What can freely available powder diffraction software via the Internet do for you? L. M. D. Cranswick, CCP 14 (Collaborative Computation Project No 14 for Single Crystal and Powder Diffraction) Department of Crystallography; Birkbeck College, University of London, Malet Street, Bloomsbury, London, WC 1 E 7 HX, UK. E-mail: l. m. d. cranswick@dl. ac. uk WWW: http: //www. ccp 14. ac. uk
Notes Free Zone - they are on the web http: //www. ccp 14. ac. uk/poster-talks/wpd_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) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
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. • Most software described can be freely usable by anyone Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
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, whethere is Oxygen in the Earth’s outer core. (unit cell volumes to obtain equations of state - EOS) “O 2 volumes at high pressure from KCl. O 4 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. Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Using the right crystallographic method can make the difference! Using Traditional UNIT CELL refinement Methods Slide Using Le Bail fitting / Rietveld Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
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. Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Why bother knowing about a variety of modern software? (1 of 2) Path of Most Resistance? Using a variety of “state-ofthe-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. Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Why bother knowing about freely available software? (2 of 2) Much freely available software is state of the art in both algorithms and usability - (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) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
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 Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
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. ccp 14. ac. uk/solution/powderdataconv/ Example of Conv. X for Windows by Mark Bowden Mass data powder diffraction data converter ·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 Con. TEXT Editor for Windows (does column editing) · http: //www. fixedsys. com/context/ Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
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. ccp 14. ac. uk/solution/search-match. htm – Free Software: Brian Toby's "Portable Logic Program" (UNIX) and "Mac. Diff" for Apple Mac freeware by Rainer Petschick – Look out for the developing Open. XRD by Stefan Krumm (UNIX and Windows) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Phase Identification/Search Match for Powder Diffraction 2 of 3 Identifying an organic – DL-Valine Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Which software, databases and methods work the best: Search Match Round Robin (2 nd May 2002 to 30 th June 2002): http: //sdpd. univ-lemans. fr/smrr/ and CCP 14 mirrors • Conclusions : – Accurate search-match without chemistry is possible but: – Need up to date database – Need good 3 rd generation search-match software – Need a skilled analyst – (the skilled analyst seems to be the most important of the 3) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Has the structure been solved already? Crystallographic Structure Databases • (UK based academics and students already have free access via the EPSRC funded CDS (Chemical Database Service): – http: //cds 3. dl. ac. uk/cds. html – Dutch equivalent is the CMBI at: http: //www. cmbi. kun. nl/cheminf/ • 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/ Slide • 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. ccp 14. ac. uk
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/ Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Structure Importing, Conversion and Transformation ·Summary list of available software at: http: //www. ccp 14. ac. uk/solution/structconv/ ·Be careful to check the results ·Best program for the moment is the shareware Cryscon · http: //www. shapesoftware. com Slide Example of Cryscon for Windows by Eric Dowty Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
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 Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
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 CAD 4 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 Slide Variable Count Time Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
