MINIMUM ZETA

From XDSwiki

As always, the authoritative documentation is at http://xds.mpimf-heidelberg.mpg.de/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.

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. 0.03) 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 .

An example

We collected data at the SLS, beamline X06SA, on a MarCCD 225 detector. Below, I show the final output of CORRECT.LP and a mapping of R-factors on the surface of the detector (file rf.pck produced by XDSSTAT).

Using the former default value of MINIMUM_ZETA= 0.15, one obtains in CORRECT.LP (this is from a 2010 version of XDS):

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

With MIMUM_ZETA=0.1 the R-factors and completeness stays the same, but a closer look (not unexpectedly) reveals that the total number of observed reflections rises:

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

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

Finally, with MINIMUM_ZETA=0.01 the number of observed reflections gets even higher:

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

Finally, we may take a look at FRAME.pck and see that very few reflections are missing. The resolution of this image is not good enough to actually see the circles but one can see that all observed reflections are indeed hit by predictions. Ms688-frame.png

From looking at rf.pck of many datasets, it is my experience that at the SLS (beamline X06SA), the R-factors along the spindle are better than perpendicular to it, which is quite surprising (and should be investigated). Therefore it is clear that in particular for these data it is a good thing to decrease MINIMUM_ZETA because accurately measured reflections are added to the data set.