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DREAR
(Data Reduction
and Error Analysis
Routines)
by Dr. Robert
Blessing
DREAR is a set of programs for processing intensity data and computing normalized structure magnitudes (|E|s). The SnB graphical user interface provides automated access to four of these programs for reducing Basic (non-difference) data and to six of them for reducing SIR (native and derivative data sets required) or single-wavelength SAS (input native data set with separate Bijvoet measurements required) substructure data. The "diffe" program computes isomorphous or anomalous difference magnitudes. FA values may be input to SnB as Basic data. In such cases, it is necessary to manually adjust the SnB parameters to values appropriate for substructures.
This section contains a brief general description of the DREAR program package including:
- Brief program descriptions.
- A data reduction flow chart.
- Descriptions of the record structure in the reflection data output from each program.
- Literature references.
Links to detailed individual program write-ups, "program.use" text files, are supplied. Output from each program is written to a file (program_name.lp) that can be examined, edited, and printed. Users with specific questions about the DREAR package should contact Dr. Robert Blessing.
All data sets are processed by the following four programs in the order given. SIR native and derivative data sets are processed separately.
- sortav
- Sorting, inter-subset scaling, empirical absorption correction based on multiple symmetry-equivalent measurements, averaging of replicate and equivalent measurements, and analysis of variance.
- bayes
- Bayesian probability expectation values of F2,
,
F and 
given
the set of unique 
and
.
Also calculates E and 
,
where is normalized by the local averaged measured intensity.
,
- levy
- Absolute scale factor and overall anisotropic mean-square atomic-displacement parameters by the method of Henri Levy and William Thiessen.
- eval
- Normalized structure factor amplitudes
, where E is normalized by the Wilson expectation value of intensity. In addition,computation of normalized difference magnitudes for SIR and SAS data requires programs "diffe" and (optionally) "locscl".
- locscl
- Evaluate and apply anisotropically variable local scale factors for SIR or SAS pairs of data sets.
- diffe
- Evaluate renormalized SIR or SAS difference E-magnitudes.
Notes:
- Be certain that both |F+| and |F-| are included in the input file for SAS data.
- For SIR cases, the sortav-bayes-levy-eval sequence is run twice, once for the native data and once for the derivative. Two input files must be specified on the "Create Es" screen. The two resulting "edata.eee" files are passed to locscl and diffe where they are combined by taking differences.
- If locally normalized |E| values are to be used (typically, this option is considered only if the resolution is less than 3.5Å), then "data.bayes", rather than "edata.eee", is passed to the subsequent programs.
- The program "make_SnB_file" is a small utility that reformats the DREAR results to create the output file specified on the "Create Es" screen. Typically, this file is then passed (via the "Reflections and Invariants" screen) as a new reflection file to the SnB phasing program.
Record Structure In Reflection Data Output Files
|
sortav |
data.sortav |
ih,ik,il,Fsq,sigFsq,rmsd,nmeas,Tbar,s0(3),s1(3) |
|
bayes |
data.bayes |
ih,ik,IL,Fsq,sigFsq,F,sigF |
|
eval |
edata.hkl |
ih,ik,IL,Fsq,sigFsq,F,sigF,E,sigE |
|
locscl |
data.locscl |
ih,ik,IL,F1,sigF1,F2,sigF2,E1,sigE1,E2,sigE2 (in a formatted ASCII file) |
|
diffe |
data.diffe |
ih,ik,IL,DiffE,sigDiffE (in a DiffE-ranked, formatted ASCII file) |
References
Blessing, R.H. (1987). Data Reduction and Error Analysis for Accurate Single Crystal Diffraction Intensities. Crystallography Reviews, 1, 3-58.
Blessing, R.H. (1986). DREAM - data reduction and error analysis routines for accurate single-crystal diffraction intensity measurements. J. Appl. Cryst. 19, 412.
Blessing, R.H. & Langs, D.A. (1987). Data Averaging with Normal Down-Weighting of Outliers. J. Appl. Cryst. 20, 427-428.
Blessing, R.H. & Langs, D.A. (1988). A Priori Estimation of Scale and Overall Anisotropic Temperature Factors From the Patterson Origin Peak. Acta Cryst. A44, 729-735.
Blessing, R.H. (1989). DREADD - data reduction and error analysis for single crystal diffractometer data. J. Appl.Cryst. 22, 396-397.
Blessing, R.H. (1995). An Empirical Correction for Absorption Anisotropy. Acta Cryst. A51, 33-38.
Blessing, R.H., Guo, D.Y. & Langs, D.A. (1996). Statistical Expectation Value of the Debye-Waller Factor and |E(hkl)| Values for Macromolecular Crystals. Acta Cryst. D52, 257- 266.
Blessing, R.H. (1997). Outlier Treatment in Data Merging. J. Appl. Cryst. 30, 421-426.
Blessing, R.H. (1997). LOCSCL: a program to statistically optimize local scaling of single-isomorphous-replacement and single-wavelength-anomalous-scattering data. J. Appl. Cryst. 30, 176-177.
Blessing, R.H., Guo, D.Y. & Langs, D.A. (1998). Intensity Statistics and Normalization. In Direct Methods for Solving Macromolecular Structures, NATO ASI Series Volume, Series C: Mathematical and Physical Sciences, Vol. 507, edited by S. Fortier, pp. 47-71. Dordrecht, The Netherlands: Kluwer Academic Publishers.
Blessing, R.H. & Smith, G.D. (1999). Difference Structure Factor Normalization for Determining Heavy-Atom or Anomalous Scattering Substructures. J. Appl. Cryst. 32, 664-670.