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, 385392 http: //www. iucr. org/cgi-bin/paper? hz 0014 Philips Friendly Fortran source code that does this Hill and Madsen method is at: http: //www. ccp 14. ac. uk/ccp 14/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 P 2. 6 NIST Special Publication No. 846, Page 210, (1992) National Institute of Standards and Technology, Gaithersburg, MD, USA. Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
VCT for trace Phase ID (1 of x) Fixed Count Time data (data collected by Jeremy Cockcroft) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
VCT for trace Phase ID (1 of x) Variable Count Time data (displayed as FCT) (data collected by Jeremy Cockcroft) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
VCT for trace Phase ID (1 of x) Fixed Count Time data (zoomed) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
VCT for trace Phase ID (1 of x) Variable Count Time data (displayed as FCT) (you only need to count excessively in the relevant angular ranges) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
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 Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
VCT to aid in phase ID and profile fitting (1 of 2) Fixed Count Time Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
VCT to aid in phase ID and profile fitting (2 of 2) Variable Count Time (you only need to count excessively in the relevant angular ranges) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
VCT for Structure Solution and Refinement (1 of 4) Variable Count Time data (as collected) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
VCT for Structure Solution and Refinement (2 of 4) Variable Count Time data (displayed as FCT) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
VCT for Structure Solution and Refinement (3 of 4) Variable Count Time data (displayed as FCT) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
VCT for Structure Solution and Refinement (4 of 4) Variable Count Time data (displayed as VCT) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Where is VCT Data Collection? Not a routine or available option in majority of commercial XRD control software Something to keep an eye on - or request from vendors. VCT is in the new Bede powder diffraction system Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Peak Profiling (indexing, unit cell refinement, size/strain, etc) For Overall Summary of available peak profiling software refer to: http: //www. ccp 14. ac. uk/solution/peakprofiling/ These include: CMPR, DRXWin, EFLECH, Fityk (GPL’d); GPLSFT, pearson. xls, SHADOW, Powder v 2. 00, Powder. X, Winfit, Winplotr, XFIT Examples of XFIT for Windows (includes fundamental parameters peak profiling) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Powder Indexing - a non trivial endeavour • For Overall Summary of available powder indexing software refer to: http: //www. ccp 14. ac. uk/solution/indexing/ • Powder Indexing: Autox, Ito, Dicvol, Treor, Taup/Powder, Lzon, Losh, Kohl, Scanix, Xrayscan, EFLECH/Index, Supercell • Linking Suites: Crysfire, Powder v 2. 00, Powder. X, PROSZKI, Win. Plotr, 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. htm ftp: //bali. saclay. cea. fr/pub/divers/fullprof. 2 k/ Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Powder Indexing - the “Crysfire” suite • At present the CRYSFIRE software by Robin Shirley links 8 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. ccp 14. ac. uk/tutorial/crys/ Example of CRYSFIRE Screen prompting the saving into one of 8 different indexing program formats: Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. 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. ccp 14. ac. uk/tutorial/lmgp/ Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Chekcell : automatic cell and spacegroup searching can trudge through a single selected unitcell; or over 1000 s of trial cells looking for the best cell and spacegroup combination based on “parsimony of extra reflections” criteria. Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
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 Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Some Alternatives to Crysfire: Winplotr, Powder. X Winplotr by Juan Rodriguez-Carvajal – http: //www-llb. cea. fr/fullweb/powder. htm Powder. X by Cheng Dong – http: //www. ccp 14. ac. uk/tutorial/powderx/ Powder v 2 by Nita Dragoe – http: //www. ccp 14. ac. uk/tutorial/powder/ CMPR for Windows and UNIX by Brian Toby (with source code) – http: //www. ccp 14. ac. uk/tutorial/cmpr/ Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
