Freely available crystallographic software for powder diffraction.

1. Freely available crystallographic software for powder diffraction. L. 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. Notes Free Zone - they are on the webhttp://www.ccp14.ac.uk/poster-talks/korea_2002/ • Some areas of this talk may resemble a rather fast computer slide show; thus detailed notes are on the web for examination at your leisure (and given out during the talk) Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

3. Talk Aims • Show there is a variety of freely available software out there that can help you with your research via diffraction and crystallographic methods • Making use of the latest software can make your difficult problems easier or doable. Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

4. For those new to Crystallography • Why bother looking into freely available crystallographic software? • Crystallography can help answer questions that may not seem very crystallographic at the time. • In the following screen images, help determine, using diffraction techniques, whether there is Oxygen in the Earth’s outer core.(unit cell volumes to obtain equations of state - EOS) “O2 volumes at high pressure from KClO4 decomposition: D" as a siderophile element pump instead of a lid on the core.” D. Walker, S.M. Clark, L.M.D. Cranswick, M.C. Johnson and R.L. Jones, (2002), Geochemistry, Geophysics, Geosystems (G^3), in press. Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

5. Using the right crystallographic method can make the difference! Using Traditional UNIT CELL refinement Methods Using Le Bail fitting / Rietveld Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

6. The risks of “not knowing what you don’t know” Thus this talk will try and get the keywords out that you can follow-up on at your leisure. Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

7. Why bother knowing about a variety of modern software? (1 of 2) Path of Most Resistance? Using a variety of “state-of-the-art” tools can improve versatility by allowing different pathways and approaches to tackle crystallographic problems. • Maximise the ability to handle present and future problems • Be able to cross hurdles that may be intractable or unnecessarily problematic if not approached the right way. Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

8. Why bother knowing about freely available software? (2 of 2) Much freely available software is state of the art in both algorithms andusability - (GUIs) • Concentrate on the crystallography • Can be installed on as many computers as you want - where-ever you like • Can take programs home and use on their personal computers (negate software piracy problems) Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

9. Single Crystal vs Powder diffraction (1 of 9) Single Crystal • “Mass transit” structure solution and refinement • There are difficulties: • Crystal not representative of the bulk • Twinning • Crystal decomposes during data collection • “Difficult” structure Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

10. Single Crystal vs Powder diffraction (2 of 9) Cambridge Database • “During 1999, 17,898 new entries were added” • (that Scale is in the 100’s of thousands) • 1999 report: http://www.ccdc.cam.ac.uk/about/annrep99/Report.html • http://www.ccdc.cam.ac.uk/prods/csd/stats.html Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

11. Single Crystal vs Powder diffraction (3 of 9) ICSD Database (inorganics - and minerals) • During first 6 months of 2002, 3073 new entries were added. • July 2002 ICSD release : a total of 64,848 entries Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

12. Single Crystal vs Powder diffraction (4 of 9) Powder Methods for solving structures • A nightmare to some • An adventure to others! Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

13. Single Crystal vs Powder diffraction (5 of 9) Number of structures solved by powder methods • 592 up to end of 2001 • http://sdpd.univ-lemans.fr/iniref.html • http://sdpd.univ-lemans.fr/iniref/SDPD-activity.html Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

14. Single Crystal vs Powder diffraction (6 of 9) Structure Determination from Powder Diffractometry Round Robin 1 • Tetracycline Hydrochloride (June 1998) • http://sdpd.univ-lemans.fr/SDPDRR/ • Armel Le Bail and Lachlan Cranswick • Powder Data: • 6 week time limit • 70 downloads of data • 2 submissions on the Tetracycline within the time limit • CSD System from Stoe • Druid/Mystic (now called Dash) • (also solved by Armel Le Bail) • http://sdpd.univ-lemans.fr/SDPDRR/sample2.html Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

15. Single Crystal vs Powder diffraction (7 of 9) Tetracycline structures obtained from microcrystal - single crystal diffraction : synchrotron X-rays • a powder can be a collection of very small single crystals • 10x20x30 micron crystal (Clegg and Teat) • Beamline 9.8 at Daresbury Synchrotron: Bruker Smart CCD • http://srs.dl.ac.uk/xrd/9.8/ • Routine structure solution - including hydrogens found from the map • Solved at the press of a button as the data was being collected. (few hours data collection) Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

16. Single Crystal vs Powder diffraction (8 of 9) What about the “inorganic unknown” in the SDPD Round Robin? • No-one bothered to solve it (except Armel Le Bail) • One participant who solved the organic said the inorganic was “too boring” and thus did not try it. • Big fad at present is to solve organic pharmaceuticals from powders • Much commercial software development reflects this emphasis on pharmaceuticals Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

17. Single Crystal vs Powder diffraction (9 of 9) 2nd SDPDRR (Indexing and solving):http://www.cristal.org/sdpdrr2/ • Round robin started on Monday 9th September • Structure solution ending on Sunday 17th November Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

