MINIMUM ZETA: Difference between revisions

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== Examples ==
== Examples ==
Using the default value of MINIMUM_ZETA= 0.15, one obtains in CORRECT.LP:


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
    6.78      76993  19828    19942      99.4%      3.5%      4.8%    76973  23.88    4.1%    3.0%  -10%  0.599    9080
    4.81      138283  35547    35595      99.9%      7.5%      7.5%  138249  15.56    8.7%    6.8%    -4%  0.792  16881
    3.94      177582  45838    45943      99.8%      8.7%      8.3%  177446  13.94    10.1%    8.4%    -2%  0.825  21918
    3.41      203352  54169    54469      99.4%      16.9%    16.0%  203075    7.93    19.8%    19.6%    9%  0.898  25847
    3.05      228865  61477    61637      99.7%      33.9%    34.4%  228019    4.08    39.6%    43.5%    1%  0.805  29056
    2.79      240279  67660    68124      99.3%      58.4%    61.1%  237748    2.33    68.8%    77.3%    2%  0.770  30609
    2.58      241037  72697    74116      98.1%      99.3%    100.1%  235667    1.42  118.4%  128.7%    6%  0.803  30621
    2.42      237676  77079    79650      96.8%    121.2%    129.7%  228955    0.98  145.8%  170.6%    2%  0.722  30204
    2.28      173189  71762    84696      84.7%    135.7%    148.8%  156159    0.71  170.1%  220.0%    2%  0.708  21582
    total    1717256  506057    524172      96.5%      18.8%    19.3%  1682291    5.40    22.2%    43.2%    2%  0.782  215798
and rf.pck generated by XDSSTAT looks like:
[[Image:zeta-0.15.png]]
[[Image:zeta-0.15.png]]


However with MIMUM_ZETA=0.1 the R-factors and completenesses get a bit better:
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
    6.78      77465  19824    19942      99.4%      3.5%      4.8%    77445  23.89    4.1%    3.0%    -7%  0.600    9078
    4.81      139162  35560    35598      99.9%      7.5%      7.5%  139162  15.62    8.7%    6.7%    -4%  0.794  16926
    3.94      178677  45842    45940      99.8%      8.7%      8.3%  178652  14.00    10.1%    8.3%    -2%  0.829  22029
    3.41      204689  54186    54467      99.5%      16.8%    15.9%  204526    7.99    19.6%    19.6%    9%  0.899  25971
    3.05      230193  61486    61641      99.7%      33.7%    34.2%  229403    4.13    39.4%    43.5%    1%  0.807  29119
    2.79      241535  67657    68124      99.3%      58.1%    60.7%  239037    2.36    68.3%    77.2%    2%  0.771  30638
    2.58      242127  72709    74118      98.1%      98.2%    99.1%  236782    1.44  117.0%  128.0%    6%  0.800  30656
    2.42      238367  77083    79650      96.8%    120.9%    129.4%  229693    0.99  145.4%  171.2%    2%  0.723  30257
    2.28      173359  71759    84698      84.7%    135.4%    148.5%  156346    0.71  169.7%  219.9%    2%  0.705  21596
    total    1725574  506106    524178      96.6%      18.6%    19.2%  1691046    5.43    22.0%    43.1%    2%  0.783  216270
and the cones along the spindle are narrower:
[[Image:zeta-0.1.png]]
[[Image:zeta-0.1.png]]


Finally, with MINIMUM_ZETA=0.01 the statistics get even better:
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
    6.78      77625  19826    19942      99.4%      3.6%      4.8%    77605  23.77    4.1%    2.9%  -11%  0.596    9077
    4.81      139571  35562    35598      99.9%      7.5%      7.5%  139571  15.60    8.7%    6.7%    -4%  0.794  16927
    3.94      179276  45840    45942      99.8%      8.7%      8.3%  179269  14.00    10.1%    8.3%    -2%  0.834  22034
    3.41      205281  54202    54465      99.5%      16.7%    15.9%  205131    8.01    19.6%    19.5%    10%  0.903  25999
    3.05      230671  61495    61643      99.8%      33.5%    34.0%  229887    4.14    39.2%    43.6%    1%  0.806  29133
    2.79      241775  67657    68124      99.3%      57.9%    60.5%  239277    2.36    68.1%    77.0%    2%  0.770  30639
    2.58      242190  72705    74122      98.1%      98.3%    99.0%  236846    1.43  117.1%  128.6%    7%  0.803  30649
    2.42      238428  77085    79650      96.8%    120.7%    129.1%  229754    0.99  145.1%  171.0%    2%  0.722  30257
    2.28      173335  71749    84693      84.7%    135.3%    148.3%  156322    0.71  169.5%  218.7%    3%  0.706  21590
    total    1728152  506121    524179      96.6%      18.6%    19.2%  1693662    5.43    22.0%    43.1%    3%  0.784  216305
and there are few reflections missing in the blind region:
[[Image:zeta-0.01.png]]
[[Image:zeta-0.01.png]]

Revision as of 16:18, 9 November 2007

As always, the authoritative documentation is at http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MINIMUM_ZETA= !

What is MINIMUM_ZETA?

MINIMUM_ZETA is a parameter determining how close reflections may be to the 'blind region' of reciprocal space to still be integrated. On the detector, the blind region consists of two cones starting at the direct beam position, and extending along the spindle, to both directions.

