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Data Visualization and Reduction for Single-Crystal Diffraction at the ILL

Data Visualization and Reduction for Single-Crystal Diffraction at the ILL. Garry McIntyre Institut Laue-Langevin, Grenoble, France. Requirements of different types of single-crystal experiments. Present capabilities. What we need, but cannot yet do!.

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Data Visualization and Reduction for Single-Crystal Diffraction at the ILL

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  1. Data Visualization and Reduction for Single-Crystal Diffraction at the ILL Garry McIntyre Institut Laue-Langevin, Grenoble, France • Requirements of different types of single-crystal experiments. • Present capabilities. • What we need, but cannot yet do!

  2. A. Collection of many Bragg reflections under fixed conditions (temperature, pressure, field,...) for structure solution or refinement B. Volumetric mapping of reciprocal space, often of diffuse and/or weak features between intense Bragg reflections, but also to detect superlattice or satellite reflections C. Study of individual reflection profiles in 1-, 2- or 3-D D. Following a few reflections vs T, P, H,.. through phase transitions Types of single-crystal experiments Laue techniques are fine forAandB, much less so forCandD.

  3. experiment orientation + statistics quantitative analysis post-experiment analysis PRL, JACS,... General single-crystal data-analysis requirements visualisation, quality check Must be on-line and fast feed back strategy Should eventually be unnecessary

  4. Brief history of PSD’s on ILL single-crystal diffractometers • 1975 D6 ( the Hedgehog) uses an array of 100 single detectors with the modified Laue technique, but is doomed by the mechanical and computational limits at the time • 1976 D14 (Arndt TV camera) in the beam behind D8 • 1977 D12 uses film techniques, but development is discontinued despite a 3-fold gain in efficiency compared with D8. Radial oscillating collimators introduced !! • 1977 S20 (tomography) and S42 (Laue camera) profit from the excellent resolution of film • 1983 The SANS instrument D17 produces the first macromolecular single-crystal structure at the ILL • 1981 D16 receives the 4° x 8° MWPC, the prototype module for the D19 banana • 1983 D19 starts up with a 4° x 64 ° vertically curved MWPC banana • 1984 DB21 uses a scintallation detector for improved spatial resolution in low- resolution protein crystallography • 1985 D9 and D15 receive 8° x 8° flat MWPC detectors • 1995 LADI shows how to achieve 2.5p sterad. of coverage by using an image-plate detector & copied 6 years later by VIVALDI • 1999 D10 receives a 10° x 10° flat MSGC • 1999 D19’s banana is supplemented, then replaced by flat MSGC and MWPC detectors up to 20° x 20° • 2005 OrientExpress starts up with a CCD detector • 2006 D19 receives the 120° x 30° horizontally curved ‘big’ banana, • 2008 CYCLOPS will start up with a CCD detector offering similar coverage to VIVALDI D16 Hedgehog D19 Big Banana CYCLOPS CCD array

  5. D9 & D15 8° x 8° MWPC, 65% efficient Individual readout, 2mm res. 4-circle or normal beam D10 10° x 10° MSGC, 65% efficient Charge division, 2 mm res 4-circle or normal beam D16 29° x 29° MWPC, 65% efficient Charge division, 2 mm res Two-axis D19 120° x 30° MWPC, 65% efficient Charge division, ~2 mm res. 4-circle or normal beam ILL single-crystal diffractometers with 2D PSD’s • LADI • 360° x 96° Image Plate, ~65% efficient • 0.15 mm resolution, 5 min readout • Normal-beam Laue • VIVALDI • 288° x 104° Image Plate, ~50% efficient • 0.15 mm resolution, 4 min readout • Normal-beam Laue • ORIENT EXPRESS • 136° x 126° CCD, ~30% efficient • 0.4 mm resolution?, fast readout • Normal-beam Laue • CYCLOPS • 360° x 90° CCD, ~30% efficient • 0.4mm resolution?, fast readout • Normal-beam Laue

  6. Data visualization

  7. Display of PSD Data: The three incommensurate magnetic reflections near the 4/3 4/3 0 in TlFeCl3 at 1.6K (D16) Three reflections along the 5 3 l line in MgSO4.6H2O. The PSD subtends 8° x 8° at the crystal. The red planes denote the limits of integration of the central reflection. (E5, HMI). • 1D projection onto w, since this is usually the direction of best resolution (monochromatic data) • Projection onto the (horizontal) DwDg plane as a surface or contour plot. Particularly advantageous at revealing subtle features in the tails of peaks. • Combination of 1D and 2D projections with an isocontour plot in 3D (mulplt) (McIntyre, Neutron News 2, 1992, 15) det Z Projection onto the w axis Projection onto the w,g plane det X Sometimes more useful is extraction of reciprocal-lattice planes from a series of scans (rlpplt) omega 3D display in angular coordinates 3D display in cartesian reciprocal-space coordinates Methods to visualize 3D count distributions Requires clarity and speed without undue loss of information How to display a voxel array often on quite a noisy background?