New MCMaille by Armel Le Bail (Sep 2002) by Armel Le Bail – http: //www. cristal. org Monte Carlo Cell finding / indexing software Whole Profile method using reconstituted peaks positions and intensities Not sensitive to trace impurities Latest version can works almost as fast as Dicvol Poor data can still give no reasonable result. Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Updated MCMaille - December 2002 Can “try” and index 2 phase materials Very experimental “ 2 phase” desparation option Could be far better to go back into the lab and try and separate out the phases As it is distributed with the source code - you can make your own modifications and add features. Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Unit Cell Refinement (powders) • For Overall Summary of available unit cell refinement software refer to: http: //www. ccp 14. ac. uk/solution/unitcellrefine/ • This includes: – Celref, LAPOD, Refcel, Unitcell, Eracel, Powder v 2. 00, XLAT, etc • Can be helpful to perform a conventional unit-cell refinement prior to a Le Bail fit (or where unit weighting of each reflection is important). Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
CELREF for Unit Cell Refinement • by Jean Laugier and Bernard Bochu http: //www. ccp 14. ac. uk/tutorial/lmgp/ • In this example, celref is performing graphical Unit Cell refinement on calcite in a multiphase mixture Knows about spacegroups Graphics can really help sort out errors or misassigned hkls Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Full Profile Fitting (Powder) • For Overall Summary of available full profile analysis refer to: Le Bail based: http: //www. ccp 14. ac. uk/solution/lebail/ Pawley Based: http: //www. ccp 14. ac. uk/solution/pawley/ • The most common method of full profile fitting is that of Le Bail fitting: which is in most Rietveld packages. It is useful for: – Spacegroup Assignment – Unit Cell Refinement (especially when overlap is a problem) – Extracting Intensities for Structure Solution Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Le Bail full profile fitting - Rietica Rietveld • By Brett Hunter – http: //www. rietica. org – http: //www. ccp 14. ac. uk/tutorial/lhpm-rietica/ • Easy to use and setup via GUI • Le Bail is Structureless whole profile fitting - just need cell and spacegroup • Easy to add and delete structures • Auto-marquardt damping for initial unstable refinement if required Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Le Bail full profile fitting - Rietica Rietveld - 2 of 2 • In this example multiphase system where the aim is to get accurate unit cell volumes. • No completely freestanding peak for KCl Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Unit Cell Refinement: Mass Le Bail fitting: multi-phase - overlapping patterns Using Le Bail fitting Slide Using Traditional Methods Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Materials Analysis Rietveld/Texture Software • Pole Figure, Texture Analysis – important also for some forms of Le Bail fitting and structure solution from powders • Summary List of available software: • MAUD (for Java PC/Mac/UNIX) Crystallite size and shape analysis http: //www. ing. unitn. it/~luttero/ http: //www. ccp 14. ac. uk/solution/pole_figure/ – – – – BEARTEX for Windows GSAS Rietveld (Windows/UNIX) MAUD for Java POFINT pop. LA Symmet for DOS Texture. Plus for Windows Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Solving Structures: Single Crystal vs Powder diffraction (1 of 5) 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 Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Single Crystal vs Powder diffraction (2 of 5) Cambridge Database • (that Scale is in the 100’s of thousands) – 2001 report: http: //www. ccdc. cam. ac. uk/about/annrep 2001/report. html – http: //www. ccdc. cam. ac. uk/prods/csd. html Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Single Crystal vs Powder diffraction (3 of 5) 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 Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Single Crystal vs Powder diffraction (4 of 5) Powder Methods for solving structures • A nightmare to some • An adventure to others! Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Single Crystal vs Powder diffraction (5 of 5) 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 Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Structure Solution from Powder Diffraction Round Robins 1 st SDPD Round Robin - 1998: (Solving only): http: //www. cristal. org/SDPDRR/ 2 nd SDPD Round Robin - 2002: (Indexing and solving): http: //www. cristal. org/sdpdrr 2/ • Indexing: – Only 6 submissions (6% return rate) – Only Index/EFLECH by Joerg Bergmann was able to suggest solutions for samples 4 to 8 within the time limit. • Solving: • 70 Downloads of data • Only two submissions using: – CSD System from Stoe – Druid/Mystic (now called Dash) Slide • Solving: • >100 Downloads of data • Only two submissions using: – Fox (GPL’d - free) – Topas (commercial from Bruker) Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
