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: [log in to unmask] Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box 647, D-78457 Konstanz
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