Re: [ccp4bb] I/sigma continued

[Kay Diederichs]

James Holton schrieb:

Frank von Delft wrote:

So, what statistic do we want to look at? That depends on what you are trying to do with the data. There is no way for Phil to know this, so it is good that he prints out lots of different statistics. That said, when talking about the data quality requirements for structure solution by MAD/SAD, I suggest looking at I/sigma(I) where: I - merged intensity (proportional to photons) assigned to a reciprocal lattice point (hkl index)

Does ANY program print this out...?

SCALA calls this "Mn(I/sd)". Sounds like d*TREK calls it "I/sig avg". With HKL you compute it "by hand" from the average I and average "error". Not sure about XDS...

XDS, like SCALA and d*TREK, gives both quantities, but in different tables.


The way the tables are printed is the same for both types of tables:




  I/Sigma  = mean intensity/Sigma of a reflection in shell
  Chi^2    = goodness of fit between sample variances of
             symmetry-related intensities and their errors
             (Chi^2 = 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:


                                   observed  expected


.... (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

  Anomal  SigAno   Nano
   LIMIT     OBSERVED  UNIQUE  POSSIBLE     OF DATA   observed  expected
   Corr


   -27%   0.740     527

   -25%   0.734     629

   -31%   0.769     449

   -19%   0.777     351

   -12%   0.644     211
(rest deleted for brevity)


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



HTH,

Kay

The unaveraged I/Sigma 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, as Phil explained for SCALA. 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]. 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: RESOLUTION RANGE I/Sigma Chi^2 R-FACTOR R-FACTOR NUMBER ACCEPTED REJECTED 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 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 6.66 12698 5958 10069 59.2% 5.3% 6.7% 11577 10.55 6.8% 5.5% 4.74 22569 11140 17519 63.6% 7.3% 7.8% 19592 8.24 9.5% 9.1% 3.88 28199 14683 22445 65.4% 7.9% 7.7% 23437 7.88 10.3% 10.6% 3.37 34407 17986 26530 67.8% 12.3% 12.0% 28131 5.25 16.1% 20.6% 3.01 39636 20921 29958 69.8% 22.7% 23.3% 31896 3.08 29.8% 42.6% My personal experience is that very few people actually read the heading of the tables, but there is little one can do about this.

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