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

$Page 1: An overview of available software for solving crystal structures from powder diffraction Lachlan M. D. Cranswick, CCP14 (Collaborative Computation Project$
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.

E-mail: [email protected]

WWW: http://www.ccp14.ac.uk

Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 2

Notes Free Zone - they are on the web

http://www.ccp14.ac.uk/poster-talks/agu_2002a/

• 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)


Talk Aims

• Give an overview of available software relevant to people doing crystallography on minerals and inorganics

• And minor ranting about other issues


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


Using the right crystallographic method can make the difference!Using Le Bail fitting / Rietveld Using Traditional UNIT CELL refinement Methods


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.


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.


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.


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)


Single Crystal vs Powder diffraction (1 of 8)

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



Cambridge Database (organics - organometallics)

• “During 1999, 17,898 new entries were added”

• (that Scale is in the 100’s of thousands)– 1999 report: http://www.ccdc.cam.ac.uk/about/annrep99/Report.html

– http://www.ccdc.cam.ac.uk/prods/csd/stats.html



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

ICSD entries by date of publication

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Cumulative ICSD entries by date of publication

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Powder Methods for solving structures• A nightmare to some

• An adventure to others!



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



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/sample2.html


Single Crystal vs Powder diffraction (7 of 8)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

– 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)


Single Crystal vs Powder diffraction (8 of 8)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


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


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.


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


VCT Literature References"Collection and analysis of powder diffraction data with near-constant

counting statistics", I. C. Madsen and R. J. Hill, J. Appl. Cryst. (1994). 27, 385-392 http://www.iucr.org/cgi-bin/paper?hz0014

Philips Friendly Fortran source code that does this Madsen and Hill method is at: http://www.ccp14.ac.uk/ccp/ccp14/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 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• http://www.ceramics.irl.cri.nz/Convert.htm


VCT for Powder Indexing (1 of 4)

Fixed Count Time data (data collected by Jeremy Cockcroft)



Variable Count Time data (normalized as FCT)(data collected by Jeremy Cockcroft)



Fixed Count Time data (zoomed)This peak position is not going to be very precise



Variable Count Time data (zoomed)This “trace” peak position will be more precise


VCT for Structure Solution and Refinement (1 of 4)

Variable Count Time data (as collected)



Variable Count Time data (normalised as FCT)



Variable Count Time data (normalised as FCT)



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.


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.ccp14.ac.uk/solution/search-match.htm

– Free Software:Brian Toby's "Portable Logic Program" (UNIX) and "MacDiff" for Apple Mac freeware by Rainer Petschick

– OpenXRD by Stefan Krumm in development (GPL’d UNIX and Windows)


Find out which software, databases and methods work the best: Search Match Round Robin (2nd May 2002 to 30th June 2002):

http://sdpd.univ-lemans.fr/smrr/ and CCP14 mirrors


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://cds3.dl.ac.uk/cds/cds.html

•ICSD (Minerals and Inorganics)– http://www.fiz-karlsruhe.de/

– Web accessible demonstration:

– http://barns.ill.fr/dif/icsd/

•MDF/CRYSTMET – (Metals and Alloys)

– http://www.tothcanada.com

•CCSD – (Organics and Organometallics)

– http://www.ccdc.cam.ac.uk/

•American Mineralogist – http://www.geo.arizona.edu/xtal-cgi/test/

•WWW Mincryst– http://database.iem.ac.ru/mincryst/

– 2398 unique phases - most with crystal structure data

•Mineral web – http://www.minweb.co.uk


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/


Powder Data Conversion / Importing Data

Initial problem in powder diffraction can be getting the data in the right format. For interconverting powder diffraction data: a variety of programs exist which in combination can pretty much get you from one format to another

Summary list of available software: http://www.ccp14.ac.uk/solution/powderdataconv/

Text Editors may occassionally be required: converting UNIX ACSII to DOS ASCII, getting rid of spaces or tabs , column editing:

Freeware PFE Editor for Windows:

http://www.lancs.ac.uk/people/cpaap/pfe/Freeware ConTEXT Editor for Windows (does column editing)

http://www.fixedsys.com/context/

Example of ConvX for Windows by Mark BowdenMass data powder diffraction data converter