18. Talk Agenda • Start from Data conversion and phase identification • Go through to photo realistically rendering crystal structures • Via stops including • Peak profiling • Unit Cell refinement • Powder indexing • Structure Solution • Structure refinement • Structure validation • Photorealistic rendering of crystal structures Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

19. Phase Identification/Search Match for Powder Diffraction • Two main parts to perform computer based search-match: • 1. Have a Powder Diffraction Database (buy or make your own) • 2. Search-match software that uses the above database to search • Databases: • ICDD has the commercial powder diffraction database area cornered http://www.icdd.com • Alternative being developed is the Pauling File: http://www.pauling.com • Editor in Chief: Dr Pierre Villars • Nearly all Search-match programs are commercial: • Refer to, "Available Search-Match Software" for a list of known software: • http://www.ccp14.ac.uk/solution/search-match.htm • Free Software:Brian Toby's "Portable Logic Program" (UNIX) and "MacDiff" for Apple Mac freeware by Rainer Petschick • Look out for the developing OpenXRD by Stefan Krumm (UNIX and Windows) Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

20. Phase Identification/Search Match for Powder Diffraction 2 of 3Identifying an organic – DL-Valine Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

21. Which software, databases and methods work the best: Search Match Round Robin (2nd May 2002 to 30th June 2002):http://sdpd.univ-lemans.fr/smrr/ and CCP14 mirrors • Conclusions : • Search-match without chemistry is possible but: • Need up to date database • Need good 3rd generation search-match software • Need a skilled analyst • (the skilled analyst seems to be the most important of the 3) Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

22. Has the structure been solved already?Crystallographic Structure Databases • (UK based academics and students already have free access via theEPSRC funded CDS (Chemical Database Service): • http://cds3.dl.ac.uk/cds/cds.html • ICSD (Minerals and Inorganics) • http://www.fiz-karlsruhe.de/ • Web accessible demonstration: • http://barns.ill.fr/dif/icsd/ • MDF/CRYSTMET • (Metals and Alloys) • http://www.tothcanada.com • CCSD • (Organics and Organometallics) • http://www.ccdc.cam.ac.uk/ • American Mineralogist • http://www.geo.arizona.edu/xtal-cgi/test/ • WWW Mincryst • http://database.iem.ac.ru/mincryst/ • 2398 unique phases - most with crystal structure data • Mineral web • http://www.minweb.co.uk Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

23. ICSD via the Web Using an Interface created by Alan Hewat at ILL, Grenoble, France There is a trend for databases to use the web due to the convenience and effectiveness. Also has advantage of being operating system independent for users. • http://barns.ill.fr/dif/icsd/ Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

24. A hopeful trend: Crystallography Suites that link directly into the crystal structure databases • Platon for UNIX (if CSD/Quest is also installed): • http://www.cryst.chem.uu.nl/platon/ • CSD Cell searching at the click of a button • Connectivity search: using the CORINA to generate a PDB file, • http://www2.ccc.uni-erlangen.de/software/corina/free_struct.html • Then use Platon/System S acting as a friendly interface for Quest. Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

25. Powder Data Conversion / Importing Data • Initial problem in powder diffraction can be getting the data in the right format. For interconverting powder diffraction data: a variety of programs exist which in combination can pretty much get you from one format to another • Summary list of available software:http://www.ccp14.ac.uk/solution/powderdataconv/ • Text Editors may occassionally be required: converting UNIX ACSII to DOS ASCII, getting rid of spaces or tabs , column editing: • Freeware PFE Editor for Windows: • http://www.lancs.ac.uk/people/cpaap/pfe/ • Freeware ConTEXT Editor for Windows (does column editing) • http://www.fixedsys.com/context/ Example of ConvX for Windows by Mark Bowden Mass data powder diffraction data converter Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

26. Structure Importing, Conversion and Transformation • Summary list of available software at:http://www.ccp14.ac.uk/solution/structconv/ • Be careful to check the results • Best program for the moment is the shareware Cryscon • http://www.shapesoftware.com • Other software such as GUI WinORTEP can import a wide variety of file formats and export these into Shelx format. http://www.chem.gla.ac.uk/~louis/software/ortep3/ Example of Cryscon for Windows by Eric Dowty Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

27. Powder Sample Preparation and Data Collection • Assumption is that you know about appropriate sample preparation and data collection • However, many hardware vendors might not provide the required flexibility in data collection Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

28. Variable Count Time data collection • Main idea here is to increase the raw intensity of selected peak areas to assist in the “required” analysis: (similar to what a CAD4 does) • Up till now, if at all, mainly done for refinement (e.g., Hill and Madsen method) • On point detector (e.g., Bragg Bretano flat plate system), do this by varying the count time in a pre-defined manner • (Can also provide more time effective counting time) Fixed Count Time Variable Count Time Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

