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Re-stating the obvious: To solve structures from powder diffraction, first they must be indexed!

Re-stating the obvious: To solve structures from powder diffraction, first they must be indexed!. Lachlan M. D. Cranswick CCP14 (Collaborative Computation Project No 14 for Single Crystal and Powder Diffraction) Department of Crystallography; Birkbeck College, University of London,

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Re-stating the obvious: To solve structures from powder diffraction, first they must be indexed!

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  1. Re-stating the obvious: To solve structures from powder diffraction, first they must be indexed! Lachlan M. D. Cranswick CCP14 (Collaborative Computation Project No 14 for Single Crystal and Powder Diffraction) Department of Crystallography; Birkbeck College, University of London, Malet Street, Bloomsbury, London, WC1E 7HX, UK. E-mail: l.m.d.cranswick@dl.ac.uk WWW: http://www.ccp14.ac.uk

  2. Robin Shirley School of Human Sciences University of Surrey Guildford, Surrey, GU2 7XH, U.K. Tel: (+44) 01483 686864 Fax: (+44) 01483 259553 E-mail: R.Shirley@surrey.ac.uk Based on a co-authored presentation at the ACA 2002 conference in San-Antonio, Texas, USA Lachlan M. D. Cranswick CCP14 (Collaborative Computation Project No 14 for Single Crystal and Powder Diffraction) Department of Crystallography; Birkbeck College, University of London, Malet Street, Bloomsbury, London, WC1E 7HX, UK. E-mail: l.m.d.cranswick@dl.ac.uk WWW: http://www.ccp14.ac.uk