“Generic” structure solution from powder diffraction data • Very non-trivial endeavour. • (though indexing can often be the limiting step in many attempted structure solutions) • EXPO - Direct Methods (Sirware Group) Makers of Sir 92/Sir 97/Sirpow – http: //www. irmec. ba. cnr. it/ • If EXPO fails, it is possible to use Le Bail or Pawley extracted data with Single Crystal Structure Solution Software: – http: //www. ccp 14. ac. uk/solution/xtalsolution/ • Then consider real space methods such as using ESPOIR (GPL’d by Armel Le bail) or FOX (GPL’d by Vincent Favre-Nicolin and Radovan Cerny) - normally real space methods use as last resort: – ESPOIR: http: //sdpd. univ-lemans. fr/sdpd/espoir/ – Web tutorial on setting up the ESPOIR files in < 10 minutes" and example of solving on an organic molecule: http: //sdpd. univ-lemans. fr/sdpd/espoir/10 mn/ – FOX: http: //objcryst. sourceforge. net/ Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
“Specialised and Commercial” Structure Solution Programs • PSSP – molecular structures – http: //powder. physics. sunysb. edu/program. PSSP/pssp. html • ZEFSA II – for Zeolites (GPL’d) – http: //www. mwdeem. rice. edu/zefsa. II/ • Focus – for Zeolites – http: //www. kristall. ethz. ch/LFK/software/ • Fullprof – Monte Carlo for structure solution and finding Magnetic Moments in neutron data – ftp: //bali. saclay. cea. fr/pub/divers/winplotr/ • “Available” Commercial Structure Solution from Powder Diffraction Data software: – – – Powder Solve: http: //www. accelrys. com Crystal Structure Determination Package (Win. CSD/CSD) : http: //imr. chem. binghamton. edu/zavalij/CSD. html DASH (Druid and Mystic of old): http: //www. ccdc. cam. ac. uk/prods/dash/ TOPAS : http: //www. bruker-axs. com Endeavour : http: //www. crystalimpact. com/endeavour/ Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
New FOX real space structure solution by Vincent Favre-Nicolin and Radovan Cerny Available for UNIX/Linux and MS-Windows GUI Based Is friendly in setting up of rigid bodies Includes automatic merging of atoms on special position with dynamic occupancy correction http: //objcryst. sourceforge. net/ Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Adding polyhedra in Fox - 1 of 5 Click on “Crystals”, “Scatterers” Icon, “Add” Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Adding polyhedra in Fox - 2 of 5 Select the central atom Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Adding polyhedra in Fox - 3 of 5 Select the corner atom(s) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Adding polyhedra in Fox - 4 of 5 Give the Bond length Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Adding polyhedra in Fox - 5 of 5 Done! Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Structure Refinement using Powder Diffraction Data (Rietveld Refinement) • Large range of programs to choose from: – http: //www. ccp 14. ac. uk/mirror. htm – http: //www. ccp 14. ac. uk/solution/rietveld_software/ • Many specialize for particular types of problems, incommensurate structures, quantitative analysis, polymers, etc. • • ARITVE, BGMN, DBWS, DEBVIN, EXPO Fullprof, GSAS, Koalariet, LHPM-Rietica, MAUD for Java (GPL’d) Premos/Remos, Pro. DD, Profil, Quanto, Riet 7/SR 5, Rietan 2000 (GPL’d) Rietquan, Simref, Win. Mprof, XND, XRS-82/DLS-76 Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Rietveld Program Interfaces · Not yet as robust and powerful as single crystal refinement programs (Single Crystal programs are very poweful and do a lot for the user) · Unlike most single crystal suites, you are not interacting directory with the structures on the screen. · Many choose their Rietveld based on what the people down the road are using. Not only human nature but learning a Rietveld program from scratch can be difficult. • Interfaces into Rietveld programs vary from GUIs to direct editing of ASCII files. Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Rietveld Programs - Rietica by Brett Hunter · Full Graphical User Interface · Still got to appreciate and know your crystallography for inserting and refining the crystal structure · http: //www. rietica. org Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Mentioning GSAS Rietveld: Some Relevant Background • by Bob von Dreele and Alan Larsen • Menu based control • Available for Windows / DOS / Linux / SGI • Separate GUI by Brian Toby (EXPGUI) • Combined X-ray / Neutron / Single Crystal / Powder Diffraction • Integrated Fourier map generation and viewing Slide • GSAS resources, tutorials and links (including links to EXPGUI) – http: //www. ccp 14. ac. uk/solution/gsas/ • Restraints – – – – Bond angle Bond length Planar Total Chemistry / charge balance Chiral volume Phi/psi group Torsion angle • Manual Marquadt damping • Atom shift limits • Lots of other features Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
