data processing has little to do with
the icerings. I guess that the indexing is not correct.
My suggestion:
1) using adxv or a similar display program, note what the inner and
outer limits of the ice rings are. These values should be used as
parameters for the EXCLUDE_RESOLUTION_RANGE= keywords in XDS.INP,
not the provided ones (which are meant for hexagonal ice).
2) start XDS from the INIT step
3) use at least half of your DATA_RANGE as SPOT_RANGE
4) make sure that ORGX and ORGY are correct - mis-indexing is in 90%
of the cases due to a wrong origin. In fact, just estimating ORGX
and ORGY from the first frame, using adxv or XDS-viewer, seems to do
a good job.
HTH,
Kay
Am 20:59, schrieb ChenTiantian:
Hi there,
I am processing a dataset which has bad ice rings (as you can see
in the
attach png file).
I tried both XDS and imosflm, and got similar results, it seems that
adding " EXCLUDE_RESOLUTION_RANGE" cannot get rid of the effects of
the
ice rings.
the following is part of the CORRECT.LP which is the second attached
file, you can find more details there.
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF
RESOLUTION
RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR
R-FACTOR COMPARED I/SIGMA R-meas Rmrgd-F Anomal SigAno Nano
LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed
expected Corr
4.24 37152 5537 5545 99.9% 46.9%
52.7% 37150 2.48 50.8% 19.4% -28% 0.513 5136
3.01 55344 9002 9840 91.5% 62.7%
65.1% 55116 1.76 68.3% 48.1% -28% 0.520 7760
2.46 84636 12699 12703 100.0% 67.4%
84.7% 84634 1.55 73.0% 54.2% -19% 0.513 12104
2.13 97910 14743 14987 98.4% 254.5%
199.3% 97908 0.16 276.2% 4899.9% -23% 0.473 14037
1.90 110260 16846 16940 99.4% 299.2%
303.3% 110245 0.06 325.0% -99.9% -17% 0.422 15995
1.74 118354 18629 18744 99.4% 1062.0%
1043.6% 118317 -0.20 1156.4% -99.9% -13% 0.380 17414
1.61 122958 20193 20331 99.3% 967.5%
1571.1% 122868 0.10 1059.7% 987.3% -2% 0.402 18348
1.51 125075 21554 21794 98.9% 838.9%
1355.1% 124933 0.08 922.6% 1116.9% -1% 0.402 18977
1.42 72057 17042 23233 73.4% 640.8%
775.3% 70391 0.08 732.5% 826.7% -8% 0.425 10003
total 823746 136245 144117 94.5% 166.4%
166.7% 821562 0.40 181.1% 296.7% -15% 0.435 119774
Note that I/SIGMA of each resolution shell is <2.5, so how should I
do
to process the dataset properly? Any suggestion about this super
ice rings?
Thanks!
Tiantian
--
Shanghai Institute of Materia Medica, Chinese Academy of Sciences
Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park,
Shanghai, 201203
--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: kay.diederi...@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box 647, D-78457 Konstanz
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--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,
Hills Road, Cambridge, CB2 0QH
