An overview of available software for solving crystal
An overview of available software for solving crystal structures from powder diffraction Lachlan 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
Talk Aims • Give an overview of available software relevant to structure solution from powder diffraction data. • On the data collection side, mention Variable Count Time (VCT) data collection as something to take an active interest in as getting the best data possible helps with the software. • Also mention Fundamental Parameters peak profiling for powder indexing Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Notes Free Zone - they are on the web http: //www. ccp 14. ac. uk/poster-talks/aca_2002 a/ • 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
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 crystallographic software Maximize your ability to handle present and future scientific 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
Single Crystal vs Powder diffraction (1 of 6) 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 6) 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/annrep 99/Report. html http: //www. ccdc. cam. ac. uk/prods/csd/stats. html Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Single Crystal vs Powder diffraction (2 a of 6) 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 (3 of 6) 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 (4 of 6) Number of structures solved by powder methods • Cumulative total of 592 up to end of 2001 – 10’s of structures added per year • • 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
Single Crystal vs Powder diffraction (5 of 6) Structure Determination from Powder Diffractometry Round Robin • 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/sample 2. html Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Single Crystal vs Powder diffraction (6 of 6) Tetracycline structures obtained from microcrystal - single crystal diffraction : synchrotron X-rays • • • a powder can be a collection of very small single crystals 10 x 20 x 30 micron crystal (Clegg and Teat) Beamline 9. 8 at Daresbury lab: 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) • When in doubt - get a single crystal!! Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Talk Agenda • Some words about data collection - Variable Count Time (VCT) • 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 Single crystal suites (also relevant to powder diffraction) 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
Sample Preparation and Data Collection • Assumption for this talk is you know the most appropriate methods for sample preparation, hardware and data collection. • However, given the lack of use of Variable Count Time (VCT) data collection, this does not seem to be the case with 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. , Madsen and Hill method). 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 Madsen and Hill method is at: http: //www. ccp 14. ac. uk/ccp 14/ftp-mirror/csirominerals-anon-ftp/pub/xtallography/variable-count-time/ (Original Madsen and Hill 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. Vctconv will inter-convert Madsen and Hill VCT format into GSAS ESD format • http: //www. ceramics. irl. cri. nz/Convert. htm Convert 4 for Windows will inter-convert x, y, esd data to GSAS ESD format • http: //www. ccp 14. ac. uk/ccp/web-mirrors/ndragoe/research/software. html Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
VCT for Powder Indexing (1 of 4) 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 Powder Indexing (2 of 4) Variable Count Time data (normalized 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 Powder Indexing (3 of 4) Fixed Count Time data (zoomed) This peak position is not going to be very precise Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
VCT for Powder Indexing (3 of 4) Variable Count Time data (zoomed) This “trace” peak position will be more precise 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 (normalized 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 (normalized 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 commercial XRD control software – Compare to the old Enraf Nonius CAD 4 single crystal diffractometer options Something to keep an eye on - or request from vendors. 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. crystalimpact. com • 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 – Open. XRD by Stefan Krumm in development (GPL’d 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
Find out 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 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 • ICSD (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 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 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
Crystallography Suites that link into the 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: //www 2. ccc. uni-erlangen. de/software/corina/free_struct. html – Then use Platon/System S acting as a friendly interface for Quest. 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
Powder Diffraction Utility Software • Examining Data, peak finding, background stripping, alpha-2 stripping • Powder v 2. 00: http: //www. ccp 14. ac. uk/tutorial/powder/ • Powder X, http: //www. ccp 14. ac. uk/tutorial/powderx/ • Win. FIT, – http: //www. geol. uni-erlangen. de/html/software/soft. html Powder X (Alpha 2 Strip, Background Strip, Peak Find) • Winplotr, http: //www-llb. cea. fr/winplotr. htm • XFIT, http: //www. ccp 14. ac. uk/tutorial/xfit-95/xfit. htm • CMPR for Windows and UNIX: – http: //www. ncnr. nist. gov/programs/crystallography/ • Example of Powder. X for Windows • • Graphical evaluation, backtground stripping, smoothing, alpha stripping, peak find and pass to treor indexing Full GUI Operation Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Peak Profiling for Powder indexing • For Overall Summary of available peak profiling software refer to: • http: //www. ccp 14. ac. uk/solution/peakprofiling/ • These include: CMPR, DRXWin, EFLECH, GPLSFT, pearson. xls, SHADOW, Powder v 2. 00, Powder. X, Winfit, Winplotr, XFIT Examples of XFIT for Windows Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Peak Profiling: high accuracy peak positions using Fundamental Parameters peak profiling in XFIT • 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. ccp 14. ac. uk/tutorial/xfit-95/fun 1. htm • Available Fundamental Parameters Peak Profiling and Rietveld software: • XFIT (no longer maintained) – http: //www. ccp 14. 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 Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Powder Indexing FOM Results XFIT Fundamental Parameters peak profiling compared to empirical Peak Fitting Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Powder Indexing - a non trivial endeavour • Very tricky to solve a structure if you don’t have cell and spacegroup • 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 : easy to see non-matching or impurity peaks 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 do not reliably determine – 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
