An overview of available software for solving crystal structures from powder diffraction Lachlan M. D. Cranswick, CCP14 (Collaborative Computation Project.

An overview of available software for solving crystal structures from powder diffraction
Lachlan M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for Single Crystal and Powder Diffraction) Department of Crystallography; Birkbeck College, University of London, Malet Street, Bloomsbury, London, WC1E 7HX, UK. WWW:

Notes Free Zone - they are on the web http://www. ccp14. ac
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 2 Lachlan M. D. Cranswick

Talk Aims Give an overview of available software relevant to people doing crystallography on minerals and inorganics And minor ranting about other issues Slide 3 Lachlan M. D. Cranswick

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

Using the right crystallographic method can make the difference!
Using Le Bail fitting / Rietveld Using Traditional UNIT CELL refinement Methods Slide 5 Lachlan M. D. Cranswick

Le Bail fitting: results of the volume of Oxygen and the earth’s other core
~10 cc/mol (This EDX / Le Bail result) means there can be Oxygen in the Earth’s outer core. Other non diffraction results of ~15 cc/mol means there cannot be Oxygen (shockwave / molecular dynamics) Refer: “O2 volumes at high pressure from KClO4 decomposition: D" as a siderophile element pump instead of a lid on the core.” D. Walker, S.M. Clark, L.M.D. Cranswick, M.C. Johnson and R.L. Jones, (2002), Geochemistry, Geophysics, Geosystems (G^3), submitted for publication. Slide 6 Lachlan M. D. Cranswick

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 7 Lachlan M. D. Cranswick

Path of Most Resistance?
Why bother knowing about a variety of modern software? (1 of 2) Path of Most Resistance? Using a variety of “state-of-the-art” tools can improve versatility by allowing different pathways and approaches to tackle crystallographic problems. Maximise the ability to handle present and future problems Be able to cross hurdles that may be intractable or unnecessarily problematic if not approached the right way. Slide 8 Lachlan M. D. Cranswick

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 9 Lachlan M. D. Cranswick

Single Crystal vs Powder diffraction (1 of 8)
“Mass transit” structure solution and refinement There are difficulties: Crystal not representative of the bulk Twinning Crystal decomposes during data collection “Difficult” structure Slide 10 Lachlan M. D. Cranswick

Cambridge Database (organics - organometallics) “During 1999, 17,898 new entries were added” (that Scale is in the 100’s of thousands) 1999 report: Slide 11 Lachlan M. D. Cranswick

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 12 Lachlan M. D. Cranswick

Powder Methods for solving structures A nightmare to some An adventure to others! Slide 13 Lachlan M. D. Cranswick

Number of structures solved by powder methods Cumulative total of 592 up to end of 2001 10’s of structures added per year Slide 14 Lachlan M. D. Cranswick

Structure Determination from Powder Diffractometry Round Robin Tetracycline Hydrochloride (June 1998) 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) Slide 15 Lachlan M. D. Cranswick

Tetracycline structures obtained from microcrystal - single crystal diffraction : synchrotron X-rays a powder can be a collection of very small single crystals 10x20x30 micron crystal (Clegg and Teat) Beamline 9.8 at Daresbury lab: Bruker Smart CCD 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 16 Lachlan M. D. Cranswick

What about the “inorganic unknown” in the SDPD Round Robin? No-one bothered to solve it (except Armel Le Bail) One participant who solved the organic said the inorganic was “too boring” and thus did not try it. Big fad at present is to solve organic pharmaceuticals from powders Much commercial software development reflects this emphasis on pharmaceuticals Slide 17 Lachlan M. D. Cranswick

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 18 Lachlan M. D. Cranswick

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 19 Lachlan M. D. Cranswick

Variable Count Time data collection
Main idea here is to increase the raw intensity of selected peak areas to assist in the “required” analysis: (similar to what a CAD4 does) Up till now, if at all, mainly done for refinement (e.g., Madsen and Hill method) due to this being the only available peer reviewed publication on this type of data collection Fixed Count Time Variable Count Time Slide 20 Lachlan M. D. Cranswick

