3CSL: Difference between revisions

3CSL (view source)

Revision as of 18:03, 18 March 2011

3,618 bytes added , 18 March 2011

→‎Peak

Kay

Bureaucrats

2,652

edits

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 frames (0.5° oscillation) at the peak wavelength were collected after the high-remote data. They can be downloaded from [ftp://turn5.biologie.uni-konstanz.de/pub/datasets/3csl-pk.tar here] (1.9 Gb). This peak dataset is somewhat difficult to index; if the results are really bad (e.g. distance refining far away from 370 mm) with the default 180 frames, then just try with 90 or 270 frames.
+This is an excerpt from [[CORRECT.LP]] :
+ REFINED PARAMETERS:  DISTANCE BEAM ORIENTATION CELL AXIS
+ USING  166758 INDEXED SPOTS
+ STANDARD DEVIATION OF SPOT    POSITION (PIXELS)     1.80
+ STANDARD DEVIATION OF SPINDLE POSITION (DEGREES)    0.61
+ CRYSTAL MOSAICITY (DEGREES)     0.557
+ DIRECT BEAM COORDINATES (REC. ANGSTROEM)   0.001590 -0.003616  1.021443
+ DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM    1536.60   1519.03
+ DETECTOR ORIGIN (PIXELS) AT                     1528.72   1536.95
+ CRYSTAL TO DETECTOR DISTANCE (mm)       370.85
+ LAB COORDINATES OF DETECTOR X-AXIS  1.000000  0.000000  0.000000
+ LAB COORDINATES OF DETECTOR Y-AXIS  0.000000  1.000000  0.000000
+ LAB COORDINATES OF ROTATION AXIS  0.999995 -0.001537 -0.002692
+ COORDINATES OF UNIT CELL A-AXIS   -41.622  -128.332    80.636
+ COORDINATES OF UNIT CELL B-AXIS    45.889    72.744   139.459
+ COORDINATES OF UNIT CELL C-AXIS  -551.193   220.474    66.370
+ REC. CELL PARAMETERS   0.006362  0.006103  0.001674  90.000  90.000  90.000
+ UNIT CELL PARAMETERS    157.174   163.848   597.351  90.000  90.000  90.000
+ E.S.D. OF CELL PARAMETERS  7.9E-01 8.7E-01 3.0E+00 0.0E+00 0.0E+00 0.0E+00
+ SPACE GROUP NUMBER     22
+ ...
+     a        b          ISa
+.764E+00  7.144E-04   13.43
+ ...
+       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
+.29       26331    7014      7090       98.9%       5.3%      5.5%    26314   20.22     6.3%     4.2%    71%   1.936    3195
+.90       48060   12542     12555       99.9%       8.4%      8.4%    48060   13.36     9.8%     8.5%    45%   1.322    5963
+.83       61534   16074     16144       99.6%      11.0%     10.6%    61534   10.69    12.9%    13.2%    27%   1.051    7728
+.19       71665   18994     19085       99.5%      12.5%     11.8%    71658    9.61    14.6%    16.0%    18%   0.920    9190
+.75       77668   21598     21677       99.6%      19.5%     19.3%    77668    6.33    23.0%    27.1%     6%   0.794   10491
+.42       78594   23767     23865       99.6%      28.3%     29.5%    78582    4.14    34.0%    45.0%     4%   0.735   11548
+.17       64135   24351     26036       93.5%      42.7%     46.4%    60830    2.18    52.9%    78.5%     2%   0.689    9568
+.97       40861   20207     27920       72.4%      63.8%     72.3%    35172    1.18    83.3%   118.6%     1%   0.657    6055
+.80       23238   15074     29715       50.7%      89.5%    104.9%    15359    0.63   122.8%   175.5%     5%   0.646    2502
+    total      492086  159621    184087       86.7%      14.8%     15.1%   475177    6.17    17.8%    30.6%    22%   0.901   66240
+ NUMBER OF REFLECTIONS IN SELECTED SUBSET OF IMAGES  501334
+ NUMBER OF REJECTED MISFITS                            8429
+ NUMBER OF SYSTEMATIC ABSENT REFLECTIONS                  0
+ NUMBER OF ACCEPTED OBSERVATIONS                     492905
+ NUMBER OF UNIQUE ACCEPTED REFLECTIONS               159845
+The verdict is clear: bad ISa, anomalous correlation > 30% only to about 5 A. The reason becomes clear if we load FRAME.cbf into [[XDS-Viewer]], and zoom in:
+[[File:3csl-frame.png]]
+It is clear that these split reflections provide bad data. Fortunately it seems that in other areas of the detector, the reflections look better.
 === Inflection ===
 frames (0.5° oscillation) at the inflection wavelength were collected after the peak data. They can be downloaded from [ftp://turn5.biologie.uni-konstanz.de/pub/datasets/3csl-ip.tar here] (1.8 Gb).