  3. Some history of Indexing of Powder Diffraction Data Peak finding and peak profiling software Fundamental Parameters Peak Fitting Available powder indexing software and indexing suites Crysfire in action Chekcell in action MCMaille by Armel Le Bail (released Sep 2002) Possibilities for the future and conclusion Talk Aims Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  4. Some History of Powder Indexing • First published manual powder indexing method: • Runge, C. (1917), "Die Bestimmung eines Kristallsystems durch Rontgenstrahlen", Physik. Z., 18, 509-515. • Candidates for first published computer based powder indexing • Haendler, H. M. & Cooney, W. A. (1963), "Computer Determination of Unit-Cell from Powder-Diffraction Data", Acta Cryst., 16, 1243-1248. • Lefker, R. (1964), "Indexing of tetragonal and hexagonal X-ray powder photographs with the aid of a small computer", Anal. Chem., 36, 332-334. Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  5. Some History of Powder Indexing - 2 • Candidates for first published publicly available powder-indexing program • Haendler, H. M. & Cooney, W. A. (1963), "Computer Determination of Unit-Cell from Powder-Diffraction Data", Acta Cryst., 16, 1243-1248. • Lefker, R. (1964), "Indexing of tetragonal and hexagonal X-ray powder photographs with the aid of a small computer", Anal. Chem., 36, 332-334. • Werner, P.-E. (1964), "Trial and error computer methods for the indexing of unknown powder patterns", Z. Krist., 120, 375-387. • Hoff, W. D. & Kitchingman, W. J. (1966), "Computer indexing of x-ray powder patterns from crystals of unknown structures", J. Sci. Instrum., 43, 952-953. Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  6. Some History of Powder Indexing - 3 • Candidates for first publically available general indexing program • Ishida, T & Watanabe, Y. (1967), "Probability Computer Method of Determining the Lattice Parameters from Powder Diffraction Data", J. Phys. Soc. Japan, 23, 556-565. • Roof, R. B. (1968), "INDX: A Computer Program to Aid in the Indexing of X-Ray Powder Patterns of Crystal Structures of Unknown Symmetry", Los Alamos Laboratory, University of California, Report LA-3920. • Taupin, D. (1968), "Une Methode Generale pour l'Indexation des Diagrammes de Poudres", J. Appl. Cryst., 1, 178-181. • Visser, J. W. (1969), "A Fully Automatic Program for Finding the Unit Cell from Powder Data", J. Appl. Cryst., 2, 89-95. Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  7. Checking Sample Purity • Powder indexing requires line-position data of the highest available quality • An important aspect of this is purity, since indexing programs don’t like to struggle with impurity lines, and several will not accept them at all. • Some suggestions from Robin for checking sample purity: • Optical (polarising) microscope • Density analysis in a gradient column • Electron microscopy and diffraction of selected crystallites • And, if time permits, see whether properties are changing with time Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  8. Peak Profiling Software • For Overall Summary of available peak profiling software refer to: http://www.ccp14.ac.uk/solution/peakprofiling/ • Some of the available freeware includes: • CMPR • DRXWin • EFLECH • GPLSFT • pearson.xls • Rawplot (with GSAS) • SHADOW • Powder v2.00 • PowderX • Winfit • Winplotr (with Fullprof) • XFIT Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  9. Empirical peak fitting : Some tricks may be required for stability and reasonable results • Peaks over small ranges may have to be linked to have the same shape and width • Usually fit small ranges of data - groups of peaks • Might have to fit large and medium peaks first, followed by trace peaks Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  10. Peak Profiling: high accuracy peak positions using Fundamental Parameters peak profiling • Example of Fundamental parameters (convoluting in the geometry elements of the diffractometer) that can provide accurate peak positions as though your sample was being run on an “ideal” diffractometer. • Tutorial at: • http://www.ccp14.ac.uk/tutorial/xfit-95/fun1.htm • Available Fundamental Parameters Peak Profiling and Rietveld software: • XFIT (no longer maintained) • http://www.ccp14.ac.uk/tutorial/xfit-95/xfit.htm • Topas (Commercial - sequel to XFIT) • http://www.bruker.com • BGMN (Commercial - academic demonstration version is freely downloadable) • http://www.bgmn.de • EFLECH/Index freeware from BGMN website • http://www.bgmn.de/related.html Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  11. XFIT Fundamental Parameters Peak Profiling mode : fit to a low angle peak on a Bragg-Brentano diffractometer Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  12. Powder Indexing FOM ResultsXFIT Fundamental Parameters peak profiling compared to empirical Peak Fitting Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  13. Powder Indexing - indexing programs • Overall Summary of available powder indexing software refer to: http://www.ccp14.ac.uk/solution/indexing/ • Powder Indexing: • Classic (widely used): Ito, Dicvol, Treor • High symmetry (exhaustive): Taup (=Powder), Dicvol • Other powerful (general symmetry): Lzon, Kohl (=TMO), Fjzn • Dominant-zone cases: Lzon, Losh, Mmap • Semi-automatic (via SIW basis set): Losh, Mmap • Fundamental parameters & covariance matrix: EFLECH/Index • Incommensurate, etc: Supercell • Monte Carlo / Random search: EFLECH/Index, McMaille • Others (better with some user guidance): Scanix, Autox Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  14. Powder Indexing - indexing suites • Overall Summary of available powder indexing software refer to: http://www.ccp14.ac.uk/solution/indexing/ • Integrated Suites: • Crysfire • Powder v2.00 • PowderX • PROSZKI • WinPlotr • and after primary indexing: • Chekcell Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  15. Powder Indexing - specialist programs • Supercel is a specialised indexing program by Juan Rodriguez-Carvajal for tackling incommensurate cells and super/sub-cell relationships. (available within Winplotr/Fullprof) Web: http://www-llb.cea.fr/winplotr/winplotr.htm FTP: ftp://bali.saclay.cea.fr/pub/divers/fullprof.2k/ Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  16. Powder Indexing - specialist programs • McMaille reconstitutes a peak listing into a full profile and performs monte carlo based searching for good cells. Because it is Monte Carlo based it can be very slow, but due to it being whole profile, can be insensitive to trace impurity peaks. Web:http://www.cristal.org/McMaille/ Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  17. Powder Indexing - Using PowderX • by Cheng Dong • http://www.ccp14.ac.uk/tutorial/powderx/ • Peak finding • Links to Treor Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  18. Powder Indexing - Using Winplotr • by Juan Rodriguez-Carvajal and T. Roisnel http://www-llb.cea.fr/fullweb/powder.htm • Peak finding / profiling • Links to • WinTreor, • Windicvol, • Winito and • supercell Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  19. Powder Indexing - the Crysfire suite (1) • by Robin Shirley (+ many contributing authors) • http://www.ccp14.ac.uk/tutorial/crys/ • Intelligent defaults for control-parameters when launching each indexing program • Data rescaling for tackling high-volume cells from macromolecular samples and zeolites • Integrated under a common interface for use by non-specialists Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  20. Powder Indexing - the Crysfire suite (2) • Principal Contributors: • Franz Kohlbeck (Kohl [=TMO]) • Daniel Louër (Dicvol, Lzon, Losh) • Robin Shirley (Overall + Mmap, Lzon, Losh, Fjzn, etc) • Ton Spek & A.Meetsma (Lepage) • Daniel Taupin (Taup [=Powder]) • Jan Visser (Ito, Fjzn, Lzon, etc) • Per-Eric Werner (Treor) Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  21. Powder Indexing - the Crysfire suite (3) Crysfire 2000: 8 different indexing programs (Ito, Dicvol, Treor, Taup, Kohl, Lzon, Fjzn, Losh) • It’s good to have a wide variety of methods available: • to cater for different types of problem • to give a feel for the range of solutions out there • and see which ones turn up repeatedly using different methods, either identically or as derivative cells Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  22. New Release - Crysfire 2002 August 2002 Now 9 indexing programs: Ito, Dicvol, Treor, Taup, Kohl, Lzon, Fjzn, Losh, Mmap • New features: • Mmap for exploring solution-space and evaluating trial cells • Le Page/Niggli reduced-cell summary • Greater ease of use, especially for first-time users • Better resilience, especially under the Windows/NT family (master program totally rewritten) Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  23. Why bother running more than one powder indexing program? • Maximize the possibility of indexing unknowns by taking advantage of different algorithms and different program implementations. Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  24. Powder Indexing - Routine Crysfire ExampleRun crysfire (giving the following screen) Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  25. Powder Indexing - Routine Crysfire Example Importing an XFIT peak file using the IM (Import command) Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  26. Powder Indexing - Routine Crysfire Example“lo” to load a CDT file estimate of expected unit cell volume is given Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  27. Powder Indexing - Routine Crysfire Example “in” to target an indexing program Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  28. Powder Indexing - Routine Crysfire Example target ITO with defaults Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  29. Powder Indexing - Routine Crysfire Example ITO runs Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  30. Powder Indexing - Routine Crysfire Example After Ito completes, press enter to see output file Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  31. Powder Indexing - Routine Crysfire Example Then “enter” again to see “one solution per line” summary Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  32. Powder Indexing - Routine Crysfire Example “Enter” again to see Le Page summary of reduced cells Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  33. Powder Indexing - Routine Crysfire Example • Repeat the sequence to run the remaining relevant indexing programs. Recommended sequence is actually: • Taup, Dicvol high sym, Ito, FJZN, Treor, Kohl, Dicvol low sym, Lzon • in to select and launch an indexing program • look at the output file • look at the summary file • look at the Le Page summary file of reduced cells • repeat Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  34. Powder Indexing - Routine Crysfire Example Finally: the complete summary file - 3332 trial solutions Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  35. Powder Indexing - Routine Crysfire Example Complete Le Page summary file of reduced cells - 3332 trial solutions Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  36. Crysfire Self CalibrationBragg-Bretano Data • Sometimes it’s hard to be sure how far the beam is penetrating into the sample, giving an unknown sample-displacement error • This can be addressed by trying self-calibration (SC) • If indexing the uncorrected data has failed, try SC • Select T (for specimen-displacement correction ratio) • A list of candidates for T will be displayed, based on 1st/2nd-order line pairs • If a particular ratio comes up several times and looks plausible, adopt it • Save it (SA) in Crysfire format under a new name, so that it can be reloaded • Do another cycle of indexing runs, this time with the “corrected” data Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  37. Crysfire Self Calibration Example • Self calibration output of an organometallic sample in histogram format Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  38. Crysfire Rescaling • Most indexing program have evolved using a range of data with solutions between 500 and 1500 • If you have cells outside this range, many indexing programs can fail • A possible solution to still index large cells it to rescale the data by changing the wavelength Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  39. Input for RAWPLOT: (1.15006 Å) 1.168100 1.656041 1.852174 1.918506 2.089703 2.345176 2.536523 2.623267 2.916919 2.992132 3.144491 3.319995 3.419907 3.458655 3.522905 3.564255 3.660448 3.712916 3.838720 3.933115 4.098415 4.151839 4.187484 4.234265 Crysfire Re-scalingProtein Data (from Bob von Dreele) Lysozyme – single peak fits for 24 reflections : Rescale factor = 0.1 Rescaled cell = a of ~7.9Å and c of ~3.8Å Unscaled cell = a of ~79Å and c of ~38Å Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  40. Crysfire Rescaling example Inorganic - on opening : Crysfire suggests rescaling Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  41. Ignoring the rescaling suggestion No obvious solutions Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  42. RS is the Rescale Command Crysfire will automatically change the filename and title Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  43. After running the indexing programs:MS, then U to unscale the summary file Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  44. Indexing using the suggested rescaling of 0.5 An obvious cubic (23.923 A) solution found by Taup Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  45. Chekcell: Interpreting Crysfire Summary Files: Powder Indexing and Spacegroup Assignment • Crysfire interlinks with Chekcell for Windows(part of the LMGP suite for Windows by Jean Laugier and Bernard Bochu).Chekcell provides a graphical interface for manually and automatically suggesting a best cell/spacegroup combination using both FOM and algorithms relating to parsimony of superfluous HKLs. http://www.ccp14.ac.uk/tutorial/lmgp/ Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  46. Chekcell : easy to see non-matching or impurity peaks Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  47. Chekcell : automatic cell and spacegroup searching can trudge through a single selected unitcell; or over 1000s of trial cells looking for the best cell and spacegroup combination based on parsimony of extra reflections criteria. Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  48. Chekcell: “integration” of Ton Spek and A. Meetsma’s Le Page(Crysfire 2001 now also provides a reduced-cell summary) • Obtaining the Reduced Cell • which in the past many powder indexing programs have not determined either reliably or at all • Refer: "'Reduced Cells', M.J. Buerger, (Zeitschift fur Kristallographie, BD 109, S. 42-60 (1957)” • Crysfire 2001 gives a LePage overview Chekcell displays a fuller analysis • Efficient Sub-cell and super-cell searching, then easy reviewing of newly derived cells within the Chekcell interface Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  49. Chekcell: GUI Cell transformation • Easily transform cells and test them withing Chekcell • Knows about common transformations • Can manually look at sub-cells and super-cells Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  50. Chekcell: Density / Z/ Mol. Vol explorer • Easily explore values of Z, density and estimated molecular volume - comparing with your found trial cells. Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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