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, Philips Friendly Fortran source code that does this Madsen and Hill method is at: (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 P2.6 NIST Special Publication No. 846, Page 210, (1992) National Institute of Standards and Technology, Gaithersburg, MD, USA. Vctconv will convert Madsen and Hill VCT format into GSAS ESD format Slide 21 Lachlan M. D. Cranswick

VCT for Powder Indexing (1 of 4) Fixed Count Time data (data collected by Jeremy Cockcroft)
Slide 22 Lachlan M. D. Cranswick

VCT for Powder Indexing (2 of 4) Variable Count Time data (normalized as FCT) (data collected by Jeremy Cockcroft) Slide 23 Lachlan M. D. Cranswick

VCT for Powder Indexing (3 of 4) Fixed Count Time data (zoomed) This peak position is not going to be very precise Slide 24 Lachlan M. D. Cranswick

VCT for Powder Indexing (3 of 4) Variable Count Time data (zoomed) This “trace” peak position will be more precise Slide 25 Lachlan M. D. Cranswick

VCT for Structure Solution and Refinement (1 of 4) Variable Count Time data (as collected)

VCT for Structure Solution and Refinement (2 of 4) Variable Count Time data (normalised as FCT)

VCT for Structure Solution and Refinement (3 of 4) Variable Count Time data (normalised as FCT)

VCT for Structure Solution and Refinement (4 of 4) Variable Count Time data (displayed as VCT)

Where is VCT Data Collection?
Not a routine or available option in commercial XRD control software Compare to the old Enraf Nonius CAD4 single crystal diffractometer options Something to keep an eye on - or request from vendors. Slide 30 Lachlan M. D. Cranswick

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 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: Free Software:Brian Toby's "Portable Logic Program" (UNIX) and "MacDiff" for Apple Mac freeware by Rainer Petschick OpenXRD by Stefan Krumm in development (GPL’d UNIX and Windows) Slide 31 Lachlan M. D. Cranswick

Find out which software, databases and methods work the best: Search Match Round Robin (2nd May 2002 to 30th June 2002): and CCP14 mirrors Slide 32 Lachlan M. D. Cranswick

Has the structure been solved already
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): ICSD (Minerals and Inorganics) Web accessible demonstration: MDF/CRYSTMET (Metals and Alloys) CCSD (Organics and Organometallics) American Mineralogist WWW Mincryst 2398 unique phases - most with crystal structure data Mineral web Slide 33 Lachlan M. D. Cranswick

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. Slide 34 Lachlan M. D. Cranswick

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: 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: Freeware ConTEXT Editor for Windows (does column editing) Example of ConvX for Windows by Mark Bowden Mass data powder diffraction data converter Slide 35 Lachlan M. D. Cranswick

Structure Importing, Conversion and Transformation
Summary list of available software at: Be careful to check the results Best program for the moment is the shareware Cryscon Other software such as GUI WinORTEP can import a wide variety of file formats and export these into Shelx format. Example of Cryscon for Windows by Eric Dowty Slide 36 Lachlan M. D. Cranswick

Powder Diffraction Utility Software
Examining Data, peak finding, background stripping, alpha-2 stripping Powder v 2.00: Powder X, WinFIT, Winplotr, XFIT, CMPR for Windows and UNIX: Example of PowderX for Windows Graphical evaluation, backtground stripping, smoothing, alpha stripping, peak find and pass to treor indexing Full GUI Operation Powder X (Alpha2 Strip, Background Strip, Peak Find) Slide 37 Lachlan M. D. Cranswick

Peak Profiling for Powder indexing
For Overall Summary of available peak profiling software refer to: These include: CMPR, DRXWin, EFLECH, GPLSFT, pearson.xls, SHADOW, Powder v2.00, PowderX, Winfit, Winplotr, XFIT Examples of XFIT for Windows Slide 38 Lachlan M. D. Cranswick

