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Single Crystal Software Workshop ECM21-2003 Louis J. Farrugia, Department of Chemistry University of Glasgow GLASGOW G12 8QQ Scotland Processing of Bruker.

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Presentation on theme: "Single Crystal Software Workshop ECM21-2003 Louis J. Farrugia, Department of Chemistry University of Glasgow GLASGOW G12 8QQ Scotland Processing of Bruker."— Presentation transcript:

1 Single Crystal Software Workshop ECM21-2003 Louis J. Farrugia, Department of Chemistry University of Glasgow GLASGOW G12 8QQ Scotland Processing of Bruker & Nonius CCD data

2 Single Crystal Software Workshop ECM21-2003 Processing of Bruker & Nonius CCD data There are two main stages of CCD data processing : First procedure is specialised, involves many corrections to the raw CCD data - no facilities in WinGX for this (Denzo, EvalCCD, SAINT). Second procedure is handled in WinGX by a variety of routes Frame integration relies on “black box” commercial software. Frame integration - extraction of intensities from images Post processing - error modelling, merging, abs corrections, etc

3 Single Crystal Software Workshop ECM21-2003

4 Denzox program Denzox was written by Bob Blessing, but extensively modified in Glasgow Reads.x files produced by Denzo and concatenates data does little massaging of reflection intensities transfers fulls transparently - no change in I or  (I) simple statistical summation of partials to provide I and  (I) some rejection criteria -  2 of fit, partials at edge of scan set, sin  / calculates direction cosines re-indexing for equivalent orientation matrices (NOT re-orientation !) various possibilities for batch number - frame, scan-set, experiment output file denzox_hkl.sortav for Sortav (or Gaussian abs correction) output file denzox.sad for Sadabs

5 Single Crystal Software Workshop ECM21-2003

6 Processing of KappaCCD data

7 Single Crystal Software Workshop ECM21-2003 Processing of KappaCCD data Most data reduction programs handled through KappaCCD GUI Load cell from various sources Filter data by sin(  ) or batch no. Quick view of data quality by Weiss or Diederich - Karplus programs Concatenation of input files Plots (Sortav)

8 Single Crystal Software Workshop ECM21-2003 Processing of KappaCCD data Most data reduction programs handled through KappaCCD GUI Load cell from various sources Filter data by sin(  ) or batch no. Quick view of data quality by Weiss or Diederich - Karplus programs Concatenation of input files Plots (Sortav)

9 Single Crystal Software Workshop ECM21-2003 Denzox GUI Denzox by R. Blessing Reads.x files and calculates direction cosines + batch no.’s Writes out files denzox_hkl.sortav denzox.sad Reads.x files from disk files or CD-ROM Allows for Denzo matrix variation

10 Single Crystal Software Workshop ECM21-2003 Sortav GUI Sortav by R. Blessing Pre-correction with GAUSSIAN abs. cor. Apply frame/batch scaling Apply empirical absorption correction Data merging & reject outliers Check that parameters are correct !

11 Single Crystal Software Workshop ECM21-2003 Sortav GUI - Empirical absorption Requires sufficient data redundancy Uses spherical harmonics to model absorption anisotropy Odd harmonics used to model non- centrosymmetric systematic errors  -dependency also possible R. H. Blessing, Acta Crystallogr., Sect A 1995, 51, 33-38.

12 Single Crystal Software Workshop ECM21-2003 Sortav GUI - Merging Several schemes for outlier rejection Normally use Tukey downweighting and rejection of outliers “Autoreject Outliers” until no further ones found R. H. Blessing, J Apply Cryst 1997, 30, 421-426

13 Single Crystal Software Workshop ECM21-2003 Sortav GUI - Output Save intermediate results here Controls number of plots and verbosity of output. Remove unwanted files R. H. Blessing, J Apply Cryst 1997, 30, 421-426

14 Single Crystal Software Workshop ECM21-2003 Sortav GUI - Results Shows outliers and rejected reflections Shown missing reflections R. H. Blessing, J Apply Cryst 1997, 30, 421-426

15 Single Crystal Software Workshop ECM21-2003 Processing of SMART/SAINT data Reads in all.RAW files found in directory Provides ranges of Intensities, exposure time, frame numbers. Necessary to provide batch numbers for scaling. In this example, files should be processed in four batches

16 Single Crystal Software Workshop ECM21-2003 Processing of SMART/SAINT data Choose which sets of RAW files to concatenate

17 Single Crystal Software Workshop ECM21-2003 Processing of SMART/SAINT data Choose which sets of RAW files to concatenate Decide on way to derive batch numbers for scaling Write file concat_hkl.sortav which is exact translation of the data in RAW file. Suitable for merging etc with Sortav

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