-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Markus,
why don't you reintegrate the data with hkl2000 telling the program to treat them as non-anomalous data-set? This should give you scalepack output with the Bijvoet pairs merged and overcome the problem you describe. Cheers, Tim On 02/13/2012 06:19 PM, Markus Meier wrote: > On 11/02/12 02:52 PM, Bryan Lepore wrote: >> did you ever get a response on this? it is interesting but nobody >> posted publicly. >> >> -Bryan >> > > Dear Bryan, > > so far no one replied ... so please find my answer below. If someone > disagrees, please post. > > None of the methods I have described are appropriate. > > If the negative Bijvoet mates and the positive Bijvoet mates have been > merged separately to one intensity value for each (i.e. I+ or I-) plus > the associated standard deviation (sigI+ or sigI-), any weighted method > to calculate the mean will bias the intensity to either the I+ or the I-. > > Therefore the only appropriate method is to use the unweighted mean: > > Imean = 0.5*( I+ + I- ) > sigImean = 0.5 * sqrt( sigI+^2 + sigI-^2 ) > > The only CCP4 program I found that actually does this is mtzMADmod. This > method also has the advantage that the original intensity values of I+ > and I- can be reconstructed from the mean and the anomalous difference > (albeit with the loss of the original standard deviations). > > Method 1 (scalepack2mtz) > should not be used. The resulting value is not the best estimate > (maximum likelihood) > > Method 2 (in book by B. Rupp) > gives the maximum likelihood average in case that the reflections are > equivalent and is thus appropriate for the merging of the negative (or > positive) set of Bijvoet mates, centric reflections (where the anomalous > differences are zero) or in the case of an non-anomalous dataset the > merging of symmetry equivalent reflections. > > Method 3 > gives a more realistic sigma value in the case that the individual > intensity values are far apart and their individual standard deviations > are small. Consider the example I have posted: > > I+: 23841.50 sigI+: 634.01 I-: 9628.57, sigI-: 264.75 > Method 2: Imean=11738.95, sigIMean=244.31 > Method 3: Imean=11738.95, sigIMean=7106.47 > > If the I+ and I- values above actually were symmetry equivalent > reflections in an non-anomalous dataset, the sigImean from method 2 is > ridiculously small and method 3 gives a far more realistic value. If > method 3 is the best mathematical solution to this problem I am not able > to judge and I have to trust the statistician (or programmer) who > implemented this solution. > > Cheers, > Markus > > On 10/02/12 01:47 PM, Markus Meier wrote: >> Dear all, >> I have a anomalous dataset, processed in HKL2000. Scalepack outputs a >> file containing the separately merged sets of the Friedel pairs I- and >> I+ and their standard deviations sigI+ and sigI-. Scalepack does not >> output the averaged intensities (Imean) and the standard deviations >> (sigIMean). >> >> The CCP4 program truncate that I use to convert the intensities to >> amplitudes requires Imean, I- and I+ and the respective standard >> deviations in its input file. >> >> I have now found at least three different methods to generate the >> averaged intensities from the Friedel pairs: >> >> 1) scalepack2mtz >> >> uses standard deviations for the weights: >> weights w = 1/sigI >> >> Imean = (w+*I+ + w-*I- ) / (w+ + w-) >> sigImean = 1 / (w+ + w-) >> >> 2) Method described in Biomolecular crystallography by Bernhard Rupp, p. >> 332/333 >> to average symmetry equivalent reflections >> >> uses variances for the weights: >> weight w = 1/sigI^2 >> >> Imean = (w+*I+ + w-*I- ) / (w+ + w-) >> sigImean = 1 / sqrt(w+ + w-) >> >> 3) Method used in cctbx >> function miller.set.average_bijvoet_mates() that calls generic >> merge.merge_equivalent_obs(): >> >> same as methods 2, except that >> >> sigImean is the larger of either >> a) sigImean = 1 / sqrt(w+ + w-) >> or >> b) sigImean = sqrt( wvariance ) >> >> where wvariance = >> (w+ + w-) / [ (w+ + w-)^2 - (w+^2 + w-^2) ] * >> [ w+*(F+ - Imean)^2 + w-*(F- - Imean)^2 ] >> >> What are the advantages and disadvantages of each method? Should method >> 1 be used at all? >> >> Some example from my dataset: >> Reflection (1, 1, 0), space group P3 2 1 >> >> I+: 23841.50 sigI+: 634.01 I-: 9628.57, sigI-: 264.75 >> Method 1: Imean=13815.32, sigImean=186.76 >> Method 2: Imean=11738.95, sigIMean=244.31 >> Method 3: Imean=11738.95, sigIMean=7106.47 >> >> Thanks a lot! >> >> Cheers, >> Markus > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPOUi5UxlJ7aRr7hoRArTUAJ4uF/sx2CcdWeETz1G+r19vi7W6SQCgzlAp nSEYj5gbOlOvZ1+KBYRUrdM= =qg83 -----END PGP SIGNATURE-----