Fundamental Parameters Peak Profiling mode : fit to a low angle peak : Bragg-Brentano diffractometer data 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: Available Fundamental Parameters Peak Profiling and Rietveld software: XFIT (no longer maintained) Topas (Commercial - sequel to XFIT) BGMN (Commercial - academic demonstration version is freely downloadable) Slide 39 Lachlan M. D. Cranswick

Powder Indexing FOM Results XFIT Fundamental Parameters peak profiling compared to empirical Peak Fitting Slide 40 Lachlan M. D. Cranswick

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: Powder Indexing: Autox, Ito, Dicvol, Treor, Taup/Powder, Lzon, Losh, Kohl, Scanix, Xrayscan, EFLECH/Index, Supercell Linking Suites: Crysfire, Powder v2.00, PowderX, PROSZKI, WinPlotr, Chekcell supercel is a specialise indexing program by Juan Rodriguez-Carvajal for indexing Super Cell and Incommensurate cells. (available within Winplotr) ftp://bali.saclay.cea.fr/pub/divers/fullprof.2k/ Slide 41 Lachlan M. D. Cranswick

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. Example of CRYSFIRE Screen prompting the saving into one of 8 different indexing program formats: Slide 42 Lachlan M. D. Cranswick

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. Slide 43 Lachlan M. D. Cranswick

Chekcell : easy to see non-matching or impurity peaks

Chekcell : automatic cell and spacegroup searching
can trudge through a single selected unitcell; or over 1000s of trial cells looking for the best cell and spacegroup combination based on “parsimony of extra reflections” criteria. Slide 45 Lachlan M. D. Cranswick

Chekcell: “integration” of Ton Spek and A. Meetsma’s Le Page
Obtaining the Reduced Cell which many powder indexing programs do not reliably determined Refer: "'Reduced Cells', M.J. Buerger, (Zeitschift fur Kristallographie, BD 109, S (1957)” Efficient Sub-cell and super-cell searching, then easy reviewing of newly derived cells within the Chekcell interface Slide 46 Lachlan M. D. Cranswick

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 47 Lachlan M. D. Cranswick

Chekcell: Density / Z / Molecular Volume Explorer
Easily look at effects of Z, Density and molecular volume Slide 48 Lachlan M. D. Cranswick

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 49 Lachlan M. D. Cranswick

Why doesn’t this powder sample index?
Why Isn’t this cell solving (Organometallic) From Armel Le Bail’s site: ESRF Synchrotron Powder Data 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 50 Lachlan M. D. Cranswick

Some Alternatives to Crysfire: Winplotr, PowderX
Winplotr by Juan Rodriguez-Carvajal PowderX by Cheng Dong Powder v2 by Nita Dragoe CMPR for Windows and UNIX by Brian Toby Slide 51 Lachlan M. D. Cranswick

Unit Cell Refinement (powders)
For Overall Summary of available unit cell refinement software refer to: This includes: Celref, LAPOD, Refcel, Unitcell, Eracel, Powder v2.00, 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 52 Lachlan M. D. Cranswick

CELREF for Unit Cell Refinement
by Jean Laugier and Bernard Bochu In this example, celref is performing graphical Unit Cell refinement on calcite in a multi-phase mixture Knows about spacegroups Graphics can really help sort out errors or misassigned Slide 53 Lachlan M. D. Cranswick

Full Profile Fitting (Powder)
For Overall Summary of available full profile analysis refer to: Le Bail based: Pawley Based: 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 54 Lachlan M. D. Cranswick

Le Bail full profile fitting - Rietica Rietveld
By Brett Hunter 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 55 Lachlan M. D. Cranswick

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 - Le Bail method can do this as peaks positions are constrained by the cell and spacegroup Slide 56 Lachlan M. D. Cranswick

Unit Cell Refinement: Mass Le Bail fitting: multi-phase - overlapping patterns
Using Le Bail fitting Using Traditional Methods Slide 57 Lachlan M. D. Cranswick

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: BEARTEX for Windows GSAS Rietveld (Windows/UNIX) MAUD for Java POFINT popLA Symmet for DOS TexturePlus for Windows MAUD (for Java PC/Mac/UNIX) Slide 58 Lachlan M. D. Cranswick