Structure Importing, Conversion and TransformationSummary list of available software at: http://www.ccp14.ac.uk/solution/structconv/

Be careful to check the resultsBest program for the moment is the shareware Cryscon

http://www.shapesoftware.com

Other software such as GUI WinORTEP can import a wide variety of file formats and export these into Shelx format.

http://www.chem.gla.ac.uk/~louis/software/ortep3/

Example of Cryscon for Windows by Eric Dowty


Powder Diffraction Utility Software

•Examining Data, peak finding, background stripping, alpha-2 stripping

•Powder v 2.00: http://www.ccp14.ac.uk/tutorial/powder/

•Powder X, http://www.ccp14.ac.uk/tutorial/powderx/

•WinFIT, – http://www.geol.uni-erlangen.de/html/software/soft.html

•Winplotr, http://www-llb.cea.fr/winplotr/winplotr.htm

•XFIT, http://www.ccp14.ac.uk/tutorial/xfit-95/xfit.htm

•CMPR for Windows and UNIX:

– http://www.ncnr.nist.gov/programs/crystallography/

•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)


Peak Profiling for Powder indexing

•For Overall Summary of available peak profiling software refer to:

•http://www.ccp14.ac.uk/solution/peakprofiling/

•These include: CMPR, DRXWin, EFLECH, GPLSFT, pearson.xls, SHADOW, Powder v2.00, PowderX, Winfit, Winplotr, XFIT

Examples of XFIT for Windows


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:http://www.ccp14.ac.uk/tutorial/xfit-95/fun1.htm

•Available Fundamental Parameters Peak Profiling and Rietveld software:

•XFIT (no longer maintained)– http://www.ccp14.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


Powder Indexing FOM Results XFIT Fundamental Parameters peak profiling compared to

empirical Peak Fitting


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.ccp14.ac.uk/solution/indexing/• Powder Indexing: Autox, Ito, Dicvol, Treor, Taup/Powder, Lzon,

Losh, Kohl, Scanix, Xrayscan, EFLECH/Index, Supercell• Linking Suites: Crysfire, Powder v2.00, PowderX, PROSZKI,

WinPlotr, Chekcell• supercel is a specialise indexing program by Juan Rodriguez-

Carvajal for indexing Super Cell and Incommensurate cells. (available within Winplotr)

http://www-llb.cea.fr/winplotr/winplotr.htm

ftp://bali.saclay.cea.fr/pub/divers/fullprof.2k/


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.ccp14.ac.uk/tutorial/crys/

Example of CRYSFIRE Screen prompting the saving into one of 8 different indexing program formats:


Chekcell: Interpreting Crysfire Summary Files: Powder Indexing and Spacegroup Assignment

•Crysfire interlinks with Chekcell for Windows (part of the LMGP suite for Windows by Jean Laugier and Bernard Bochu). Chekcell provides a graphical interface for manually and automatically suggesting a best cell/spacegroup combination using both FOM and algorithms relating to parsimony of superfluous HKLs.

http://www.ccp14.ac.uk/tutorial/lmgp/


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.


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. 42-60 (1957)”

•Efficient Sub-cell and super-cell searching, then easy reviewing of newly derived cells within the Chekcell interface


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


Chekcell: Density / Z / Molecular Volume Explorer•Easily look at effects of Z, Density and molecular volume


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


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.


Some Alternatives to Crysfire: Winplotr, PowderX

Winplotr by Juan Rodriguez-Carvajal– http://www-llb.cea.fr/fullweb/powder.htm

PowderX by Cheng Dong– http://www.ccp14.ac.uk/tutorial/powderx/

Powder v2 by Nita Dragoe– http://www.ccp14.ac.uk/tutorial/powder/

CMPR for Windows and UNIX by Brian Toby

– http://www.ccp14.ac.uk/tutorial/cmpr/


Unit Cell Refinement (powders)

•For Overall Summary of available unit cell refinement software refer to:

http://www.ccp14.ac.uk/solution/unitcellrefine/

•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).


