Re: [ccp4bb] data processing problem with ice rings

[Kay Diederichs]

Hi ChenTiantian,


My suggestion:

2) start XDS from the INIT step
3) use at least half of your DATA_RANGE as SPOT_RANGE



HTH,

Kay


Am 20:59, schrieb 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. 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). 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.

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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