CAD4 Reflection profile within WinGX
Single Crystal Absorption Correction Options Using WinGX Single crystal suite by Louis Farrugia as an example: Viewing or HKL Profiles Blessing DREAR Software Sortav (Kappa CCD data processing) Numerical: Gaussian, Analytical, Spherica l, Cylindrical Semi Empirical: Psi-scans, Camel-Jockey, Multiscan RefDelF: Difabs, XABS2, Shelxa CAD4 Reflection profile within WinGX Slide 59 Lachlan M. D. Cranswick

Platon options for absorption correction
Platon by Ton Spek: DELrefABS ABSPsiScan ABSTompa ABSGauss ABSXtal ABSSphere MULscanABS Links to FaceLift - program to refine the initial crystal description (HABITUS style approach) XTALHabit within Platon Slide 60 Lachlan M. D. Cranswick

Single Crystal Indexing / Twinning
DIRAX for difficult Indexing problems: ftp://xraysoft.chem.uu.nl/pub/msdos/DIRAX/ Twindex: ftp://laue.chem.ncsu.edu/pub/X-ray/twindex/ The Merohedral Crystal Twinning Server: TWIN3.0 for Windows (test for merohedry): Contact V. Kahlenberg Spacegroup Assignment: ABSEN Single Crystal Program by Patrick McArdle (comes with the ORTEX and WinGX suites) Platon spacegroup assignment options Slide 61 Lachlan M. D. Cranswick

ROTAX Single Crystal Twinning Software
New ROTAX style: (Determine Twin Matrix from Fo/Fc Data) Platon incorporates LePageTwin WinGX and Crystals suites link seamlessly into ROTAX (by Simon Parsons and Bob Gould) Slide 62 Lachlan M. D. Cranswick

“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 Sir92/Sir97/Sirpow 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: 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: FOX: Slide 63 Lachlan M. D. Cranswick

“Specialised and Commercial” Structure Solution Programs
PSSP – molecular structures ZEFSA II – for Zeolites (GPL’d) Focus – for Zeolites 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: Crystal Structure Determination Package (WinCSD/CSD) : DASH (Druid and Mystic of old): TOPAS : Endeavour : Slide 64 Lachlan M. D. Cranswick

EXPO direct methods in Action (1 of 4) Edit the input / control file - inorganic

EXPO direct methods in action (2 of 4) Click on the OK button to start

EXPO direct methods in action (3 of 4) Le Bail fitting of the powder pattern (not the full range of data as high angle data can be just noise and spoil the direct methods) Slide 67 Lachlan M. D. Cranswick

EXPO direct methods in action (4 of 4) Structure after being solved and auto built

Important with realspace programs to input good starting information (too much bad or too little good can put you in a world of not getting anywhere fast) Slide 69 Lachlan M. D. Cranswick

New FOX real space structure solution by Vincent Favre-Nicolin and Radovan Cerny
Available for UNIX/Linux and MS-Windows GUI Based Very user friendly in setting up rigid bodies Includes automatic merging of atoms on special position with dynamic occupancy correction Thus very good for minral/inorganic structures Slide 70 Lachlan M. D. Cranswick

Adding polyhedra in Fox - 1 of 5
Click on “Crystals”, “Scatterers” Icon, “Add” Slide 71 Lachlan M. D. Cranswick

Select the central atom Slide 72 Lachlan M. D. Cranswick

Select the corner atom(s) Slide 73 Lachlan M. D. Cranswick

Give the Bond length Slide 74 Lachlan M. D. Cranswick

Done! Slide 75 Lachlan M. D. Cranswick

Single Crystal Structure Solution
Also can be applied to powder problems - is a range of programs to choose from: CAOS (also inside part of Sir97) – 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 (SnB) – Weeks, Miller, et al. Dual-space direct methods. (Linux, SGI, IBM AIX, Alpha executables via web) ShakePSD/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 Sir92/97/2000 – Sirware Group: Cascarano, Giacovazzo el al Solver – in NRCVAX Suite – based on Multan Slide 76 Lachlan M. D. Cranswick

