7

Workshop Powder Diffraction Structure Determination and Refinement from Powder Diffraction Data

University of Bayreuth, Laboratory of Crystallography, Germany

(11.00am, Saturday, October 7, 2000)

 

 

Freely Available Software tools to aid in Structure Solution from Powder Diffraction

Lachlan M.D. Cranswick

Collaborative Computational Project No 14 (CCP14) for Single Crystal and Powder Diffraction

Daresbury Laboratory, Warrington, WA4 4AD U.K

E-mail: L.Cranswick@dl.ac.uk

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

 

 

Freely Available Software tools to aid in Structure Solution from Powder Diffraction

Notes on the Web

Lachlan M.D. Cranswick (L.Cranswick@dl.ac.uk)

CCP14 Project for Single Crystal and Powder Diffraction

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

 

 

 

 

 

Hand Written Note Free Zone!!!!

Put down those pens!!

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:

http://www.ccp14.ac.uk/poster-talks/powd2000/

Link Via:

http://www.ccp14.ac.uk

 

Single Crystal Methods

(Mass tourism structure solution)

Some Possible Problems:

Crystal not representative of the bulk material

Twinning

Crystal explodes during take-off/data collection

Structure Validation

 

Cambridge Database Stats:

( http://www.ccdc.cam.ac.uk/about/annrep99/Report.html )

"During 1999, 17,898 new entries were added"

(that Scale is in the 100’s of thousands)

MicroCrystal Beamline 9.8 at Daresbury Lab.

(managed by Simon Teat: http://srs.dl.ac.uk/xrd/9.8/)

(is your powder really just a collection of small crystals?)

82 publications in 3.5 years (35 publications in 1999)

Estimated 1,000 to 1,500 structures solved in that 3.5 years on 9.8 (30 minutes to 12 hours per data collection).

 

Powder Methods

(a nightmare to some? – an Adventure to Others!)

Powder Solving Stats:

( http://sdpd.univ-lemans.fr/iniref.html )

Powder: "During 1999: 55 publications"

( http://sdpd.univ-lemans.fr/iniref/a1999.html )

(a cumulative scale would be in the 100’s)

 

(Cambridge: "During 1999: 17,898 new entries")

 

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

http://www.stoe.com/products/

http://imr.chem.binghamton.edu/zavalij/CSD.html

Druid/Mystic (now called Dash)

http://www.esrf.fr/info/science/highlights/1999/chemistry/powder.html

(solved by Armel Le Bail)

http://sdpd.univ-lemans.fr/SDPDRR/sample2.html

 

Structure Determination from Powder Diffractometry Round Robin

Single Crystal Data?

(a powder can be a collection of small crystals)

10x20x30 micron crystal (Clegg and Teat).

http://srs.dl.ac.uk/xrd/9.8/

"Routine" structure solution within the hour (before all the data was collected)

Bruker Smart CCD: BL 9.8, Daresbury:

 

Implies that in practise Solving Structures from Powder Diffraction Data is Still an Adventure compared to single crystal methods!

 

 

 

Freely Available Software tools to aid in Structure Solution from Powder Diffraction

CCP14 Sponsored Back-Packer Tours for Structure Solution

Lachlan M.D. Cranswick (L.Cranswick@dl.ac.uk)

CCP14 Project for Single Crystal and Powder Diffraction

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

Normally much nicer if you have a single crystal

(if that is not practical)

Powders are doable:

This talk will now concentrate on the freely available software you can obtain.

 

General Methodology for Solving Structures from Powder Diffraction Data

(many attempted structure solutions can fail here)

(possible multiple cells and spacegroups)

Organics: Restraints

Organics: Hydrogen placement

 

Has the structure been found already?

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

Known exceptions being:

Brian Toby's "Portable Logic Program" (UNIX)

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

"MacDiff" for Apple Mac freeware by Rainer Petschick

http://www.geol.uni-erlangen.de/macsoftware/macdiff/

 

Has the structure been solved already?