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 Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. 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 Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
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 T 3 R 3 human insulinzinc complex produced by grinding", Acta Cryst. (2000). D 56, 1549 -1553. 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 now 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
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) 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
“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/Uk/uk-software. htm • If EXPO fails, it is possible to use Le Bail or Pawley extracted data with Single Crystal Structure Solution Software • 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. chemeng. ucla. 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
Important with realspace programs to input good starting information (too much bad or too little good can put your in a world of “not getting anywhere”) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Single Crystal Structure Solution Also can be applied to powder problems - is a range of programs to choose from: http: //www. ccp 14. ac. uk/solution/xtalsolution/ • CAOS (also inside part of Sir 97) – Ricardo Spagna, et. al. – Patterson Solution Option. • Crisp – Part of the GPL’d Xtal Suite – Direct Methods • Crunch – R. de Gelder, R. A. G. de Graaff & H. Schenk, – Direct Methods and automatic structure building • Dirdif - P. T. Beurskens, G. Beurskens, R. de Gelder, et al. - UNIX and Windows – Patterson Methods for heavy atoms and fragments and automatic structure building • “Patsee” – E. Egert and G. Sheldrick – Fragment Search • SAPI and DIMS – Fan Hai-Fu, et al. – Direct methods including ability to handle pseudo-symmetry and incommensurate modulated structures and composite structures (Windows) • Shake’n’Bake (Sn. B) – Weeks, Miller, et al. – Dual-space direct methods. (Linux, SGI, IBM AIX, Alpha executables via web) • Shake. PSD/DS*SYSTEM – Kenji Okada – Windows based direct methods for large structures up to 500 atoms • “Shelxs” 86/97/d- George Sheldrick – Direct Methods and Patterson Option • Sir 92/97/2000 – Sirware Group: Cascarano, Giacovazzo el al – Direct Methods and automatic structure building • Solver – in NRCVAX Suite – based on Multan – Direct Methods Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
2 D to 3 D model building software • Applicable for Generating 3 D fragments for Patsee/Dirdif Orient – single crystal/powder - and real space methods for solving structures • Summary list at: – http: //www. ccp 14. ac. uk/solution/2 d_3 d_model_builders/ • E. g. , CORINA (COo. Rd. INAtes) (Use web based direct submission): http: //www 2. ccc. uni-erlangen. de/software/corina/free_struct. html Comes with a Java Molecule Editor for building up the 2 D structure over the web which generates the required SMILES string from the drawn molecule. In this example a 2 D tetracyline PDB file is generated: CN(C)C 3 C(O)=C(C(N)=O)C(O)C 4(C)C(O)C 2 C(=O)c 1 c(O)cc cc 1 C(C)(O)C 2 CC 34 (Word of warning: the CORINA “energy minisation” may generate an inaccurate 3 D model where different conformations are possible) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Getting fragments into Dirdif and Patsee for Windows • One of the User Friendliest methods is to use is Win. GX’s “SXGRAPH” GUI Shelx INS/RES file Editor – http: //www. chem. gla. ac. uk/~louis/software/wingx/ • Either graphically Browse and Edit the Orbase Entries or Open an imported structure file (CSSR, CSD, Shelx or CIF from existing structure refinement), clean it up, then save it as a fragment ready for immediate use with Dirdif for Windows. (or any Dirdif) • For Dirdif: File, Save ATMOD File • For Patsee: File, Save PATSEE File • Or ready for powder real space structure solver Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Single Crystal Structure Refinement Software (Applicable to powder diffraction for helping build up the structure) • Range of programs to choose from: – http: //www. ccp 14. ac. uk/solution/xtalrefine/ • CAOS (also inside Sir 97) • Crystals • DS*SYSTEM/LSBF • NRCVAX • Shelxl – (Shelxl is within 3 freely available crystallographic suites) – Win. GX – Platon/System S – ORTEX • Xtal (GPL’d) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Using Crystals to help add hydrogens Automatic Hydrogen Addition http: //www. xtl. ox. ac. uk • Just select: – Structure – Add hydrogens geometrically • New Auto-bond display gives extra graphical feedback Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Crystals : Manual Hydrogen Addition - 1 of 2 • Crystals explains what is going on in a language organic chemists and students can understand Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Crystals : Manual Hydrogen Addition - 2 of 2 • A “Wizard” then guides the user to complete the hydrogen addition 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 • 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, 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 powerful 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 crystallographyfor 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 scales : 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 (This and a new combined