(if nothing solves, it could be twinning - or other problems?)
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 77 Lachlan M. D. Cranswick

Shelxs direct methods (Cesium Titanium Silicate) via WinGX as an interface

Sir97 direct methods with auto-building (Cesium Titanium Silicate) via WinGX as an interface (in this case - first try does not solve - just leave Sir97 to automatically continue on) Slide 79 Lachlan M. D. Cranswick

Dirdif automatic Patterson methods (Cesium Titanium Silicate) via WinGX as an interface (solves and auto-builds in default mode - all atoms correctly found and labelled) Slide 80 Lachlan M. D. Cranswick

Single Crystal Structure Refinement Software (Applicable to powder diffraction for helping build up the structure) Range of chemical crystallography dominated programs to choose from at: CAOS (also inside Sir97) Crystals DS*SYSTEM/LSBF GSAS (single crystal and powder) Jana (single crystal and powder) NRCVAX Shelxl (Shelxl is within 3 freely available crystallographic suites) WinGX : Platon/System S : ORTEX Xtal (GPL’d) Slide 81 Lachlan M. D. Cranswick

Single Crystal Structure Refinement Software JANA Single Crystal and Powder Diffraction Refinement
Developed for handling inorganics / metals - commensurate and incommensurate by Vaclav Petricek and Michal Dusek Single crystal and powder diffraction (not Neutron Time of Flight (TOF)) Powder tutorial at: UNIX, Windows and Mac Os X Menu driven Complicated inorganic solid state structure refinement Commensurate, incommensurate and composite structures Electron density and anharmonic refinement (automatically sets the required symmetry constraints for anharmonic) Refinement of f’ and f’’ Equation editor based constraints make it possible to link any one parameter to another Can handle multiple twins Many other features Slide 82 Lachlan M. D. Cranswick

Structure Refinement using Powder Diffraction Data (Rietveld Refinement)
Large range of programs to choose from: Many specialize for particular types of problems, incommensurate structures, quantitative analysis, polymers, etc. ARITVE, BGMN, DBWS, DEBVIN, EXPO Fullprof, GSAS, Jana, Koalariet, LHPM-Rietica, MAUD for Java (GPL’d) Premos/Remos, ProDD, Profil, Riet7/SR5, Rietan 2000 (GPL’d) Rietquan, Simref, WinMprof, XND, XRS-82/DLS-76 Slide 83 Lachlan M. D. Cranswick

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 84 Lachlan M. D. Cranswick

Rietveld Programs - Rietica by Brett Hunter
Full Graphical User Interface Still got to appreciate and know your crystallographyfor inserting and refining the crystal structure Slide 85 Lachlan M. D. Cranswick

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 GSAS resources, tutorials and links (including links to EXPGUI) 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 Slide 86 Lachlan M. D. Cranswick

Brian Toby’s EXPGUI Interface for GSAS
Can be user friendlier to start using GSAS via EXPGUI (A new combined installer makes it very easy to start using GSAS.) Slide 87 Lachlan M. D. Cranswick

Restrained Rietveld structure refinement of organics
Software not as routine as single crystal but there are some tutorials with tricks on the CCP14 website Slide 88 Lachlan M. D. Cranswick

Fourier capability in Rietveld Software
GSAS (including VRML output) Fullprof / GFOUR for Windows Summary list of Fourier friendly Rietveld software at: Slide 89 Lachlan M. D. Cranswick

Single Crystal Suites (applicable to powder diffraction)
Again, a large range of programs to choose from: Crystals for Windows - David Watkin, Richard Cooper, et al DS*SYSTEM - Kenji Okada ORTEX - Patrick McArdle Platon / System S for UNIX - Ton Spek WinGX for Windows - Louis Farrugia Xtal (GPL’d) - Syd Hall, Doug du Boulay & R. Olthof-Hazekamp NRCVAX - Eric Gabe, Peter White, et al Slide 90 Lachlan M. D. Cranswick