Crystallographic Structure Databases

ICSD (Inorganics)

http://www.fiz-karlsruhe.de/icsd_.html

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 many types of databases to use the web due to the convenience and effectiveness. Also has advantage of being operating system independent.

 

http://barns.ill.fr/dif/icsd/

 

A hopeful new trend - Crystallography Suites that link directly into structure databases:

(Platon/System S and Crystals linking into the Cambridge Database)

Platon/System S as a user-friendly interface into CSD Quest

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

Platon: http://www.crystal.chem.uu.nl/software.html

CSD Cell searching via a point and click interface in Platon

 

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 vareity of programs exist which in combination can pretty much get you from one format to another.

Use of a text editor and spreadsheet may be occassionally required.

A very good text editor is the freeware PFE Editor for Windows:

http://www.lancs.ac.uk/people/cpaap/pfe/

Refer: Data Conversion/Importing data/structures

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

These Include: ConvX, Powder v2.00, Powder X, Winfit

Example of the ConvX for Windows : mass conversion of powder diffraction data (http://www.ceramics.irl.cri.nz/Convert.htm):

 

 

Structure Importing, Conversion and Transformation

Summary List at:

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

Be careful with these and check the results.

Best program at the moment is the shareware program CRYSCON

http://www.shapesoftware.com

 

Other software such as Ortep-3 can import a wide variety of formats and output these as Shelx files.

 

Powder Diffraction Utility Software

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

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

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

Alpha2 Strip, Background Strip, Peak Find

 

Peak Finding/Peak Profiling

 

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

Example of XFIT for Windows (this can also perform fundamental parameters peak profiling for high accuracy peak positions from laboratory diffractometer data). This can be the difference between a convincing and unconvincing powder indexing from laboratory X-ray data.

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

E.g., 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

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:

 

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 has gone through the ~4000 solutions generated by Crysfire and recommended that a lower FOM (76.6) Rhombohedral (R3, R-3, R32, R-3M) cell is the best solution as found by Dicvol within Crysfire. (this is an Inorganic Structure)

NOTE: IT IS A GRAPHICAL and CONTROLLED BY A GUI!

Takes much of the drudge work out of evaluating possible solutions

Crysfire/Chekcell: Framework Structure

Unsolvable Cell! (defined as "Treor does not solve it")

10 Minutes work for Crysfire and Chekcell to give cell and spacegroup!

ITO Solves it in this case:1 impurity peak

Unexpected Cell and Spacegroup

(though visually very compelling)

Validated after the event from a single crystal

 

Crysfire/Chekcell: Organometallic

Structure cannot fit into found monoclinic Cell!

(near identical to monoclinic/rhombohedral problem of first example)

~45 Minutes work for Crysfire and Chekcell!

No "indexing" program finds the "best" cell:

Chekcell’s TrueCell option finds what turns out to be a slightly better FOM Rhombohedral cell by looking for higher symmetry higher volume cells based on best FOM hit)

(Truecell is a way of getting out the problem of indexing programs favouring low volume low symmetry solutions)

 

Crysfire/Chekcell for Indexing and Spacegroup Assignment

High Presssure "Angular Dispersive" Data

Kohl within Crysfire is the program that works

Structure Solved using Powder Cell menu driven Structure Transformation options

-------------------------------------------------

Very Low Resolution High Presssure

"Energy Dispersive" Data

(1.5 weeks due to care in finding the best data files)

1 impurity peak on the best data files

 

Manual Single Crystal Indexing/Spacegroup Assignment

Brian Toby’s CMPR Suite (UNIX and Windows)

(slide bars to dynamically change the cell – select spacegroup or operators)

(supercell/sub cell relationships)

http://www.ncnr.nist.gov/programs/crystallography/software/cmpr/

 

Single Crystal Spacegroup Assignment

(can be applicable to powder diffraction)

Platon by Ton Spek (UNIX and Windows).

http://www.cryst.chem.uu.nl/platon/

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/

Unit Cell Refinement (Powders)

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

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

This include:

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.