  8. Facilitating experiments – constructing reciprocal space Large-Array Manipulation ProgramMany scans are accumulated to give an extensive view in reciprocal space.Diffuse reflections from short range magnetic order can be more easily seen.Bragg reflections are “snowballs”.Planes help to index reflections. TbMnO3 on D9 with a small area detector . Didier Richard et al. - www.ill.fr/data_treat/lamp/front.html

  9. Visualization of spallation Laue data (SXD) Asymmetric profiles along the time axis - not a simple Gaussian profile Perspective view from time origin aids identification of lattice planes

  10. ImageJ - http://rsb.info.nih.gov/ij/ Extraction of line profiles, surface plots and much more VIVALDI LAUE pattern from an Fe porphyrin (Dougan & Xue)

  11. Reflection integration

  12. All ILL routines for automatic integration of reflections, whether in 1D, 2D or 3D, use the minimum s(I)/I method: 1D: Lehmann & Larsen, Acta Cryst. A30 (1974) 580 (coll5) 2D & 3D: Wilkinson, Khamis, Stansfield & McIntyre, J. Appl. Cryst. 21 (1988) 471 A. Automatic reflection integration For weak reflections the optimum envelope within which to integrate is smaller than that containing the entire peak. Negative bias in the weak reflections is corrected by knowledge of the shapes of nearby strong reflections. This reduces s(I) by up to a factor 3 for weak reflections on a high background. Least-squares profile fitting further decreases s(I)/I, but only very slightly, and then even only when the true profile isknown.

  13. retreat (Stansfield, Wilkinson, McIntyre) for multi-reflection scans racer (Wilkinson, McIntyre) for single-reflection scans Boxes around rlp’s which are then treated like single-reflection scans Size of the box is given by a 2D resolution surface in g and n Reflection prediction includes conventional extinction rules Multiple UB’s for twins and multiple crystals Close-lying neighbours, twin reflections etc are simply masked off Correction for powder contribution by 2q projection of local background Incommensurate reciprocal lattices are presently hard-coded individually based on Wilkinson, Khamis, Stansfield & McIntyre, J. Appl. Cryst. 21 (1988) 471 3D integration using retreat & racer

  14. Masking off neighbours in retreat

  15. Zoom-in on part of the observed pattern Quick inspection of integration ellipsoid boundaries Predicted Laue pattern superimposed 2D data allow quick inspection of integration ellipses Spots are tomographic projections of the crystal Improvements needed for spatial overlap A. LADI & VIVALDI - Data Analysis Reduction of conventional structures on LADI & VIVALDI is (mostly) by programs of the CCP4 X-ray Laue suite www.dl.ac.uk/SRS/PX/jwc_laue/laue_top.html First user experiment, Feb 2002.Vitamin B12. Nearly 10000 measurable reflections in an 8-hour exposure from a 10 mm3 crystal. Mean I/s(I) = 10.

  16. Already very good, but lacks: Magnetic space groups Easy generation of incommensurate reflections Pattern manipulations, e.g. differences, background flattening Easy lattice manipulations, e.g. a x a x c to a√2 x a√2 x c More interaction with diffraction pattern, e.g. spot identification Plotting of profiles along arbitrary lines (use ImageJ) Crystal shape and size from the forms of the spots Local multi-peak fitting to recover overlapped reflections … CCP4 Laue suite:www.dl.ac.uk/SRS/PX/jwc_laue/laue_top.html Tutorial for use at ILL, including some local programs (by John Cowan): www.ill.fr/YellowBook/LADI/ladimanual/Lmain.html ImageJ:http://rsb.info.nih.gov/ij/ lauegen

  17. A. Pushing the limits on D19 Xylose isomerase*:I222, a = 94 Å, b = 100 Å, c = 103 Å, l = 1.46 Å, ~3500 active refs/frame (Kovalevsky, Langan, Forsyth et al. D19) One frame for 111 seconds Our present integration programs consider that each reflection can be isolated within a small box around the ideal reciprocal lattice point. (*Kovalevsky et al. Biochemistry. 2008 Jul 22;47(29):7595-7)