GSAS : Solving and refining a protein from powder data • As cited in R. B. Von Dreele, P. W. Stephens, G. D. Smith and R. H. Blessing, "The first protein crystal structure determined from highresolution X-ray powder diffraction data: a variant of T 3 R 3 human insulin-zinc complex produced by grinding", Acta Cryst. (2000). D 56, 1549 -1553. http: //journals. iucr. org/d/issues/2000/12/00/issconts. html Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Brian Toby’s EXPGUI Interface for GSAS User friendlier to start using GSAS via EXPGUI (A new combined installer makes it very easy to start using GSAS. ) http: //www. ncnr. nist. gov/programs/crystallography/software/expgui_intro. html Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Restrained Rietveld structure refinement of organics • Software not as powerful as single crystal but there are some tutorials with tricks on the CCP 14 website http: //www. ccp 14. ac. uk/solution/restrained_rietveld/ Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Fourier capability in Rietveld Software Example of GSAS 2 D contour maps and also VRML output (below) Summary list of Fourier friendly Rietveld software at: http: //www. ccp 14. ac. uk/solution/rietveld_fourier_maps/ Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Some Specialist Applications • Anharmonic Refinement – List of Software: – http: //www. ccp 14. ac. uk/solution/anharmonic/ • Incommensurate Structure Refinement – List of Software: – http: //www. ccp 14. ac. uk/solution/incomm. htm • PDF / High Q Analysis – List of Software: – http: //www. ccp 14. ac. uk/solution/high_q_pdf/ Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Quantitative Phase Analysis • Non-trivial and in many cases, custom solutions may be required. (accurate Quantitative analysis is a complete world in itself) • Rietveld programs are commonly used for Quantitative Analysis (refer list in a previous slide). • Following using Koalariet / XFIT (fundamental parameters) http: //www. ccp 14. ac. uk/tutorial/xfit-95/ Refer to non-Rietveld references cited in: http: //www. ccp 14. ac. uk/poster-talks/david-hay-quant-notes-axaa 99/ Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
MAUD for Java : GPL’d (you get the source code) Tutorial on “Performing an x-ray quantitative analysis in seven easy steps!”: http: //www. ing. unitn. it/~luttero/maud/tutorial/ http: //www. ccp 14. ac. uk/ccp/web-mirrors/lutterotti/~luttero/maud/tutorial/ Including options for standardless quantitative analysis on amorphous material Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
New for 2002: Fullpat (runs within MS-Excel) By Steve Chipera and Dave Bish of Los Alamos National Laboratory, USA http: //www. ccp 14. ac. uk/ccp/web-mirrors/fullpat/ Full profile non-Rietveld method using standards Described in the IUCr Commission on Powder Diffraction Newsletter: http: //www. se. iucr. org/iucr-top/comm/cpd/Newsletters/no 27 jul 2002/ Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Quantitative Phase Analysis - is it routinely easy? Based on the IUCr CPD Quant Round Robin (http: //www. iucr. org/iucr-top/comm/cpd/QARR/) The answer seems to be No! A quote from Armel Le Bail’s Tmacle “twinned refinement” software manual seems appropriate: http: //sdpd. univ-lemans. fr/museum/tmacle 92. zip GOOD LUCK IT'S VERY HARD! DON'T YOU THINK SO? ONLY THE BOSS SAID THAT IT IS EASY, BUT HE NEVER TRIED! Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Graphically interacting with the structure • Number of programs available with list available at: http: //www. ccp 14. ac. uk/solution/structuredrawing/ • http: //www. ccp 14. ac. uk/tutorial/lmgp/#gretep Most single crystal suites include structure viewing by default but not powder refinement programs • Gretep by Jean Laugier and Bernard Bochu Some can read common file formats (CIF, Shelx, etc) – Gui Win. ORTEP reads the widest variety of formats • Software includes: Crystals, Cameron, PIG (part of the Xtal suite), ORTEX, Gretep, Platon, GUI Win. ORTEP, GUI Win. STRUPLO Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Validation - why take an interest? • For perhaps the same reason that Columbia University Law/Journalism professors teach their students (at least one - circa late 1940’s): “If your mother says she loves you, ” “CHECK IT OUT!!” • If you want to publish anything that can stand the test of time - you need to be validating your results as much as possible. Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Platon’s Addsym (by Ton Spek): checking for extra symmetry : e. g. , Structure Published in 1997 P 1 - Triclinic: 42 non-H atoms Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Platon’s Addsym: Correction Published in 1999: C 2 - Monoclinic: 22 non-H atoms Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Platon’s Addsym: Press of a button: 2000: FDD 2 - Orthorhombic: 11 non-H atoms (Short Communication Abstract: "P 1 or P-1? Corrigendum", Acta Cryst B 56 (2000) 744 from Richard E. Marsh) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Platon’s Addsym: for powders • Some powder based structures at the Royal Institution and Birkbeck College in London solved using EXPO direct methods • Triclinic P 1 - found by Addsym to be P -1 • Orthorhombic: – P 21 21 21 - found by Addsym to be P n m a – P 2 21 21 - found by Addsym to be P m m n • Platon is not free for commercial use Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Powder diffraction pattern calculation Powder Cell for Windows • Most Rietveld Programs can calculate powder patterns but they may not be all that friendly to use • Two dedicated GUI programs for calculating powder patterns - 1 st being: • Powder Cell by Werner Kraus and Gert Nolze at BAM in Germany http: //www. ccp 14. ac. uk/tutorial/powdcell/ Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Powder diffraction pattern calculation Poudrix for Windows • Powder Cell by Jean Laugier and Bernard Bochu http: //www. ccp 14. ac. uk/tutorial/lmgp/#pdw • Poudrix can handle anomalous dispersion at non X-ray tube wavelengths with the option of two models: – Brenann and Cowan – Sasaki Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Photorealistic hardcopy output of structures Using GRETEP by Jean Laugier and Bernard Bochu http: //www. ccp 14. ac. uk/tutorial/lmgp/ http: //www. ccp 14. ac. uk/ccp/web-mirrors/lmgp-laugier-bochu/ Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Freeware for photorealistic hardcopy output of structures Balls and Sticks by Sung J. Kang & Tadashi C. Ozawa • http: //www. toycrate. org • http: //www. ccp 14. ac. uk/ccp/web-mirrors/toycrate/ • Individual point and click creation of polyhedra and bonds via a Windows graphical user interface Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Photorealistic hardcopy output of Fourier Maps Marching Cubes by Michal Husak (http: //www. ccp 14. ac. uk/tutorial/marchingcube/) • Interlinks with Win. GX, Crystals and can read Project XD files. Software for converting GSAS Fourier files is available. Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Other Internet Resources • Crystallographic Mailing lists and internet newsgroups: – http: //www. ccp 14. ac. uk/maillist/ – Including: • • • Sci. techniques. xtallography Internet newsgroup Rietveld Users’ Mailing List SDPD - Structure Determination from Powder Diffractometery XRD - discussions on X-ray Diffraction Hardware Clay Minerals Mailing List • IUCr Commission on Powder Diffraction Newsletter: – http: //www. iucr. org/iucr-top/comm/cpd/Newsletters/ Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Dual Boot UNIX / Windows PC and Crystallographic Nexus CD-ROMs for those isolated from the internet • Tutorials for creating dual boot Windows / UNIX PCs: • Linux – refer: http: //www. ccp 14. ac. uk/solution/linux/ • Free. BSD (can run linux binaries) – refer: http: //www. ccp 14. ac. uk/solution/bsdunix/ • (be careful of hackers invading your systems when running Linux/UNIX. CCP 14 tutorials try to be security conscious and leave no “open” services) • • Free Xtal Nexus CD-ROMs for academics and students http: //www. unige. ch/crystal/stxnews/nexus/index. htm (Supported & Sponsored by the IUCr and CCP 14) Contact the author (Lachlan Cranswick) for a free air-mailed CD-ROM. Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Don’t be a “passive kitten” · Just looking over someone’s shoulder will not teach you how to use this software. You have to use it yourself on your real scientific problems. Image from: http: //www. cs. umbc. edu/~rheingan/SIGGRAPH/motion. slides. pdf Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Summary · · Large Genetic Diversity of Software This diversity is necessary to help you get the job done. Getting better all the time (some areas faster than others) Freely available for Academics and Students · Much is free for commercial applications • Downloadable via the EPSRC funded CCP 14 website: http: //www. ccp 14. ac. uk E-mail: ccp 14@dl. ac. uk Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
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