and Error Analysis
by Dr. Robert
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
This section contains a brief general description of the DREAR program
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.
All data sets are processed by the following four
programs in the order given. SIR native and derivative data sets are processed
- Sorting, inter-subset scaling, empirical absorption correction based
on multiple symmetry-equivalent measurements, averaging of replicate
and equivalent measurements, and analysis of variance.
- 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.
- Absolute scale factor and overall anisotropic mean-square atomic-displacement
parameters by the method of Henri Levy and William Thiessen.
- 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".
- Evaluate and apply anisotropically variable local scale factors for
SIR or SAS pairs of data sets.
- Evaluate renormalized SIR or SAS difference E-magnitudes.
- 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
(in a formatted ASCII file)
(in a DiffE-ranked, formatted ASCII file)
Blessing, R.H. (1987). Data Reduction and Error Analysis for Accurate
Single Crystal Diffraction Intensities. Crystallography Reviews,
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.