WinGX 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 WinGX distribution Slide 91 Lachlan M. D. Cranswick

WinGX for Windows single crystal suite Families of programs included/linkable with WinGX
Importing/viewing data and models Absorption Correction Solution (Shelx, difdif, sir, patsee) GUI / manual shelxl97 refinement Hydrogen addition options Shelxl, GUI CalcOH, GUI XHYDEX Fourier Contour Map viewing Platon, Contour, Mapview, Marching cubes Structure Plotting Validation / publishing Slide 92 Lachlan M. D. Cranswick

WinGX for Windows single crystal suite Viewing the raw CCD frames and raw profile data
Nonius Raw Frame image files CAD4 peak Profiles HKLs displayed as precession data Simple to advanced HKL processing, sorting, merging, etc Slide 93 Lachlan M. D. Cranswick

WinGX for Windows single crystal suite Structure Solution
Shelxs97, Shels86, (Shelxd) Sir97, Sir 92 Dirdif (Patterson and fragment) Patsee fragment searching SXGRAPH GUI with WinGX SXGRAPH Shelxl GUI allows an easy interface for loading of fragments for passing to Patsee or Dirdif Slide 94 Lachlan M. D. Cranswick

WinGX for Windows single crystal suite Absorption Correction
Sortav for Nonius CCD data 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 XtalView Slide 95 Lachlan M. D. Cranswick

WinGX for Windows single crystal suite Refinement - Shelxl 97 (WinGX now links to Crystals as well)
GUI control of Shelx via WinGX’s SXGRAPH program In the following SXGRAPH screen - only allowing heavy atom co-ords to refine or Shelx ASCII INS File Slide 96 Lachlan M. D. Cranswick

WinGX 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 97 Lachlan M. D. Cranswick

WinGX for Windows single crystal suite Easy Interlinking with Ton Spek’s Platon
ADDSYM Other Platon Features Slide 98 Lachlan M. D. Cranswick

WinGX for Windows single crystal suite Structure Plotting
GUI WinORTEP GUI WinSTRUPLO Platon/Pluton/ADP GRETEP (plugin) Schakal (plugin) Rasmol Photo realistic rendering Povray Render / RASTER 3D Slide 99 Lachlan M. D. Cranswick

WinGX for Windows single crystal suite Validation and Structure Checking
Platon (Addsym, etc) CIF Validation Parst GEOM THMA 14c IDEAL SYMMOL WTANAL R-tensor Slide 100 Lachlan M. D. Cranswick

Graphically interacting with the structure
Number of programs available with list available at: Most single crystal suites include structure viewing by default Some can read common file formats (CIF, Shelx, etc) Gui WinORTEP reads the widest variety of formats Software includes: Crystals, Cameron, PIG (part of the Xtal suite), ORTEX, Gretep, Platon, GUI WinORTEP, GUI WinSTRUPLO Slide 101 Lachlan M. D. Cranswick

Graphically interacting with the structure (and the ability to open GSAS, Rietica and Fullprof files) GUI WinORTEP ( GUI WinSTRUPLO ( Slide 102 Lachlan M. D. Cranswick

Some Specialist Applications
Charge Density (single crystal) Project XD Anharmonic Refinement List of Software: Incommensurate Structure Refinement PDF / High Q Analysis Slide 103 Lachlan M. D. Cranswick

Platon: Validation - why taking 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 solve, refine and publish structures that can stand the test of time - that means doing a variety of validation and using a variety of programs to assist in validation! Slide 104 Lachlan M. D. Cranswick

Structure validation and quality checking
(Each suite can offer different features) e.g., ORTEX by Patrick McArdle: 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 105 Lachlan M. D. Cranswick

WinGX for Windows single crystal suite Validation and Structure Checking
Platon (Addsym, etc) CIF Validation Parst GEOM THMA 14c IDEAL SYMMOL WTANAL R-tensor Slide 106 Lachlan M. D. Cranswick

Platon’s Addsym (by Ton Spek) (finding missing symmetry): Structure Published in P1 - Triclinic: 42 non-H atoms Slide 107 Lachlan M. D. Cranswick

Platon’s Addsym: Correction Published in 1999: C2 - Monoclinic: 22 non-H atoms

Platon’s Addsym: Press of a button: 2000: FDD2 - Orthorhombic: 11 non-H atoms (Short Communication Abstract: "P1 or P-1? Corrigendum", Acta Cryst B56 (2000) 744 from Richard E. Marsh) Slide 109 Lachlan M. D. Cranswick

New triclinic refinement:
Platon’s Addsym - finding extra symmetry in inorganics and minerals - P1 triclinic starting structure. Unpublished Mineral Example - “tiny crystal” and “marginal data” Default Addsym gives C2/C Tighten the addsym values: calc ADDSYM SHELX addsym gives P 2/c and exact fit on Pc New triclinic refinement: Lower R factor in Shelx Addsym now finds P21/c in default mode Thus need to be careful! Slide 110 Lachlan M. D. Cranswick

Platon’s Addsym: for powders
Some powder based structures at the Royal Institution and Birkbeck College in London solved using EXPO Triclinic P 1 - found by Addsym to be P -1 Orthorhombic: P found by Addsym to be P n m a P found by Addsym to be P m m n Slide 111 Lachlan M. D. Cranswick

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 - 1st being: Powder Cell by Werner Kraus and Gert Nolze Slide 112 Lachlan M. D. Cranswick

Powder diffraction pattern calculation Poudrix for Windows
Powder Cell by Jean Laugier and Bernard Bochu Poudrix can handle anomalous dispersion at non X-ray tube wavelengths with the option of two models: Brenann and Cowan Sasaki Slide 113 Lachlan M. D. Cranswick

Photorealistic hardcopy output of structures
Many programs can do this. E.g, ORTEX (Images and Movie Animations): Just open up a Shelx format *.INS/*.RES file and go for it Slide 114 Lachlan M. D. Cranswick

Photorealistic hardcopy output of structures GUI WinORTEP / GUI Struplo / WinGX
Can open a wide variety of file formats including Shelx, CIF, GSAS, Fullprof, CDS, etc Slide 115 Lachlan M. D. Cranswick

Photorealistic hardcopy output of structures Balls and Sticks - Polyhedral, etc

Photorealistic hardcopy output of Fourier Maps Marching Cubes by Michal Husak ( Interlinks with WinGX, Crystals and can read Project XD files. Slide 117 Lachlan M. D. Cranswick

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: FreeBSD (can run linux binaries) refer: (be careful of hackers invading your systems when running Linux/UNIX. CCP14 tutorials try to be security conscious and leave no “open” services) Free Xtal Nexus CD-ROMs for academics and students (Supported & Sponsored by the IUCr and CCP14) Contact the author (Lachlan Cranswick) for a free air-mailed CD-ROM. Slide 118 Lachlan M. D. Cranswick

Summary http://www.ccp14.ac.uk E-mail: ccp14@dl.ac.uk
Large Genetic Diversity of Software is out there This diversity is necessary to help you get the job done. Getting better all the time (some areas faster than others) Most of it is freely available for Academics and Students Downloadable via the EPSRC funded CCP14 website: Slide 119 Lachlan M. D. Cranswick

An overview of available software for solving crystal structures from powder diffraction Lachlan M. D. Cranswick, CCP14 (Collaborative Computation Project.

Similar presentations

Presentation on theme: "An overview of available software for solving crystal structures from powder diffraction Lachlan M. D. Cranswick, CCP14 (Collaborative Computation Project."— Presentation transcript:

Similar presentations

About project

Feedback

Log in

Auth with social network:

An overview of available software for solving crystal structures from powder diffraction Lachlan M. D. Cranswick, CCP14 (Collaborative Computation Project.

Similar presentations

Presentation on theme: "An overview of available software for solving crystal structures from powder diffraction Lachlan M. D. Cranswick, CCP14 (Collaborative Computation Project."— Presentation transcript:

Similar presentations

About project

Feedback