Crunching problems into solutions: freely available crystallographic software for single crystal and powder diffraction. L. M. D. Cranswick, CCP14 (Collaborative

$Page 1: Crunching problems into solutions: freely available crystallographic software for single crystal and powder diffraction. L. M. D. Cranswick, CCP14 (Collaborative$
Crunching problems into solutions: freely available crystallographic software for single crystal and powder diffraction.

L. 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

Aims of the EPSRC funded CCP14 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.ccp14.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


Notes Free Zone - they are on the web

http://www.ccp14.ac.uk/poster-talks/thai_2002/

• Some areas of this talk may resemble a rather fast computer slide show; thus detailed notes are on the web for examination at your leisure (and given out during the talk)


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)


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


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 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.


Why bother knowing about a variety of modern software? (2 of 4)

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.

– When to use a scalpal

– When to unlock the sledgehammer cabinet

– When to declare that Defcon 1 has been activated!


Why bother knowing about freely available software? (4 of 4)

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)

Crystallographic Weaponry 102


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



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/annrep99/Report.html

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



Powder Methods for solving structures

• Nightmare to some

• An adventure to others



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



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 (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

• 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)


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


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.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

– Look out for the developing OpenXRD by Stefan Krumm (UNIX and Windows)


Phase Identification/Search Match for Powder Diffraction 2 of 3Identifying an organic – DL-Valine

33- 1954 DL-VALINE

File Name: c:\...\valine.cpi

Valine

2-Theta Angle (deg)10.00 20.00 30.00 40.00 50.00

1

Inte

nsity

(C

ount

s) X

100

000


Phase Identification/Search Match for Powder Diffraction 3 of 3Multiphase mixture: Flourite, Corundum, Zincite

35- 816 FLUORITE, SYN 46- 1212 CORUNDUM, SYN 36- 1451 ZINCITE, SYN

File Name: c:\...\cpd-1g.cpi

SampleIdent CPD RR S

2-Theta Angle (deg)30.00 40.00 50.00 60.00 70.00

Inte

nsity

(Cou

nts)

X 1

0000

0


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 (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/


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/


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://www2.ccc.uni-erlangen.de/software/corina/free_struct.html

– Then use Platon/System S acting as a friendly interface for Quest.


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 Sample Preparation and Data Collection

–Assumption is that you know about appropriate sample preparation and data collection

–However, many hardware vendors might not provide the required flexibility in data collection


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., Hill and Madsen method)

• On point detector (e.g., Bragg Bretano flat plate system), do this by varying the count time in a pre-defined manner

– (Can also provide more time effective counting time)

Fixed Count Time 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 Hill and Madsen method is at: http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/csirominerals-anon-ftp/pub/xtallography/variable-count-time/

(Original Hill and Madsen VCT (variable count time) Paper), I. C. Madsen and

R. J. Hill, Adv. X-ray Anal. (1992), 35, 39-47

W. I. F. David, Accuracy in Powder Diffraction, Abstract P2.6 NIST Special

Publication No. 846, Page 210, (1992) National Institute of Standards and Technology, Gaithersburg, MD, USA.


VCT for trace Phase ID (1 of x)

Fixed Count Time data (data collected by Jeremy Cockcroft)



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



Fixed Count Time data (zoomed)



Variable Count Time data (displayed as FCT)


Variable Count Time applications

Equally relevant to problems where you need to adequately profile fit small / trace peaks which might not be significantly above background in a “routine”, time effective fixed count time data collection - e.g.,;

– Powder Indexing– Unit Cell refinement– Quantitative Rietveld Analysis


VCT to aid in phase ID and profile fitting (1 of 3)

Fixed Count Time



Variable Count Time



Overlaying VCT and FCT


Where is VCT Data Collection?

Not a routine or available option in commercial XRD control software

Something to keep an eye on - or request from vendors.


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

•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 (indexing, unit cell refinement, size/strain, etc)

•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


Powder Indexing - a non trivial endeavour• 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 : 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 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


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


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 T3R3 human insulin-zinc complex produced by grinding", Acta Cryst. (2000). D56, 1549-1553.


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.


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

•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 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


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)Crystallite size and shape analysis

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

Reflection profile within WinGX


Single Crystal Absorption Correction : WinGX

Define and view single crystalfaces within WinGXBefore 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.


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:

– 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

• Summary of available software at:– http://www.ccp14.ac.uk/solution/twinning/

• 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 as described in following slides.

• 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

• 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


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


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


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

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(tetracycline hydrochloride) via WinGX as an interface


Sir direct methods and auto Fourier building(tetracycline hydrochloride) via WinGX as an interface


Dirdif Patterson methods and auto Fourier building(tetracycline hydrochloride) via WinGX as an interface


Crunch for UNIX direct methods and Fourier building(tetracycline hydrochloride) via Platon/System S as an interface


2D to 3D model building software

•Applicable for Generating 3D fragments for Patsee/Dirdif Orient – single crystal/powder

•Summary list at:

–http://www.ccp14.ac.uk/solution/2d_3d_model_builders/

•E.g., CORINA (COoRdINAtes) (Use web based direct submission):http://www2.ccc.uni-erlangen.de/software/corina/free_struct.html

Comes with a Java Molecule Editor for building up the 2D structure over the web which generates the required SMILES string from the drawn molecule. In this example a 2D tetracyline PDB file is generated: CN(C)C3C(O)=C(C(N)=O)C(O)C4(C)C(O)C2C(=O)c1c(O)cccc1C(C)(O)C2CC34

