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

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 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

Notes Free Zone - they are on the web http://www. ccp14. ac Slide 3 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Talk Aims 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 Mmap with Crysfire 2002 (released August 2002) MCMaille by Armel Le Bail (released Sep 2002) Possibilities for the future and conclusion Slide 4 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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. Slide 5 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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. Slide 6 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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. Slide 7 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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 Slide 8 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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 Slide 9 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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 Slide 10 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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 Slide 11 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

XFIT Fundamental Parameters Peak Profiling mode : fit to a low angle peak on a Bragg-Brentano diffractometer Slide 12 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Powder Indexing FOM Results XFIT Fundamental Parameters peak profiling compared to empirical Peak Fitting Slide 13 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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 Slide 14 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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 Slide 15 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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/ Slide 16 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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/ Slide 17 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Powder Indexing - Using PowderX by Cheng Dong http://www.ccp14.ac.uk/tutorial/powderx/ Peak finding Links to Treor Slide 18 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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 Slide 19 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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 Slide 20 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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) Slide 21 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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 Slide 22 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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) Slide 23 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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. Slide 24 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Powder Indexing - Routine Crysfire Example Run crysfire (giving the following screen) Slide 25 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Powder Indexing - Routine Crysfire Example Importing an XFIT peak file using the IM (Import command) Slide 26 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Powder Indexing - Routine Crysfire Example “lo” to load a CDT file estimate of expected unit cell volume is given Slide 27 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Powder Indexing - Routine Crysfire Example “in” to target an indexing program Slide 28 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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

Powder Indexing - Routine Crysfire Example ITO runs Slide 30 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Powder Indexing - Routine Crysfire Example After Ito completes, press enter to see output file Slide 31 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Powder Indexing - Routine Crysfire Example Then “enter” again to see “one solution per line” summary Slide 32 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Powder Indexing - Routine Crysfire Example “Enter” again to see Le Page summary of reduced cells Slide 33 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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 Slide 34 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Powder Indexing - Routine Crysfire Example Finally: the complete summary file - 3332 trial solutions Slide 35 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Powder Indexing - Routine Crysfire Example Complete Le Page summary file of reduced cells - 3332 trial solutions Slide 36 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Crysfire Self Calibration Bragg-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 Slide 37 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Crysfire Self Calibration Example Self calibration output of an organometallic sample in histogram format Slide 38 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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 Slide 39 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Crysfire Re-scaling Protein Data (from Bob von Dreele) 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-scaling Protein 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 Slide 40 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Crysfire Rescaling example Inorganic - on opening : Crysfire suggests rescaling Slide 41 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Ignoring the rescaling suggestion No obvious solutions Slide 42 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

RS is the Rescale Command Crysfire will automatically change the filename and title Slide 43 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

After running the indexing programs: MS, then U to unscale the summary file Slide 44 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Indexing using the suggested rescaling of 0. 5 An obvious cubic (23 Indexing using the suggested rescaling of 0.5 An obvious cubic (23.923 A) solution found by Taup Slide 45 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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/ Slide 46 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Chekcell : easy to see non-matching or impurity peaks Slide 47 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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. Slide 48 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Chekcell: “integration” of Ton Spek and A 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 Slide 49 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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 Slide 50 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Chekcell: Density / Z/ Mol. Vol explorer Easily explore values of Z, density and estimated molecular volume - comparing with your found trial cells. Slide 51 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Chekcell: example of it running Load the raw diffraction data Slide 52 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Chekcell: example of it running Load the peak position file Slide 53 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Chekcell: example of it running Load the Crysfire summary file Slide 54 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Chekcell: example of it running Use the tools to evaluate the trial cells Slide 55 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Crysfire / Chekcell: indexing powder Protein data Using the “Lepage” feature in Chekcell Can find the correct rhombohedral cell as published in: R. B. Von Dreele, P. W. Stephens, G. D. Smith and R. H. Blessing, "The first protein crystal structure determined from high-resolution X-ray powder diffraction data: a variant of T3R3 human insulin-zinc complex produced by grinding", Acta Cryst. (2000). D56, 1549-1553. Slide 56 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Crysfire / Chekcell: indexing powder Protein data Even on rescaled data, if Crysfire and the various indexing programs do not find the “true cell”, Chekcell and possibly can find a derivative cell which LePage (combined with Chekcell’s “parsimony and superflous reflections” criteria), can find the true cell. In the case of reindexing of the protein data: Crysfire and Dicvol finds 73.2645 70.5256 40.7430 90.000 90.000 90.000 Orthorhomic P222 or PMM2 or PMMM : 157 hkls to match 41 reflections LePage followed by Chekcell “parsimony check” then finds: 81.449 81.449 73.265 90 .000 90.000 120.00 Hexagonal setting 52.988 52.988 52.988 100.45 100.45 100.45 Rhombohedral R-3 or R3 etc : 60 hkls to match 41 reflections Slide 57 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