  18. Indexed using lauegen A single frame indexed using lauegen A. Treating monochromatic data as Laue data Clive Wilkinson is exploring the possibility of using standard Laue programs to analyse monochromatic data. Typical monochromatic neutron Dl/l ~ 3% One frame for 111 seconds Radial projection of a 51-step w scan as a Laue pattern The Laue projection is very useful at identifying the presence of extra reflections, superlattices, etc … Once indexed the projection can then be expanded into 3D for integration.

  19. Separation of 6 domains in D19 data (in progress) A. Integration of overlapping reflections For overlapping reflections we need multi-dimensional fitting separation of twinned and incommensurate reflections separation of spatial overlaps in Laue data (not resolved in time) Unlike complete integration within an envelope, we need good knowledge of the individual peak profiles Fitting of the projection of the TlFeCl3 reflections onto the w-g plane allowed separation of the individual peaks, and a good fit by the peaks of each domain to the model magnetic structure. (D16, l = 4.52Å) (McIntyre & Visser, J. de Phys. 47, 1986, C5-183)

  20. B. Modelling of volumetric data Analysis of diffuse scattering generally needs matching of the model to the 2D Laue projection or the full 3D monochromatic or time-sorted data. FeTaO6: 3-D antiferromagnetic order at 8 K, 2-D order above 8 K. Chung, Balakrishnan, Visser & Paul (Warwick), McIntyre (ILL) 10 K minus 2 K -> rods of magnetic scattering along l

  21. Diffit: estimate peaks, positions, heights and widths Diffit: Fit peak positions, heights and widths; Put out Lorentz-corrected integrated intensities Interactive user-driven execution 1 0 1 fundamental nuclear reflection Helical magnetic reflections and satellites Bilayer nuclear satellite reflections C. Analysis of individual reflection profiles [Tb20/Y30]60 Subiger et al. JMMM, submitted For ‘single-reflection’ experiments, profile fitting often gives the best information if the ideal profile of individual reflections is known Even for Q-scans, the general Lorentz correction is straightforward (McIntyre & Stansfield, Acta Cryst. A44, 1998, 257) For 1D data, commercial software (Igor, Origin, Matlab, etc) can be used to good effect, or local programs (diffit: Brueckel & Vrtis)

  22. Repeated analysis of series of Laue patterns or monochromatic scans to extract: integrated intensity, peak position (angle, q), peaks widths, background,… Needs: Input or plug-ins to standard applications (Igor, Origin, ImageJ, Matlab,..) D. Temperature, pressure, field,... variations FeTaO6 on D10 magnetic Bragg reflection magnetic diffuse rod

  23. C & D. Profile fitting and temperature variation Spin-slip magnetic structure of Ho, Bates et al. J.Phys. C. 21 (1988) 4125

  24. Other programs Peak search pfind (Turner), prewash (Wilkinson) Indexing Often by inspection and trial and error index (Savariault) - brute force using a known cell and a few reflections centred by hand latfit (Wilkinson), dirax (Duisenberg)- identification of zones in full 3D data; being tested http://www.crystal.chem.uu.nl/distr/dirax/ Cell refinement rafin, rafd9, rafd19, rafnb (Filhol) - all based on codrub (Ellis & Pryor, AAEC) Visualization fly (Allibon), dview (Turner), mulplt, qscplt (McIntyre) Geometry transformations euler (Stansfield) Attenuation correction Several programs, all using Gaussian integration (Coppens, Leiserowitz & Rabinovich), plus correction for attentuation in heat shields etc. datap (Coppens), d19abs (Stansfield), ladiabs (Cowan), abscan (Mason)

  25. Analysis software must be: On-line and fast to guide the experimental strategy Intuitive, to relieve the instrument responsible of repetitive instruction Offer several modes of visualization Offer input to many of the standard crystallographic packages, and to commercial fitting programs Data formats: TIFF or NeXus for raw Laue data (16 Mb per image, 1 CD per experiment) CIF for reduced crystallographic data ? for results of repeated profile fits What we should really aim for: Full 3D fitting of monochromatic data Full 2D (multi-)pattern refinement of Laue data (8,000,000 pixels per VIVALDI pattern, 1 - 10 patterns per data collection) Conclusions

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