Example of Celref for Windows by Jean Laugier and Bernard Bochu performing Graphical Unit Cell refinement on calcite in a multi-phase mixture (http://www.ccp14.ac.uk/tutorial/lmgp/)

 

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. Is useful for:

Spacegroup Assignment

Unit Cell Refinement (when overlap is a problem)

Extracting Intensities for Structure Solution

Following is an example of using Fullprof Rietveld with the Winplotr for Windows program:

 

 

Materials Analysis Rietveld/Texture Software

Pole Figure, Texture Analysis – important for some forms of Le Bail fitting and structure solution from powders

BEARTEX for Windows

Rudy Wenk - wenk@seismo.berkeley.edu

Texture, Pole figure, Calculates Orientation Distribution

http://www.seismo.berkeley.edu/~wenk/beartex.htm

http://www.ccp14.ac.uk/ccp/web-mirrors/beartex/~wenk/beartex.htm

GSAS for UNIX and PC

Bob Von Dreele - vondreele@lanl.gov

Menu driven interface with large vareity of functionality including Fourier map generation and viewing, ORTEP, Texture Analysis

ftp://ftp.lanl.gov/public/gsas/

http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/gsas/public/gsas/

EXP Tcl/Tk GUI - new GUI replacement of expedit being developed by Brain Toby:

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

http://www.ccp14.ac.uk/ccp/web-mirrors/briantoby/programs/crystallography/

MAUD for Java

Luca Lutterotti - Luca.Lutterotti@ing.unitn.it

Sequel to Rietquan and all menu driven; concentrating on size/strain/stress analysis

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

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

ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/web-mirrors/lutterotti/~luttero/index.html

POFINT

Daniel Chateigner - daniel.chateigner@univ-lemans.fr

Pole Figure Interpretation and Corrections

http://pecdc.univ-lemans.fr/pofint/pofint.htm

http://www.ccp14.ac.uk/ccp/web-mirrors/pofint/pofint/pofint.htm

popLA

John Bingert - bingert@lanl.gov

Texture Analysis and Modeling.

http://www.mst.lanl.gov/cms/poplalapp.html

http://www.ccp14.ac.uk/ccp/web-mirrors/popla/cms/poplalapp.html

Symmet

John Root

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

 

Materials Analysis Rietveld

MAUD (for Java PC/Mac/UNIX)

Crystallite size and shape

Pole figure/Refinement wizard

 

"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

http://www.ba.cnr.it/IRMEC/SirWare_main.html

http://www.ccp14.ac.uk/ccp/web-mirrors/sirware/IRMEC/SirWare_main.html

 

If EXPO fails, used Le Bail or Pawley extracted data with Single Crystal Structure Solution Software as described below.

 

 

ESPOIR (GPL’d by Armel Le bail) Monte Carlo and pseudo simulated annealing - normally use as last resort (new version for Windows has "real space molecule and fragment location").

http://www.cristal.org/sdpd/espoir/

http://www.ccp14.ac.uk/ccp/web-mirrors/armel/sdpd/espoir/

 

"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:

(Tend to have optimised algorithms and interfaces not easily available in freely obtained programs)

Cerius 2 by Molecular Simulations

http://www.msi.com/life/products/cerius2/

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/dash/bayreuth/

DIFFRACplus TOPAS

http://www.bruker-axs.com/production/products/xrd/software/topas/

Endeavour Structure Solution from Powder Diffraction Software

http://www.crystalimpact.com/endeavour/

 

EXPO :

Direct Methods Structure Solution from Powder Data (or extracted intensities)

Initially Run with an ASCII Input File

Then Controlled by the GUI Menu

Starting Information:

%struct cime

%job cimetidine -- Synchrotron data

%init

%data

range 8.01 84.99 0.01

pattern cime.pow

cont s 4 c 40 n 24 h 64

wave 1.52904

cell 10.6986 18.8181 6.8246 90.000 111.284 90.000

space p 21/n

sync

double

%extraction

%continue

Select the Control File and Start the Solution:

 

 

Profile Fitting/ Le Bail Extraction:

Starting the Direct Methods (at this point looks very similar to Sir 97):

 

 

Fourier Cycling:

Presenting the Final Result for Evaluation (along side the idealised connectivity from the ICDD database):

 

 

 

 

 

 

 

 

 

If EXPO seems to solve the structure but looses it on the auto-building (possibly indicating a data quality problem) there are a few things that can be tried:

Lower the upper limit of the powder diffraction data

RECYCLE n (placed under FOURIER, n= cycle number)

 

Single Crystal Structure Solution

(Applicable to extracted Powder Data)

 

CAOS (also inside part of Sir97) – Ricardo Spagna, et. al.