CELREF for Unit Cell Refinement

•by Jean Laugier and Bernard Bochu http://www.ccp14.ac.uk/tutorial/lmgp/

•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


Full Profile Fitting (Powder)

•For Overall Summary of available full profile analysis refer to:

Le Bail based: http://www.ccp14.ac.uk/solution/lebail/

Pawley Based: http://www.ccp14.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


Le Bail full profile fitting - Rietica Rietveld

•By Brett Hunter– http://www.rietica.org– http://www.ccp14.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


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


Unit Cell Refinement: Mass Le Bail fitting: multi-phase - overlapping patterns

Using Le Bail fitting Using Traditional Methods


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:• http://www.ccp14.ac.uk/solution/pole_figure/

– BEARTEX for Windows

– GSAS Rietveld (Windows/UNIX)

– MAUD for Java

– POFINT

– popLA

– Symmet for DOS

– TexturePlus for Windows

MAUD (for Java PC/Mac/UNIX)http://www.ing.unitn.it/~luttero/


Single Crystal Absorption Correction Options• Using WinGX 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:– Gaussian, Analytical, Spherica l, Cylindrical

• Semi Empirical:– Psi-scans, Camel-Jockey, Multiscan

• RefDelF:– Difabs, XABS2, Shelxa

CAD4 Reflection profile within WinGX


Platon options for absorption correction• Platon by Ton Spek:

– http://www.cryst.chem.uu.nl/platon/• DELrefABS

• ABSPsiScan

• ABSTompa

• ABSGauss

• ABSXtal

• ABSSphere

• MULscanABS

• Links to FaceLift - program to refine the initial crystal description (HABITUS style approach)

XTALHabit within Platon


Single Crystal Indexing / Twinning• Twinning: http://www.ccp14.ac.uk/solution/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:

• http://www.doe-mbi.ucla.edu/Services/Twinning/

– TWIN3.0 for Windows (test for merohedry): • Contact V. Kahlenberg ([email protected])

Spacegroup Assignment:– ABSEN Single Crystal Program by Patrick McArdle (comes with the ORTEX and

WinGX 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 Single Crystal Twinning Software

• New ROTAX style: (Determine Twin Matrix from Fo/Fc Data)

– Platon incorporates LePageTwin• http://www.cryst.chem.uu.nl/platon/

– WinGX and Crystals suites link seamlessly into ROTAX (by Simon Parsons and Bob Gould)

• http://www.ccp14.ac.uk/ccp/web-mirrors/rotax/

• http://www.xtl.ox.ac.uk/

• http://www.chem.gla.ac.uk/~louis/software/


“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

– 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/10mn/

– FOX: http://objcryst.sourceforge.net/


“Specialised and Commercial” Structure Solution Programs

• PSSP – molecular structures – http://powder.physics.sunysb.edu/programPSSP/pssp.html

• ZEFSA II – for Zeolites (GPL’d)

– http://www.mwdeem.chemeng.ucla.edu/zefsaII/

• 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 (WinCSD/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/


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)


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)


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

http://objcryst.sourceforge.net/


Adding polyhedra in Fox - 1 of 5

Click on “Crystals”, “Scatterers” Icon, “Add”



Select the central atom



Select the corner atom(s)



Give the Bond length



Done!


Single Crystal Structure Solution

•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–Direct Methods and automatic structure building

•Solver – in NRCVAX Suite – based on Multan–Direct Methods

Also can be applied to powder problems - is a range of programs to choose from:http://www.ccp14.ac.uk/solution/xtalsolution/


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?)


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)


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)


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:

–http://www.ccp14.ac.uk/solution/xtalrefine/

•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)


Single Crystal Structure Refinement SoftwareJANA Single Crystal and Powder Diffraction Refinement

–Developed for handling inorganics / metals - commensurate and incommensurate

–by Vaclav Petricek and Michal Dusek

–http://www-xray.fzu.cz/jana/jana.html

–Single crystal and powder diffraction (not Neutron Time of Flight (TOF))

–Powder tutorial at: http://www-xray.fzu.cz/jana/Jana2000/powders.html

–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


Structure Refinement using Powder Diffraction Data(Rietveld Refinement)

• Large range of programs to choose from:

– http://www.ccp14.ac.uk/mirror/mirror.htm

• 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


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.