A high value (corresponding to a large blind region) is "safe" but produces lower completeness because more pixels of the detector are considered to be in the blind region. The default of 0.15 is on the safe side. I routinely use 0.1, and 0.05 turns out to still be good.

How could I check if a low value of MINIMUM_ZETA is beneficial for my data reduction?

It does not hurt to use a low value of MINIMUM_ZETA (e.g. 0.05) in INTEGRATE, because in CORRECT you may still choose higher values (i.e. you don't then have to re-run INTEGRATE if you want to test a different value).

Then, run CORRECT with the low values and with higher values and compare the resulting completeness and R-factors.

For a finer evaluation, you might want to inspect with VIEW the file 'rf.pck' of XDSSTAT .

Examples

Using the default value of MINIMUM_ZETA= 0.15, one obtains in CORRECT.LP:

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
    6.78       76993   19828     19942       99.4%       3.5%      4.8%    76973   23.88     4.1%     3.0%   -10%   0.599    9080
    4.81      138283   35547     35595       99.9%       7.5%      7.5%   138249   15.56     8.7%     6.8%    -4%   0.792   16881
    3.94      177582   45838     45943       99.8%       8.7%      8.3%   177446   13.94    10.1%     8.4%    -2%   0.825   21918
    3.41      203352   54169     54469       99.4%      16.9%     16.0%   203075    7.93    19.8%    19.6%     9%   0.898   25847
    3.05      228865   61477     61637       99.7%      33.9%     34.4%   228019    4.08    39.6%    43.5%     1%   0.805   29056
    2.79      240279   67660     68124       99.3%      58.4%     61.1%   237748    2.33    68.8%    77.3%     2%   0.770   30609
    2.58      241037   72697     74116       98.1%      99.3%    100.1%   235667    1.42   118.4%   128.7%     6%   0.803   30621
    2.42      237676   77079     79650       96.8%     121.2%    129.7%   228955    0.98   145.8%   170.6%     2%   0.722   30204
    2.28      173189   71762     84696       84.7%     135.7%    148.8%   156159    0.71   170.1%   220.0%     2%   0.708   21582
   total     1717256  506057    524172       96.5%      18.8%     19.3%  1682291    5.40    22.2%    43.2%     2%   0.782  215798

and rf.pck generated by XDSSTAT looks like: Zeta-0.15.png

However with MIMUM_ZETA=0.1 the R-factors and completenesses get a bit better:

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
    6.78       77465   19824     19942       99.4%       3.5%      4.8%    77445   23.89     4.1%     3.0%    -7%   0.600    9078
    4.81      139162   35560     35598       99.9%       7.5%      7.5%   139162   15.62     8.7%     6.7%    -4%   0.794   16926
    3.94      178677   45842     45940       99.8%       8.7%      8.3%   178652   14.00    10.1%     8.3%    -2%   0.829   22029
    3.41      204689   54186     54467       99.5%      16.8%     15.9%   204526    7.99    19.6%    19.6%     9%   0.899   25971
    3.05      230193   61486     61641       99.7%      33.7%     34.2%   229403    4.13    39.4%    43.5%     1%   0.807   29119
    2.79      241535   67657     68124       99.3%      58.1%     60.7%   239037    2.36    68.3%    77.2%     2%   0.771   30638
    2.58      242127   72709     74118       98.1%      98.2%     99.1%   236782    1.44   117.0%   128.0%     6%   0.800   30656
    2.42      238367   77083     79650       96.8%     120.9%    129.4%   229693    0.99   145.4%   171.2%     2%   0.723   30257
    2.28      173359   71759     84698       84.7%     135.4%    148.5%   156346    0.71   169.7%   219.9%     2%   0.705   21596
   total     1725574  506106    524178       96.6%      18.6%     19.2%  1691046    5.43    22.0%    43.1%     2%   0.783  216270

and the cones along the spindle are narrower: Zeta-0.1.png

Finally, with MINIMUM_ZETA=0.01 the statistics get even better:

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
    6.78       77625   19826     19942       99.4%       3.6%      4.8%    77605   23.77     4.1%     2.9%   -11%   0.596    9077
    4.81      139571   35562     35598       99.9%       7.5%      7.5%   139571   15.60     8.7%     6.7%    -4%   0.794   16927
    3.94      179276   45840     45942       99.8%       8.7%      8.3%   179269   14.00    10.1%     8.3%    -2%   0.834   22034
    3.41      205281   54202     54465       99.5%      16.7%     15.9%   205131    8.01    19.6%    19.5%    10%   0.903   25999
    3.05      230671   61495     61643       99.8%      33.5%     34.0%   229887    4.14    39.2%    43.6%     1%   0.806   29133
    2.79      241775   67657     68124       99.3%      57.9%     60.5%   239277    2.36    68.1%    77.0%     2%   0.770   30639
    2.58      242190   72705     74122       98.1%      98.3%     99.0%   236846    1.43   117.1%   128.6%     7%   0.803   30649
    2.42      238428   77085     79650       96.8%     120.7%    129.1%   229754    0.99   145.1%   171.0%     2%   0.722   30257
    2.28      173335   71749     84693       84.7%     135.3%    148.3%   156322    0.71   169.5%   218.7%     3%   0.706   21590
   total     1728152  506121    524179       96.6%      18.6%     19.2%  1693662    5.43    22.0%    43.1%     3%   0.784  216305

and there are few reflections missing in the blind region: File:Zeta-0.01.png