MMAP Mmap explores sections of solution-space (e.g. sections with varying alpha* and beta*, holding the other 4 parameters constant) The results are displayed as a map, with the high-ground colored It lists all the peaks in the map and refines them - each is a trial solution So it can act as an indexing program in its own right (taking the basis set containing the first 4 constants from Lzon’s output) This offers another way to search for trial cells Use the new “LC” (Load a trial cell from the Crysfire summary file) to then run MMAP (using the MM command) on it. Slide 58 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

MMAP - what does the output look like? Example MMap thumbnail output from a high FOM trial cell Slide 59 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

MMAP - what does the output look like? Example MMap output from a high FOM trial cell Slide 60 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

MMAP But another use is for checking out trial solutions taken from the summary lists generated by other indexing programs The usual guides to which solutions are the most promising are ones like figures of merit, numbers of lines indexed, etc., but only at the position of the refined cell in the map That’s like having a list of high points in a landscape, and trying to tell tall buildings from natural features with only their heights to go on Knowing the surroundings of the high-point tells us which are man-made, and similarly which Mmap peak corresponds to the physical solution Slide 61 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Height of 80 Height of 78 Height of 65 MMAP - which of these objects is man made? Using peak height as the selection criteria. Height of 80 Height of 78 Height of 65 Slide 62 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

MMAP - which of these peaks is man made? 2 It’s obvious once you can see the landscape Slide 63 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Analogous problem with powder indexing Traditional indexing only gives you the numbers (and possibly a Chekcell style fit) where a large number of trial cells can give reasonable matches Mmap shows you the actual “landscape” Slide 64 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

An Mmap landscape Quick scan of an alpha*/beta* section for some real data for a triclinic cell (a finely-divided triclinic biological sample showing some line broadening) There are a number of high points scattered across the map Each of these peaks is a potential solution (+others others out of section) Slide 65 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Mmap Looking at some real data and see how figure-of-merit lists can be illuminated by looking at the landscapes that they come from. Slide 66 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Mmap After refinement, though one peak has reached a figure of merit of 21, it still has a long list of competitors - no one solution really stands out There are 48 peaks in the whole list, all non-equivalent 17 of these have M>10 and index all of the first 20 lines Slide 67 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Mmap : Is the following a good solution? Here is the traditional set of information that we have for solution 1 from that list: a = 10.631A alpha = 101.56 deg b = 10.212 A beta = 93.80 deg c = 3.5704 A gamma = 112.24 deg V = 347.152 A3 M20 = 21.02 Slide 68 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Mmap : Yes looks a good solution Here is a magnification of the region around map-peak 1 (M=21.0), reloaded into Crysfire from the Mmap summary file using LC and then selecting a cell. It’s relatively compact (though sitting on a lowish diagonal ridge) Slide 69 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Mmap : Is the following a good solution? Similarly for the solution that corresponds to map-peak 2: a = 10.787 A alpha = 107.14 deg b = 10.470 A beta = 79.52 deg c = 3.6227 A gamma = 115.47 deg V = 352.236 A3 M20 = 16.05 Slide 70 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Mmap A similar magnified map around map-peak 2 (M=16.0) This is revealed to be less well defined as well as lower, with its central region extending as a broad ridge right off the top of the map Slide 71 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Mmap: Is the following a good solution? And for map-peak 3: a = 10.760 A alpha = 100.33 deg b = 10.170 A beta = 80.33 deg c = 3.5307 A gamma = 114.75 deg V = 343.288 A3 M20 = 14.57 Slide 72 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Mmap Map-peak 3 (M=14.6) is broader still, and also drifts off the top of the map Slide 73 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Mmap We can also avoid wasting time on landscapes that are broad and featureless, indicating data problems or wrong initial assumptions, and so not worth pursuing Slide 74 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

MCMaile by Armel Le Bail Developed in September 2002 (on from the ESPOIR code) GPL’d (free and you get the source code) Whole profile Monte Carlo and Grid Search methods using a pattern reconstituted from the peak list Columnar peak shape - can increase/decrease width Can make “important” trace peaks more likely to be part of a solution by increasing their intensities. Insensitive to impurity peaks 20,000 tests per second - but can still take many hours Thus a method of last resort Slide 75 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

A MCMaile ASCII input file Slide 76 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

MCMaile is running Slide 77 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

MCMaile output files Chekcell *.ckm summary file of all trial cells and Fullprof PRF profile file of top solution: viewable in Winplotr Slide 78 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

MCMaile : on large cubic Finds cubic cell easily - even with trace “impurity” peaks Via outputted Chekcell *.ckm summary file. Top solution is not correct solution (possible effect of impurity peaks) Slide 79 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

MCMaile : on large cubic Finds cubic cell easily - even with trace “impurity” peaks Via outputted Chekcell *.ckm summary file. Second set of solutions is correct Slide 80 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