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


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)– http://www.ccp14.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


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.)

http://www.ncnr.nist.gov/programs/crystallography/software/expgui/expgui_intro.html


Restrained Rietveld structure refinement of organics

• Software not as routine as single crystal but there are some tutorials with tricks on the CCP14 website

http://www.ccp14.ac.uk/solution/restrained_rietveld/


Fourier capability in Rietveld Software

GSAS (including VRML output)

Summary list of Fourier friendly Rietveld software at: http://www.ccp14.ac.uk/solution/rietveld_fourier_maps/

Fullprof /

GFOUR for Windows


Single Crystal Suites(applicable to powder diffraction)

• Again, a large range of programs to choose from:

– http://www.ccp14.ac.uk/solution/xtalsuites/

• 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


WinGX for Windows single crystal suiteLouis 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


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


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


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


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


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


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


WinGX for Windows single crystal suite Easy Interlinking with Ton Spek’s Platon

• ADDSYM

• Other Platon Features


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


WinGX for Windows single crystal suite Validation and Structure Checking

• Platon (Addsym, etc)

• CIF Validation

• Parst

• GEOM

• THMA 14c

• IDEAL

• SYMMOL

• WTANAL

• R-tensor


Graphically interacting with the structure

• Number of programs available with list available at:http://www.ccp14.ac.uk/solution/structuredrawing/

• 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


Graphically interacting with the structure (and the ability to open GSAS, Rietica and Fullprof files)

GUI WinORTEP (http://www.chem.gla.ac.uk/~louis/software/ortep3/)

GUI WinSTRUPLO (http://www.chem.gla.ac.uk/~louis/software/struplo/)


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.ccp14.ac.uk/solution/anharmonic/

• Incommensurate Structure Refinement


– http://www.ccp14.ac.uk/solution/incomm.htm

• PDF / High Q Analysis


– http://www.ccp14.ac.uk/solution/high_q_pdf/


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!


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


WinGX for Windows single crystal suite Validation and Structure Checking

• Platon (Addsym, etc)

• CIF Validation

• Parst

• GEOM

• THMA 14c

• IDEAL

• SYMMOL

• WTANAL

• R-tensor


Platon’s Addsym (by Ton Spek) (finding missing symmetry): Structure Published in 1997

P1 - Triclinic: 42 non-H atoms


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)


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 1 0.2 0.4 0.2

– 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!


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 21 21 21 - found by Addsym to be P n m a– P 2 21 21 - found by Addsym to be P m m n


Powder diffraction pattern calculationPowder 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

http://www.ccp14.ac.uk/tutorial/powdcell/


Powder diffraction pattern calculationPoudrix for Windows

• Powder Cell by Jean Laugier and Bernard Bochu

http://www.ccp14.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


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


Photorealistic hardcopy output of structuresGUI WinORTEP / GUI Struplo / WinGX

http://www.ccp14.ac.uk/tutorial/wingx/

• Can open a wide variety of file formats including Shelx, CIF, GSAS, Fullprof, CDS, etc


Photorealistic hardcopy output of structuresBalls and Sticks - Polyhedral, etc

• http://www.toycrate.org/


Photorealistic hardcopy output of Fourier MapsMarching Cubes by Michal Husak

(http://www.ccp14.ac.uk/tutorial/marchingcube/)

• Interlinks with WinGX, Crystals and can read Project XD files.


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.ccp14.ac.uk/solution/linux/

• FreeBSD (can run linux binaries)– refer: http://www.ccp14.ac.uk/solution/bsdunix/

• (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

• http://www.unige.ch/crystal/stxnews/nexus/index.htm

• (Supported & Sponsored by the IUCr and CCP14)

• Contact the author (Lachlan Cranswick) for a freeair-mailed CD-ROM.


Summary

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:

http://www.ccp14.ac.ukE-mail: [email protected]

Documents

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