CORRECT.LP

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Revision as of 07:28, 7 April 2009 by Kay (talk | contribs) (fix wraparound)

XDS, like SCALA and d*TREK, gives statistics about unaveraged and averaged quantities, but in different tables. The unaveraged values are in a table that is fine-grained in terms of resolution, at the beginning of CORRECT.LP. The Sigma values in that table are corrected to match the RMS scatter.

The table that has information about the averaged data (suitably weighted) is repeated several times. It is less fine-grained in resolution (9 shells, and overall). [if a user wants this table in fine-grained form, s/he can use XSCALE].

The way the tables are printed is the same for both types of tables: at first the definitions of the quantities in the table are given, and then the table itself is printed.

Specifically, the heading of the table which talks about the unaveraged data looks like this:

 I/Sigma  = mean intensity/Sigma of a reflection in shell
 Chi2    = goodness of fit between sample variances of
            symmetry-related intensities and their errors
            (Chi2 = 1 for perfect agreement)
 R-FACTOR
 observed = (SUM(ABS(I(h,i)-I(h))))/(SUM(I(h,i)))
 expected = expected R-FACTOR derived from Sigma(I)

  NUMBER  = number of reflections in resolution shell
            used for calculation of R-FACTOR
 ACCEPTED = number of accepted reflections
 REJECTED = number of rejected reflections (MISFITS),
            recognized by comparison with symmetry-related
            reflections.

and then the table itself is:

RESOLUTION RANGE  I/Sigma  Chi2  R-FACTOR  R-FACTOR  NUMBER ACCEPTED REJECTED
                                  observed  expected

  39.660  19.587     8.23   0.96      6.36      7.12     929     940     75
  19.587  14.780     7.39   0.88      5.94      7.46    1956    1959     66
.... (many resolution shells deleted for brevity)



and later it gives the table for the averaged intensities with heading

R-FACTOR
observed = (SUM(ABS(I(h,i)-I(h))))/(SUM(I(h,i)))
expected = expected R-FACTOR derived from Sigma(I)

COMPARED = number of reflections used for calculating R-FACTOR
I/SIGMA  = mean of intensity/Sigma(I) of unique reflections
           (after merging symmetry-related observations)
Sigma(I) = standard deviation of reflection intensity I
           estimated from sample statistics

R-meas   = redundancy independent R-factor (intensities)
Rmrgd-F  = quality of amplitudes (F) of this data set
           For definition of R-meas and Rmrgd-F see
           Diederichs & Karplus (1997), Nature Struct. Biol. 4, 269-275.
(rest of heading deleted for brevity)

and the table itself is

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    
  LIMIT     OBSERVED  UNIQUE  POSSIBLE     OF DATA   observed  expected                                      Corr

    6.66       12698    5958     10069       59.2%       5.3%    6.7%    11577   10.55     6.8%     5.5%    -27%    0.740     527
    4.74       22569   11140     17519       63.6%       7.3%    7.8%    19592    8.24     9.5%     9.1%    -25%    0.734     629
    3.88       28199   14683     22445       65.4%       7.9%    7.7%    23437    7.88    10.3%    10.6%    -31%    0.769     449
    3.37       34407   17986     26530       67.8%      12.3%   12.0%    28131    5.25    16.1%    20.6%    -19%    0.777     351
    3.01       39636   20921     29958       69.8%      22.7%   23.3%    31896    3.08    29.8%    42.6%    -12%    0.644     211
(rest deleted for brevity)


So, the program indicates quite clearly what the statistics refer to.