2VB1: Difference between revisions

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Revision as of 19:07, 11 March 2011

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   SILICON=34.812736 ! account for theta-dependant absorption in the CCD's phosphor. The correction is only
   ! significant for hi-res data; 34.812736=32*(value for silicon as printed to CORRECT.LP if SILICON= not given)
-  MAXIMUM_NUMBER_OF_PROCESSORS=4 ! for fast processing on a machine with many cores, use (e.g. for 16 cores)
+  MAXIMUM_NUMBER_OF_PROCESSORS=4 ! for fast processing on a machine with many cores (e.g. for 16 cores)
-  MAXIMUM_NUMBER_OF_JOBS=6 ! This "overcommits" the available cores but on the whole this produces results faster (see below).
+  MAXIMUM_NUMBER_OF_JOBS=6 ! "overcommit" the available cores but on the whole this produces results faster (see below)
   SPACE_GROUP_NUMBER=1                   ! this is known
   UNIT_CELL_CONSTANTS=  27.07 31.25 33.76 87.98 108.00 112.11  ! from 2vb1
@@ Line 187: / Line 187: @@
   NUMBER OF UNIQUE ACCEPTED REFLECTIONS               171714
+=== further optimization ===
+Another round of optimization again improves the R-factors and I/sigma at high resolution a bit, but it also increased the misfits back to 8200. At this point I decided to switch to FRIEDEL'S_LAW=FALSE, and the resulting table is:
+       NOTE:      Friedel pairs are treated as different reflections.
+ 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
+.77        9599    9023     19002       47.5%       1.5%      1.5%     1152   36.81     2.1%     1.6%     0%   0.000       0
+.26       31196   28239     33446       84.4%       1.4%      1.6%     5914   34.40     2.0%     1.6%     0%   0.000       0
+.03       40125   35205     43274       81.4%       1.7%      1.7%     9840   30.09     2.4%     2.0%     0%   0.000       0
+.89       46987   40188     51124       78.6%       2.3%      2.3%    13598   22.03     3.2%     3.4%     0%   0.000       0
+.80       52229   43723     57738       75.7%       3.9%      3.9%    17012   14.44     5.5%     6.6%     0%   0.000       0
+.73       56830   46674     64088       72.8%       7.1%      6.8%    20312    9.30    10.1%    13.2%     0%   0.000       0
+.68       60488   48814     69544       70.2%      13.9%     13.5%    23348    5.26    19.6%    27.1%     0%   0.000       0
+.63       36190   28598     74736       38.3%      28.2%     29.7%    15184    2.70    39.8%    57.3%     0%   0.000       0
+.60        9246    7246     79466        9.1%      57.8%     62.4%     4000    1.26    81.8%   122.0%     0%   0.000       0
+    total      342890  287710    492418       58.4%       2.8%      2.8%   110360   16.19     3.9%     9.9%     0%   0.000       0
+ NUMBER OF REFLECTIONS IN SELECTED SUBSET OF IMAGES  345355
+ NUMBER OF REJECTED MISFITS                            2448
+ NUMBER OF SYSTEMATIC ABSENT REFLECTIONS                  0
+ NUMBER OF ACCEPTED OBSERVATIONS                     342907
+ NUMBER OF UNIQUE ACCEPTED REFLECTIONS               287724
+Indeed this brings the number of misfits to well below 1%, and it does make some sense.
 == XSCALE results ==
-a few sweeps were optimized by copying the two lines containing mosaicity and beam divergence values from INTEGRATE.LP to XDS.INP
+The same strategy as shown for sweep e was used for sweeps a-d and f-h. XSCALE.INP is:
-=== main table ===
+ SPACE_GROUP_NUMBER=    1
+ UNIT_CELL_CONSTANTS= 27.07 31.25 33.76 87.98 108.00 112.11 !  from 2vb1 PDB entry
+ ! cellparm for a-h gives  27.083    31.269    33.773    87.978   107.998   112.133
+ OUTPUT_FILE=lys-xds.ahkl
+ FRIEDEL'S_LAW=TRUE
+ RESOLUTION_SHELLS=2.91 2.06 1.68 1.45 1.30 1.19 1.10 1.03 0.97 0.92 0.88 0.84 0.81 0.78 0.75 0.73 0.71 0.69 0.67 0.65
+ INPUT_FILE=../a/XDS_ASCII.HKL
+ INCLUDE_RESOLUTION_RANGE=30 0.65
+ INPUT_FILE=../b/XDS_ASCII.HKL
+ INCLUDE_RESOLUTION_RANGE=30 0.65
+ INPUT_FILE=../c/XDS_ASCII.HKL
+ INCLUDE_RESOLUTION_RANGE=30 0.65
+ INPUT_FILE=../d/XDS_ASCII.HKL
+ INCLUDE_RESOLUTION_RANGE=30 0.65
+ INPUT_FILE=../e/XDS_ASCII.HKL
+ INCLUDE_RESOLUTION_RANGE=30 0.65
+ INPUT_FILE=../f/XDS_ASCII.HKL
+ INCLUDE_RESOLUTION_RANGE=30 0.65
+ INPUT_FILE=../g/XDS_ASCII.HKL
+ INCLUDE_RESOLUTION_RANGE=30 0.65
+ INPUT_FILE=../h/XDS_ASCII.HKL
+ INCLUDE_RESOLUTION_RANGE=30 0.65
+=== XSCALE.LP main table ===
@@ Line 221: / Line 274: @@
      total     1433128  190017    191232       99.4%       3.3%      3.5%  1431595   33.18     3.5%     3.5%     2%   0.801  170074
+Remark: The first frames of sweeps g and h show a shadow in one corner of the detector. Nothing was done by me to exclude this shadow from processing (but one should do so if the resolution should be expanded beyond 0.65 A which the XSCALE statistics suggest to be possible). There is however no facility in XDS to exclude bad areas of specific frames in a dataset; one would need to chop the dataset into two parts.
 == Comparison of data processing: published (2006) ''vs'' XDS results ==