SDPDRR-II (Structure Determination by Powder Diffractometry Round Robin - 2 ) WWW: http://www.cristal.org/sdpdrr2/ Started: Monday 9th September Part 1 (powder indexing): Start: Monday 9th September Finish: Sunday 13th October 8 samples 1 - 3 : Powder indexing and structure solution 4 - 8 : Powder Indexing only > 100 downloads of the data (samples 1 to 3) Slide 81 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

SDPDRR-II - Indexing Results WWW: http://sdpd.univ-lemans.fr/sdpdrr2/results/ 6 returns/100 downloads = 6% return rate Slide 82 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

SDPDRR-II - Sample 1 WWW: http://sdpd.univ-lemans.fr/sdpdrr2/results/ Organisers: 10.323 7.395 8.535 90 91.29 90 Reduced cell: 7.395 8.535 10.323 91.29 90.00 90.00 P1: 10.318 7.393 8.527 90 91.3 90 P2: 10.321 7.392 13.236 90 139.90 90 P3: 10.322 14.787 8.529 90 91.35 90 Reduced cell: 8.529 10.322 14.787 90.00 90.00 91.30 P4: No solution P5: 8.523 10.327 7.397 90 90 91.34 P6: 8.525 7.394 13.230 90 128.748 90 Slide 83 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

SDPDRR-II - Sample 2 WWW: http://sdpd.univ-lemans.fr/sdpdrr2/results/ Organisers: 11.239 8.194 19.943 90 106.727 90 Reduced cell: 8.194 11.239 19.875 106.06 90.00 90.00 P1: 19.880 8.195 11.242 90 106.06 90 P2: 11.242 8.195 19.948 90 106.72 90 P3: 19.878 8.193 11.240 90 106.06 90 P4: 19.880 8.194 11.243 90 106.06 90 P5: 11.244 19.882 8.196 90 90 106.06 P6: 11.243 8.195 19.949 90 106.72 90 Slide 84 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

SDPDRR-II - Sample 3 WWW: http://sdpd.univ-lemans.fr/sdpdrr2/results/ Organisers: 18.881 18.881 18.881 90 90 90 (vol 6734Å3) P1: 13.349 13.349 9.439 90 90 90 (Tet - 1638Å3) P2: 18.878 18.878 18.878 90 90 90 P3: 13.354 13.354 9.442 90 90 90 (Tet - 1638Å3) P4: No Solution P5: 18.878 18.878 18.878 90 90 90 P6: 18.88 18.88 18.88 90 90 90 Slide 85 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

SDPDRR-II - Sample 3 Tetragonal or Cubic? 2 participants (1 and 3) obtained the same tetragonal cell instead of the correct cubic. Possibly due to default volume restrictions in the programs used(?) What happens if you run LePage (via Chekcell) followed by a “parsimony of extra reflections” check on the tetragonal solution Slide 86 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

SDPDRR-II - Sample 3: Tetragonal: 1 peak unmatched - 46 hkl’s (P42MC et al) to match 25 reflections Slide 87 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

SDPDRR-II - Sample 3: Tetragonal: Running LePage shows a cubic cell (18.885Å) Slide 88 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

SDPDRR-II - Sample 3: Visual inspection of cubic cell implies “bad”peak could still be an impurity Slide 89 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

SDPDRR-II - Sample 3: Cubic: 37 hkl’s to match 25 reflections (I23 et al) (vs 46 hkl’s in tetragonal) Slide 90 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

SDPDRR-II - Samples 4 to 8 WWW: http://sdpd.univ-lemans.fr/sdpdrr2/results/ Only one response - using the EFLECH/Index software of Joerg Bergmann (http://www.bgmn.de/related.html) S4: none suggested S5: 6.011 16.937 18.229 90 90 92.19 S6: none suggested S7: 4.417 11.479 17.126 77.87 85.09 82.67 S8: 3.796 9.368 28.915 90 90 90 Summary: Powder indexing is not easy and not routine! Slide 91 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Be on the lookout for bugs in the Software Be on the lookout for bugs in the Software! Found in LePage - within Chekcell Slide 92 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

The Future The message has got through that indexing has become a bottleneck for solving structures from powder diffraction data. New Indexing programs are being developed. MCMaille (Free GPL’d - get the source code as well) Bruker SVD Indexing (commercial) Accerlys Indexing program (commercial) EFLECH/Index (new developments due to the SDPDRR-2) Slide 93 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Conclusion Don’t give up if your lab’s favorite indexing program doesn’t work on a particular dataset Suites like Crysfire offer a wide range of indexing tools Follow on with Chekcell to help pin down the correct physical cell If that does not work - whole profile methods such as MCMaille (still using Chekcell to evaluate trial solutions) Relevant web links: CCP14 Summary Page: http://www.ccp14.ac.uk/solution/indexing/ Crysfire: http://www.ccp14.ac.uk/tutorial/crys/ Chekcell: http://www.ccp14.ac.uk/tutorial/lmgp/ McMaille: http://www.cristal.org/McMaille/ Slide 94 Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk