Dissolving problems into solutions: freely available crystallographic software for single crystal and powder diffraction. 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
Aims of the EPSRC funded CCP 14 Project Get free Crystallographic software and related resources to academics and students relevant to their research. – Tutorials – Software mirrors – Mirror free compilers and software tools Via: http: //www. ccp 14. ac. uk 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. • Where time permits, give screen dumps of actual examples 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/qmul_2001/ • 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
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) 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 Le Bail fitting / Rietveld Slide Using Traditional UNIT CELL refinement Methods 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
Why bother knowing about a variety of modern software? (2 of 4 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. – When to use a scalpal – When to unlock the sledgehammer cabinet – When to declare that Defcon 1 has been activated! 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? (3 of 4) Crystallographic Weaponry 101 • You can benefit from having access to a variety of state of the art tools 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? (4 of 4) Crystallographic Weaponry 102 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
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 (3 of 6) Powder Methods for solving structures • 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 • 484 up to mid 2001 • “During 2000: 58 publications” • 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) 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 (single crystal and powder diffraction) Structure refinement (single crystal and powder diffraction) Single crystal suites 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
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 • 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 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
Phase Identification/Search Match for Powder Diffraction 3 of 3 Multiphase mixture: Flourite, Corundum, Zincite 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
A hopeful trend: 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
Structure Importing, Conversion and Transformation ·Summary list of available software at: http: //www. ccp 14. ac. uk/solution/structconv/ Example of Cryscon for Windows by Eric Dowty ·Be careful to check the results ·Best program for the moment is the shareware Cryscon · http: //www. shapesoftware. com ·Other software such as GUI Win. ORTEP can import a wide variety of file formats and export these into Shelx format. http: //www. chem. gla. ac. uk/~louis/software/ortep 3/ 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 • 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 (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, 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: Crystallite size and strain using Fundamental Parameters peak profiling in XFIT • Example of Fundamental parameters (convoluting in the geometry elements of the diffractometer) to profile peaks and also provide size and strain information (though be careful on how you intepret this) • 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 version is downloadable) – http: //www. bgmn. de 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
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: 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 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
Why doesn’t this powder sample index? Why Isn’t this cell solving (Organometallic) From Armel Le Bail’s site: ESRF Synchrotron Powder Data as well Very difficult problems can still be difficult on any available software program. But it may solve in the future when tried on updated software. 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 • Graphics can really help sort out errors or misassigned 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
Single Crystal Absorption Correction Options • Using Win. GX Single crystal suite by Louis Farrugia as an example: – http: //www. chem. gla. ac. uk/~louis/software/wingx/ • • Viewing or HKL Profiles Blessing DREAR Software Sortav (Kappa CCD data processing) Numerical: Reflection profile within Win. GX – Gaussian, Analytical, Spherica l, Cylindrical • Semi Empirical: – Psi-scans, Camel-Jockey, Multiscan • Ref. Del. F: – Difabs, XABS 2, Shelxa Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Single Crystal Absorption Correction : Win. GX Before making use of the data (e. g. , for refinement) the user is prompted which form of absorption corrected data to use. Thus users can easily check the various absorption algorithms. Slide Define and view single crystal faces within Win. GX Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Platon options for absorption correction • Platon by Ton Spek: – http: //www. cryst. chem. uu. nl/platon/ • • DELref. ABSPsi. Scan ABSTompa ABSGauss ABSXtal ABSSphere MULscan. ABS XTALHabit within Platon • Links to Face. Lift - program to refine the initial crystal description (HABITUS style approach) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Single Crystal Indexing / Twinning • Twinning: – DIRAX for difficult Indexing problems: ftp: //ftp. chem. uu. nl/pub/dirax/ – Twindex: ftp: //laue. chem. ncsu. edu/pub/X-ray/twindex/ • • The Merohedral Crystal Twinning Server: http: //www. doe-mbi. ucla. edu/Services/Twinning/ TWIN 3. 0 for Windows (test for merohedry): Contact V. Kahlenberg (vkahlen@uni-bremen. de) • Spacegroup Assignment: • • ABSEN Single Crystal Program by Patrick Mc. Ardle (comes with the ORTEX and Win. GX suites) – http: //www. nuigalway. ie/cryst/software. htm – http: //www. chem. gla. ac. uk/~louis/software/wingx/ Platon spacegroup assignment options – http: //www. cryst. chem. uu. nl/platon/ • ROTAX style or inspired twinning software (Fo / Fc) (by Simon Parsons and Bob Gould) – Platon Twin. Rot. MAt - http: //www. cryst. chem. uu. nl/platon/ – ROTAX in Crystals - http: //www. xtl. ox. ac. uk/crystals. html 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 as described in following slides. • Then consider real space methods such as using ESPOIR (GPL’d by Armel Le bail) Monte Carlo and pseudo simulated annealing - normally use as last resort (new version for Windows has “real space molecule and fragment location”). • http: // sdpd. univ-lemans. fr /sdpd/espoir/ • http: //www. ccp 14. ac. uk/ccp/web-mirrors/armel/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/ Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
“Specialised and Commercial” Structure Solution Programs • Obj. Cryst++ & FOX - modular toolbox - including special features for inorganics – http: //objcryst. sourceforge. net/ • 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
EXPO in Action (1 of 4) Edit the input / control file Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
EXPO in action (2 of 4) Click on the OK button to start Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
EXPO in action (3 of 4) Le Bail fitting of the powder pattern Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
EXPO in action (4 of 4) Structure after solved by direct methods Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Single Crystal Structure Solution 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 • 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 • XFPA – Frantisek Pavelcik – Patterson Methods and automatic structure building Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Single Crystal Structure Solution (What’s it like to use the software? ) 1) Push the “start” button 2) Structure solves 3) If not, try next program (using the benefits of having access to multiple programs with different strengths) Single Crystal Suites make it trivial to easily use multiple programs (if nothing solves, it could be twinning - or other problems? ) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Shelxs direct methods (tetracycline hydrochloride) via Win. GX as an interface Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Sir direct methods and auto Fourier building (tetracycline hydrochloride) via Win. GX as an interface Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Dirdif Patterson methods and auto Fourier building (tetracycline hydrochloride) via Win. GX as an interface Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Crunch for UNIX direct methods and Fourier building (tetracycline hydrochloride) via Platon/System S as an interface 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 • 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 “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 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
Example of Crystals for Windows David Watkin, Richard Cooper, et al. : http: //www. xtl. ox. ac. uk/ • Will focus on Guided refinement Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Guided structure refinement using Crystals Import Shelx INS file of structure solved by DIRDIF • Asymmetric unit is always in view Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Guided structure refinement using Crystals • Crystals Superviser can then try and take the user (including students and chemistrs) through the refinement - giving guidance where appropriate Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Guided structure refinement using Crystals Have now refined atom positions Isotropically • The Crystals Supervisor will then make further recommendations • (Crystals Scripts means custom tutorials and refinement logic can be added) Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Guided structure refinement using Crystals Have now refined atom positions anisotropically • Atoms can be displayed anisotropically Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Guided structure refinement using Crystals Automatic Hydrogen Addition • Graphically compare calculated hydrogens (white) to possible hydrogens found in the difference map (pink). Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Interrupt the Guided Refinement in Crystals Manual Hydrogen Addition - 1 of 2 • Crystals explains what is going on in a language organic chemists and students can understand (who may be learning single crystal methods as a tool for a larger project) and displayed in organic chemistry text books. • May be easier teaching crystallographic methods to a specialist audience starting out with their jargon. Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Interrupt the Guided Refinement in 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
