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Freely available crystallographic software for powder diffraction.

Freely available crystallographic software for powder diffraction.

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Freely available crystallographic software for powder diffraction.

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  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