(Word of warning: the “energy minisation” may generate an inaccurate 3D model where different conformations are possible)


Getting fragments into Dirdif and Patsee for Windows

•One of the User Friendliest methods is to use is WinGX’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


Single Crystal Structure Refinement Software(Applicable to powder diffraction for helping build up the structure)

•Range of programs to choose from:

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

•CAOS (also inside Sir97)

•Crystals

•DS*SYSTEM/LSBF

•NRCVAX

•Shelxl–(Shelxl is within 3 freely available crystallographic suites)

–WinGX

–Platon/System S

–ORTEX

•Xtal (GPL’d)


Example of Crystals for Windows David Watkin, Richard Cooper, et al.: http://www.xtl.ox.ac.uk/

• Will focus on Guided refinement


Guided structure refinement using Crystals Import Shelx INS file of structure solved by DIRDIF

• Asymmetric unit is always in view


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


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)


Guided structure refinement using Crystals Have now refined atom positions anisotropically

• Atoms can be displayed anisotropically


Guided structure refinement using Crystals Automatic Hydrogen Addition

• Graphically compare calculated hydrogens (white) to possible hydrogens found in the difference map (pink).


Interrupt the Guided Refinement in CrystalsManual 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.


Interrupt the Guided Refinement in Crystals Manual Hydrogen Addition - 2 of 2

• A “Wizard” then guides the user to complete the hydrogen addition


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.


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.

BondlengthsRED="too long" and BLUE="too short".

RED ---- GREY ---- GREY ---- BLUE

3sigma 2sigma 1sigma 0sigma 1sigma 2sigma 3sigma


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



• Using the GUI (or scripts) make the offending Nitrogen a Carbon and re-refine.



• 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.



• CSD results now imply/infer that local geometry is consistent with what is already in the database.


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, 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 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.


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


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 high-resolution X-ray powder diffraction data: a variant of T3R3 human insulin-zinc complex produced by grinding", Acta Cryst. (2000).

D56, 1549-1553.

http://journals.iucr.org/d/issues/2000/12/00/issconts.html


Brian Toby’s EXPGUI Interface for GSAS

User friendlier to start using GSAS via EXPGUI(A new combined installer makes it very easy to start using GSAS.)

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


Rietveld: Rod Hill and Ian Madsen VCT data collection• Important to know how to

appropriate collect your data that is optimized for the analysis.

• For Rietveld: If you do have a choice of data collection strategies for XRD - consider variable count time (VCT)

• VCTCONV for DOS by Mark Bowden will convert VCT Hill and Madsen data into GSAS ESD format.

• VCT Fortran Source Code with references is available

http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/csirominerals-anon-ftp/pub/xtallography/


Restrained Rietveld structure refinement of organics

• Software not as powerful 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(also 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 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 XtalView


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 Refinement - Shelxl 97

• GUI control of Shelx via WinGX’s SXGRAPH program

• or Shelx ASCII INS File


WinGX for Windows single crystal suite Hydrogen Addition options

• Shelx97 (G. Sheldrick)– Manually edit INS file

– Via SXGRAPH GUI

• GUI XHYDEX (G Orphen)

• GUI CalcOH (M Nardelli)


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

• Squeeze/disordered solvent effects

• ADDSYM

• Other Platon Features


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 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


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/


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).

• Refer to non-Rietveld references cited in:

Following using Koalariet / XFIT(fundamental parameters)

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

http://www.ccp14.ac.uk/poster-talks/david-hay-quant-notes-axaa99/


MAUD for Java : GPL’d (you get the source code)

Tutorial on “Performing an x-ray quantitative analysis in seven easy steps!”:

http://www.ing.unitn.it/~luttero/maud/tutorial/

http://www.ccp14.ac.uk/ccp/web-mirrors/lutterotti/~luttero/maud/tutorial/


Quantitative Phase Analysis - is it routinely easy?

Based on the IUCr CPD Quant Round Robin(http://www.iucr.org/iucr-top/comm/cpd/QARR/)

The answer seems to be No!A quote from Armel Le Bail’s Tmacle “twinned refinement” manual seems appropriate:

http://sdpd.univ-lemans.fr/museum/tmacle92.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.......


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

Gretep by Jean Laugier and Bernard Bochuhttp://www.ccp14.ac.uk/tutorial/lmgp/#gretep


Graphically interacting with the structure (more examples)

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

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


Crystal Structure validation - Why Bother?

• Better to publish work that can stand the test of time

• Thus is very helpful doing a variety of validation and using a variety of programs!


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)


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): checking for extra symmetry : e.g., 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 - (1 of 2) finding extra symmetry in inorganics and minerals - P1 triclinic starting structure.

• Unpublished Mineral Example– 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• Loosening defaults:

– calc addsym shelx exact 1 .2 .4 .4

– P-31m


Platon’s Addsym - (2 of 2) finding extra symmetry in inorganics and minerals - P1 triclinic starting structure.

• Update new refinement in triclinic:– Lower R factor in Shelx

– Addsym now finds P21/c in default mode

• Thus need to be careful!


Platon’s Addsym - Be wary when using Addsym with Tilt Models

• With subtle tilts - (e.g., 0.3 A shifts)

• Increasing the Addsym defaults may give you the ideal non-tilt model


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 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 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 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 CCP14 website:

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

Documents

Crunching problems into solutions: freely available crystallographic software for single crystal and powder diffraction. L. M. D. Cranswick, CCP14 (Collaborative