Interrupt the Guided Refinement in Crystals Generating Fourier maps and Marching Cubes for Windows • Easily generate Fourier contour maps to show the electron density. In this case: electron density due to the missing hydrogens. Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Structure refinement using Crystals Validation via Cambridge database: geometry checking • To students and new users, every structure must seem like a new structure type. Thus using CSD geometry check can encourage students to look for errors or novel features of the structure. Bondlengths RED="too long" and BLUE="too short". RED ---- GREY ---- BLUE 3 sigma 2 sigma 1 sigma 0 sigma 1 sigma 2 sigma 3 sigma Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Validation using Crystals Cambridge database geometry check (1 of 4) • Doing a CSD check shows a bond in red (too long) displaying a geometry of which is completely novel in reference to what is already known Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Validation using Crystals Cambridge database geometry check (2 of 4) • Using the GUI (or scripts) make the offending Nitrogen a Carbon and re-refine. Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Validation using Crystals Cambridge database geometry check (3 of 4) • Black bonds around the renamed atom tells the user that the new geometry has not been tested against the CSD. So interrogate the CSD again to obtain this information. Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Validation using Crystals Cambridge database geometry check (4 of 4) • CSD results now imply/infer that local geometry is consistent with what is already in the database. 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 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
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
GSAS: Individual Histogram Weighting • In this example, you need to zoom up a bit. – XRD pattern is ~1500 times more intense than the corresponding neutron pattern – Problematic for combined refinement Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
GSAS: Individual Histogram Weighting (use Sum(w*d**2) as a guide) • Set via EXPEDT • (changing weight on Histogram 1 - XRD) – – – y !backup p !powder prep h !histograms f 1 !weighting on hist 1. 001 !set the weighting x x x !exit expedt • Run Powpref for new weighting to take effect Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
GSAS : Combined refinement on both XRD and Neutron X-ray 7. 6% R(F**2) Neutron 4. 2% R(F**2) (~3. 8% R Bragg) (~2. 1% R Bragg) 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) 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 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 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 Families of programs included/linkable with Win. GX • Importing/viewing data and models • Absorption Correction • Solution (Shelx, difdif, sir, patsee) • GUI / manual shelxl 97 refinement • Hydrogen addition options – Shelxl, GUI Calc. OH, GUI XHYDEX • Fourier Contour Map viewing – Platon, Contour, Mapview, Marching cubes • Structure Plotting • Validation / publishing 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 Absorption Correction • DREAR - Blessing software • Numerical – Gaussian, Analytical, Spherical, Cylindrical, Needle • Semi-empirical – Psi Scans, Camel Jockey, Multiscan • DIFABS Style – Difabs, Xabs, Shelxa • Interactive Visualisation of crystal faces using Xtal. View 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 Refinement - Shelxl 97 • GUI control of Shelx via Win. GX’s SXGRAPH program • or Shelx ASCII INS File 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 • Squeeze/disordered solvent effects • 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 Fourier Electron Density Contour Maps • Use LIST 3 command in Shelxl • Point and click map generation • View resulting maps in: – Contour – Mapview – Marching Cubes by Michak Husak 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
Some Specialist Applications • Charge Density (single crystal) – Project XD – http: //www. chem. gla. ac. uk/~paul/paul. html • 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 previous slide). • Following using Koalariet / XFIT (fundamental parameters) http: //www. ccp 14. ac. uk/tutorial/xfit-95/ Maud for Java Quantitative Analysis Tutorial: http: //www. ing. unitn. it/~luttero/maud/tutorial/ • 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
Quantitative Phase Analysis - pharmaceuticals • No-one using a Rietveld method could take on the IUCr CPD QARR samples due to lack of crystal structures. From the IUCr CPD Quant Round Robin (draft results for publication) http: //www. iucr. org/iucr-top/comm/cpd/QARR/ • A quote from Armel Le Bail’s Tmacle “twinned refinement” 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! TO HAVE THE SOLUTION DEPENDS ON YOU, NOT ON THIS PROGRAM WHICH IS JUST ABLE TO TEST YOUR HYPOTHESIS. . . . 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 • 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
Graphically interacting with the structure (more examples) 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? • 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!!” • 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) 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): 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 - (1 of 2) finding extra symmetry in inorganics and minerals - P 1 triclinic starting structure. • Unpublished Mineral Example – Default Addsym gives C 2/C • Tighten the addsym values: – calc ADDSYM SHELX 1 0. 2 0. 4 0. 2 – addsym gives P 2/c and exact fit on Pc • Loosening defaults: – calc addsym shelx exact 1. 2. 4. 4 – P-31 m Slide Lachlan M. D. Cranswick (l. m. d. cranswick@dl. ac. uk) http: //www. ccp 14. ac. uk
Platon’s Addsym - (2 of 2) finding extra symmetry in inorganics and minerals - P 1 triclinic starting structure. • Update new refinement in triclinic: – Lower R factor in Shelx – Addsym now finds P 21/c in default mode • Thus need to be careful! 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 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, 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 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. 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 This diversity is necessary to help you get the job done. Getting better all the time (some areas faster than others) Free available for Academics and Students • 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
Скачать презентацию Dissolving problems into solutions freely available crystallographic software
dcacd7446ab8c3d542ed63b5a9fe291c.ppt