installer makes it very easy to start using GSAS. ) http: //www. ncnr. nist. gov/programs/crystallography/software/expgui_intro. html Can spawn Ton Spek’s Platon for structure plotting and structure validation Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Rietveld: Rod Hill and Ian Madsen VCT data collection • • Important to know how to appropriate collect your data that is optimized for the analysis. For Rietveld: If you do have a choice of data collection strategies for XRD - consider variable count time (VCT) VCTCONV for DOS by Mark Bowden will convert VCT Hill and Madsen data into GSAS ESD format. VCT Fortran Source Code with references is available http: //www. ccp 14. ac. uk/ccp 14/ftp-mirror/csirominerals-anon-ftp/pub/xtallography/ 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 routine 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 GSAS (including VRML output) Fullprof / GFOUR for Windows 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
Single Crystal Suites (applicable to powder diffraction) • Again, a large range of programs to choose from: – http: //www. ccp 14. ac. uk/solution/xtalsuites/ • • Crystals for Windows - David Watkin, Richard Cooper, et al DS*SYSTEM - Kenji Okada ORTEX - Patrick Mc. Ardle Platon / System S for UNIX - Ton Spek Win. GX for Windows - Louis Farrugia Xtal (GPL’d) - Syd Hall, Doug du Boulay & R. Olthof-Hazekamp NRCVAX - Eric Gabe, Peter White, et al Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Win. GX for Windows single crystal suite Louis Farrugia: http: //www. chem. gla. ac. uk/~louis/software/ • Complete Single Crystal Suite for Windows • Links to dozens of other programs (new and old) via GUI interfaces • Nearly all programs are included with Win. GX distribution Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Win. GX for Windows single crystal suite Structure Solution • • • Shelxs 97, Shels 86, (Shelxd) Sir 97, Sir 92 Dirdif (Patterson and fragment) Patsee fragment searching SXGRAPH GUI with Win. GX – SXGRAPH Shelxl GUI allows an easy interface for loading of fragments for passing to Patsee or Dirdif Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Win. GX for Windows single crystal suite Hydrogen Addition options • Shelx 97 (G. Sheldrick) – Manually edit INS file – Via SXGRAPH GUI • GUI XHYDEX (G Orphen) • GUI Calc. OH (M Nardelli) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Win. GX for Windows single crystal suite Easy Interlinking with Ton Spek’s Platon • ADDSYM • Other Platon Features Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Win. GX for Windows single crystal suite Structure Plotting • • GUI Win. ORTEP GUI Win. STRUPLO Platon/Pluton/ADP GRETEP (plugin) Schakal (plugin) Rasmol Photo realistic rendering – Povray – Render / RASTER 3 D Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Win. GX for Windows single crystal suite Validation and Structure Checking • • • Platon (Addsym, etc) CIF Validation Parst GEOM THMA 14 c IDEAL SYMMOL WTANAL R-tensor 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/ • Most single crystal suites include structure viewing by default • Some can read common file formats (CIF, Shelx, etc) Gretep by Jean Laugier and Bernard Bochu http: //www. ccp 14. ac. uk/tutorial/lmgp/#gretep – 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
Graphically interacting with the structure (and the ability to open GSAS, Rietica and Fullprof files) GUI Win. ORTEP GUI Win. STRUPLO (http: //www. chem. gla. ac. uk/~louis/software/ortep 3/) (http: //www. chem. gla. ac. uk/~louis/software/struplo/) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Crystal Structure validation - Why Bother? • Better to publish work that can stand the test of time • Thus is very helpful doing a variety of validation and using a variety of programs to assist in validation! Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Structure validation and quality checking (Each suite can offer different features) e. g. , ORTEX by Patrick Mc. Ardle: Example of the Void Finding and graphical viewing within ORTEX (including estimate of time to completion) Platon can do this as well, including display of the void areas as shown on the right Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Win. GX for Windows single crystal suite Validation and Structure Checking • • • Platon (Addsym, etc) CIF Validation Parst GEOM THMA 14 c IDEAL SYMMOL WTANAL R-tensor Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Platon’s Addsym (by Ton Spek) (finding missing symmetry): 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 (by Ton Spek): for powders • Some powder based structures at the Royal Institution and Birkbeck College in London solved using EXPO • Triclinic P 1 - found by Platon’s Addsym to be P -1 • Orthorhombic: – P 21 21 21 - found by Platon’s Addsym to be P n m a – P 2 21 21 - found by Platon’s Addsym to be P m m n • Refer to Howard Harvey and Martin Attfield’s and Talk on the 29 th May – 10. 02: From Structures to Materials Science – 09: 15 - 09: 30 AM (10. 02. 03) (W 0121) – The Design, Synthesis, and Characterization of Novel Group IIIb Bisphonate Materials. 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 • 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 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 Many programs can do this. E. g, ORTEX (Images and Movie Animations): • http: //www. nuigalway. ie/cryst/ • Just open up a Shelx format *. INS/*. RES file and go for it Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Photorealistic hardcopy output of structures GUI Win. ORTEP / GUI Struplo / Win. GX http: //www. ccp 14. ac. uk/tutorial/wingx/ • Can open a wide variety of file formats including Shelx, CIF, GSAS, Rietica, Fullprof, CDS, etc 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
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
Summary · Large Genetic Diversity of Software to help you solve structures from powder diffraction · This diversity is necessary to help you get the job done. · Getting better all the time (some areas faster than others) · Great majority of it is freely available for Academics and Students • Most is mirrored 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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