29. VCT Literature References "Collection and analysis of powder diffraction data with near-constant counting statistics", I. C. Madsen and R. J. Hill, J. Appl. Cryst. (1994). 27, 385-392 http://www.iucr.org/cgi-bin/paper?hz0014 Philips Friendly Fortran source code that does this Hill and Madsen method is at: http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/csirominerals-anon-ftp/pub/xtallography/variable-count-time/ (Original Hill and Madsen VCT (variable count time) Paper), I. C. Madsen and R. J. Hill, Adv. X-ray Anal. (1992), 35, 39-47 W. I. F. David, Accuracy in Powder Diffraction, Abstract P2.6 NIST Special Publication No. 846, Page 210, (1992) National Institute of Standards and Technology, Gaithersburg, MD, USA. Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

30. VCT for trace Phase ID (1 of x) Fixed Count Time data (data collected by Jeremy Cockcroft) Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

31. VCT for trace Phase ID (1 of x) Variable Count Time data (displayed as FCT)(data collected by Jeremy Cockcroft) Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

32. VCT for trace Phase ID (1 of x) Fixed Count Time data (zoomed) Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

33. VCT for trace Phase ID (1 of x)Variable Count Time data (displayed as FCT) Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

34. Variable Count Time applications Equally relevant to problems where you need to adequately profile fit small / trace peaks which might not be significantly above background in a “routine”, time effective fixed count time data collection - e.g.,; • Powder Indexing • Unit Cell refinement • Quantitative Rietveld Analysis Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

35. VCT to aid in phase ID and profile fitting (1 of 2) Fixed Count Time Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

36. VCT to aid in phase ID and profile fitting (2 of 2) Variable Count Time Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

37. VCT for Structure Solution and Refinement (1 of 4)Variable Count Time data (as collected) Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

38. VCT for Structure Solution and Refinement (2 of 4)Variable Count Time data (displayed as FCT) Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

39. VCT for Structure Solution and Refinement (3 of 4)Variable Count Time data (displayed as FCT) Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

40. VCT for Structure Solution and Refinement (4 of 4)Variable Count Time data (displayed as VCT) Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

41. Where is VCT Data Collection? Not a routine or available option in commercial XRD control software Something to keep an eye on - or request from vendors. Is in the new Bede powder diffraction system Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

42. Powder Diffraction Utility Software • Examining Data, peak finding, background stripping, alpha-2 stripping • Powder v 2.00: http://www.ccp14.ac.uk/tutorial/powder/ • Powder X, http://www.ccp14.ac.uk/tutorial/powderx/ • WinFIT, • http://www.geol.uni-erlangen.de/html/software/soft.html • Winplotr, http://www-llb.cea.fr/winplotr/winplotr.htm • XFIT, http://www.ccp14.ac.uk/tutorial/xfit-95/xfit.htm • Example of PowderX for Windows • Graphical evaluation, backtground stripping, smoothing, alpha stripping, peak find and pass to treor indexing • Full GUI Operation Powder X (Alpha2 Strip, Background Strip, Peak Find) Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

43. Peak Profiling (indexing, unit cell refinement, size/strain, etc) • For Overall Summary of available peak profiling software refer to: • http://www.ccp14.ac.uk/solution/peakprofiling/ • These include: CMPR, DRXWin, EFLECH, GPLSFT, pearson.xls, SHADOW, Powder v2.00, PowderX, Winfit, Winplotr, XFIT Examples of XFIT for Windows Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

44. Powder Indexing - a non trivial endeavour • For Overall Summary of available powder indexing software refer to: http://www.ccp14.ac.uk/solution/indexing/ • Powder Indexing: Autox, Ito, Dicvol, Treor, Taup/Powder, Lzon, Losh, Kohl, Scanix, Xrayscan, EFLECH/Index, Supercell • Linking Suites: Crysfire, Powder v2.00, PowderX, PROSZKI, WinPlotr, Chekcell • supercel is a specialise indexing program by Juan Rodriguez-Carvajal for indexing Super Cell and Incommensurate cells. (available within Winplotr) http://www-llb.cea.fr/winplotr/winplotr.htm 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

45. Powder Indexing - the “Crysfire” suite • At present the CRYSFIRE software by Robin Shirley links8 different indexing programs (ito, dicvol, treor, taup, kohl, lzon, fjzn and losh)together with a common interface and using intelligent defaults. Important to have access to as many indexing programs as possible so you can get a feel for the range of possible solutions. http://www.ccp14.ac.uk/tutorial/crys/ Example of CRYSFIRE Screen prompting the saving into one of 8 different indexing program formats: Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

46. 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

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 • Obtaining the Reduced Cell • which many powder indexing programs to not reliably determined • Refer: "'Reduced Cells', M.J. Buerger, (Zeitschift fur Kristallographie, BD 109, S. 42-60 (1957)” • 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: example of using Le Page • Orthorhombic cell with good FOM (Figure of Merit) • Le Page combined with automatic “Best Solution”easily finds a better hexagonal cell based on parsimony of extra reflections criteria Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

50. Crysfire / Chekcell: indexing powder Protein data Using the “Rescale” feature in Crysfire Finds 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. Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk