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Revision as of 17:28, 15 March 2011

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→‎dataset E1
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== dataset E1 ==
== dataset E1 ==


These are the spacegroup statistics from CORRECT.LP - they obviously indicate an orthorhombic spacegroup.
Use generate_XDS.INP and run xds once. Based on R-factors and an inspection of BKGPIX.cbf, I modified the resulting XDS.INP to have
INCLUDE_RESOLUTION_RANGE=50 2.1
VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=8000. 30000.
and ran xds again. This is the excerpt from CORRECT.LP :
  SPACE-GROUP        UNIT CELL CONSTANTS            UNIQUE  Rmeas  COMPARED  LATTICE-
  SPACE-GROUP        UNIT CELL CONSTANTS            UNIQUE  Rmeas  COMPARED  LATTICE-
   NUMBER      a      b      c  alpha beta gamma                            CHARACTER
   NUMBER      a      b      c  alpha beta gamma                            CHARACTER
Line 19: Line 23:
       1    102.9  103.2  131.4  90.0  90.0  90.1  18040    6.9    14871    44 aP
       1    102.9  103.2  131.4  90.0  90.0  90.1  18040    6.9    14871    44 aP
   
   
...
REFINED PARAMETERS:  DISTANCE BEAM ORIENTATION CELL AXIS                 
USING  219412 INDEXED SPOTS
STANDARD DEVIATION OF SPOT    POSITION (PIXELS)    1.01
STANDARD DEVIATION OF SPINDLE POSITION (DEGREES)    0.11
CRYSTAL MOSAICITY (DEGREES)    0.191
DIRECT BEAM COORDINATES (REC. ANGSTROEM)  -0.004789  0.003758  1.021015
DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM    1027.25  1064.20
DETECTOR ORIGIN (PIXELS) AT                    1036.84  1056.68
CRYSTAL TO DETECTOR DISTANCE (mm)      209.38
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  0.999997  0.000527  0.002187
COORDINATES OF UNIT CELL A-AXIS    21.922    52.895    85.337
COORDINATES OF UNIT CELL B-AXIS    3.771    87.158  -54.992
COORDINATES OF UNIT CELL C-AXIS  -128.130    18.914    21.191
REC. CELL PARAMETERS  0.009731  0.009697  0.007620  90.000  90.000  90.000
UNIT CELL PARAMETERS    102.766  103.125  131.241  90.000  90.000  90.000
E.S.D. OF CELL PARAMETERS  1.3E-01 8.6E-02 9.3E-02 0.0E+00 0.0E+00 0.0E+00
SPACE GROUP NUMBER    16
So CORRECT chooses an orthorhombic spacegroup. Please note that the "UNIT CELL PARAMETERS" and the "E.S.D. OF CELL PARAMETERS" lines give a difference between the a and the b axis of 0.359 A, whereas the sum of their E.S.D.s is only 0.13+0.086 = 0.22 A.
The file continues:
...
      a        b          ISa
6.058E+00  3.027E-04  23.35
  ...
  ...
   
   
Line 43: Line 78:
  NUMBER OF SYSTEMATIC ABSENT REFLECTIONS                  0
  NUMBER OF SYSTEMATIC ABSENT REFLECTIONS                  0
  NUMBER OF ACCEPTED OBSERVATIONS                    479004
  NUMBER OF ACCEPTED OBSERVATIONS                    479004
NUMBER OF UNIQUE ACCEPTED REFLECTIONS              157108
Some comments:
* CORRECT obviously indicates an orthorhombic spacegroup.
* the number of MISFITS is higher than 1%. Running "xdsstat > XDSSTAT.LP" we obtain, among other files, the file "misfits.pck" which can be visualized using VIEW or XDS-Viewer. This clearly shows that many misfits are due to faint high-resolution ice rings - so nothing to worry about.
To my surprise, pointless does not agree with CORRECT's standpoint:
<pre>
Scores for each symmetry element
Nelmt  Lklhd  Z-cc    CC        N  Rmeas    Symmetry & operator (in Lattice Cell)
  1  0.959  9.91  0.99  65030  0.034    identity
  2  0.959  9.91  0.99  132222  0.035 *** 2-fold l ( 0 0 1)  {-h,-k,+l}
  3  0.958  9.87  0.99  110073  0.044 *** 2-fold h ( 1 0 0)  {+h,-k,-l}
  4  0.942  9.55  0.96  132646  0.109 *** 2-fold  ( 1 1 0)  {+k,+h,-l}
  5  0.958  9.87  0.99  111819  0.043 *** 2-fold k ( 0 1 0)  {-h,+k,-l}
  6  0.941  9.54  0.95  131842  0.109 *** 2-fold  ( 1-1 0)  {-k,-h,-l}
  7  0.937  9.50  0.95  224393  0.107 *** 4-fold l ( 0 0 1)  {-k,+h,+l} {+k,-h,+l}
</pre>
and
<pre>
    Laue Group        Lklhd  NetZc  Zc+  Zc-    CC    CC-  Rmeas  R-  Delta ReindexOperator
> 1  P 4/m m m  ***  1.000  9.73  9.73  0.00  0.97  0.00  0.07  0.00  0.2 [h,k,l]
- 2    P m m m      0.000  0.35  9.88  9.53  0.99  0.95  0.04  0.11  0.0 [h,k,l]
  3    C m m m      0.000  -0.02  9.72  9.74  0.97  0.97  0.07  0.07  0.2 [h+k,-h+k,l]
  4      P 4/m      0.000  0.07  9.77  9.70  0.98  0.97  0.06  0.08  0.2 [h,k,l]
  5  P 1 2/m 1      0.000  0.25  9.91  9.66  0.99  0.97  0.03  0.08  0.0 [-h,-l,-k]
  6  P 1 2/m 1      0.000  0.22  9.89  9.67  0.99  0.97  0.04  0.08  0.0 [h,k,l]
  7  P 1 2/m 1      0.000  0.21  9.88  9.67  0.99  0.97  0.04  0.08  0.0 [-k,-h,-l]
  8  C 1 2/m 1      0.000  -0.01  9.72  9.73  0.97  0.97  0.07  0.07  0.2 [h-k,h+k,l]
  9  C 1 2/m 1      0.000  -0.02  9.71  9.73  0.97  0.97  0.07  0.07  0.2 [h+k,-h+k,l]
10      P -1      0.000  0.21  9.91  9.70  0.99  0.97  0.03  0.08  0.0 [h,k,l]
</pre>
and
  Spacegroup        TotProb SysAbsProb    Reindex        Conditions
  <P 41 21 2> ( 92)    0.823  0.823                        00l: l=4n, h00: h=2n (zones 1,2)
  <P 43 21 2> ( 96)    0.823  0.823                        00l: l=4n, h00: h=2n (zones 1,2)
    ..........
    <P 4 21 2> ( 90)    0.095  0.095                        h00: h=2n (zone 2)
    ..........
  <P 42 21 2> ( 94)    0.077  0.077                        00l: l=2n, h00: h=2n (zones 1,2)
Thus suggesting #92 or #96 - the latter of which agrees with the PDB deposition. Running CORRECT in #96, we obtain:


To my surprise, pointless does not agree:
REFINED PARAMETERS: DISTANCE BEAM ORIENTATION CELL AXIS                 
USING  220320 INDEXED SPOTS
STANDARD DEVIATION OF SPOT    POSITION (PIXELS)    1.17
STANDARD DEVIATION OF SPINDLE POSITION (DEGREES)    0.14
CRYSTAL MOSAICITY (DEGREES)    0.191
DIRECT BEAM COORDINATES (REC. ANGSTROEM)  -0.004790  0.004009  1.021014
DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM    1027.19  1064.23
DETECTOR ORIGIN (PIXELS) AT                    1036.79  1056.20
CRYSTAL TO DETECTOR DISTANCE (mm)      209.52
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  0.999996  0.000901  0.002534
COORDINATES OF UNIT CELL A-AXIS    21.926    53.087    85.553
COORDINATES OF UNIT CELL B-AXIS    3.794    87.060  -54.995
COORDINATES OF UNIT CELL C-AXIS  -128.212    18.926    21.115
REC. CELL PARAMETERS  0.009704  0.009704  0.007616  90.000  90.000  90.000
UNIT CELL PARAMETERS    103.045  103.045  131.310  90.000  90.000  90.000
E.S.D. OF CELL PARAMETERS  2.1E-01 2.1E-01 2.1E-01 0.0E+00 0.0E+00 0.0E+00
SPACE GROUP NUMBER    96
...
    a        b          ISa
7.890E+00  8.793E-04  12.01
...
      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
    6.23      16770    2983      3017      98.9%      5.2%      6.1%    16752  26.20    5.7%    2.6%    55%  1.247    1223
    4.43      30598    5392      5393      100.0%      5.8%      6.2%    30596  25.25    6.3%    3.0%    50%  1.072    2420
    3.62      39822    6992      6994      100.0%      6.9%      6.6%    39820  22.27    7.6%    4.0%    32%  0.975    3215
    3.14      49620    8240      8242      100.0%      9.2%      8.7%    49619  17.14    10.1%    6.2%    19%  0.876    3847
    2.81      59388    9379      9379      100.0%      17.7%    18.1%    59387  10.44    19.3%    12.3%    0%  0.736    4410
    2.56      65652  10308    10310      100.0%      34.6%    39.1%    65652    6.08    37.7%    23.6%    -1%  0.680    4872
    2.37      71744  11258    11259      100.0%      71.3%    83.8%    71744    3.23    77.6%    52.1%    -2%  0.652    5352
    2.22      74888  12065    12082      99.9%    111.0%    116.9%    74888    1.98  121.2%    86.9%    2%  0.718    5753
    2.09      65727  12386    12874      96.2%    151.3%    176.1%    65517    1.12  168.0%  148.4%    -3%  0.631    5797
    total      474209  79003    79550      99.3%      10.3%    11.0%  473975    9.44    11.3%    17.2%    13%  0.772  36889
NUMBER OF REFLECTIONS IN SELECTED SUBSET OF IMAGES  492346
NUMBER OF REJECTED MISFITS                          17898
NUMBER OF SYSTEMATIC ABSENT REFLECTIONS                141
NUMBER OF ACCEPTED OBSERVATIONS                    474307
NUMBER OF UNIQUE ACCEPTED REFLECTIONS                79022
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