Comes with an automatic Patterson Solution Option.

http://www.mlib.cnr.it/isc/caos/

http://www.ccp14.ac.uk/ccp/web-mirrors/caos/isc/caos/

Crisp – Part of the GPL’d Xtal Suite

Direct Methods

http://xtal.crystal.uwa.edu.au/

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

Crunch – R. de Gelder, R.A.G. de Graaff & H. Schenk,

Direct Methods and automatic structure building

http://www-xtal.sci.kun.nl/xtal/documents/software/crunch.html

http://www.ccp14.ac.uk/ccp/web-mirrors/dirdif/xtal/documents/software/crunch.htmL

Dirdif - P.T. Beurskens, G. Beurskens, R. de Gelder, et al.

Patterson Methods for heavy atoms and fragments and automatic structure building

http://www-xtal.sci.kun.nl/xtal/documents/software/dirdif.html

http://www.ccp14.ac.uk/ccp/web-mirrors/dirdif/xtal/documents/software/dirdif.html

Windows: http://www.chem.gla.ac.uk/~louis/dirdif/

http://www.ccp14.ac.uk/ccp/web-mirrors/farrugia/~louis/dirdif/

Patsee – E. Egert and G. Sheldrick

Fragment Search

http://www.org.chemie.uni-frankfurt.de/egert/html/patsee.html

http://www.ccp14.ac.uk/ccp/web-mirrors/patsee/egert/html/patsee.html

 

 

Single Crystal Structure Solution (cont’d)

 

Shake’n’Bake (SnB) – Weeks, Miller, et al.

Dual-space direct methods. (Linux, SGI, IBM AIX, Alpha executables via web)

http://www.hwi.buffalo.edu/SnB/

http://www.ccp14.ac.uk/ccp/web-mirrors/snb/SnB/index.html

ShakePSD/DS*SYSTEM – Kenji Okada

Windows based direct methods for large structures up to 500 atoms

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

Shelxs 86/97/d- George Sheldrick

Direct Methods and Patterson Option

http://shelx.uni-ac.gwdg.de/SHELX/index.html

(SHELXD – for large structures. Beta versions are available from shelx ftp site )

Sir92/97/2000 – Sirware Group: Cascarano, Giacovazzo el al

Direct Methods and automatic structure building

http://www.ba.cnr.it/IRMEC/SirWare_main.html

http://www.ccp14.ac.uk/ccp/web-mirrors/sirware/IRMEC/SirWare_main.html

Solver – in NRCVAX Suite – based on Multan

Direct Methods

Peter White (pwhite@pyrite.chem.unc.edu)

XFPA – Frantisek Pavelcik

Patterson Methods and automatic structure building

E-mail: pavelcik@fns.uniba.sk

 

Using Single Crystal Structure Solution Software on HKL files extracted from Powder Diffraction Data:

May have to play with the data : sequentially elliminating excessively reflections using software such as Armel Le Bail’s "overlap":

http://sdpd.univ-lemans.fr/ftp/overlap.zip

http://www.cristal.org/ ftp/overlap.zip

http://www.ccp14.ac.uk/ccp/web-mirrors/armel/ftp/overlap.zip

May require Imagination

May require Tenacity

And that "Spirit of Adventure"

 

 

Different structures (even if supposedly similar or of related complexity) may require different "tricks" to solve.

 

 

Comparing single crystal structure solution programs on powder derived data and single crystal data for tetracycline:

 

Solving powder structures using single crystal software.

This is potentially where adventures in structure solution from powders can go into that grey transition area of becoming nightmares.

 

 

 

Shelxs97 direct methods:

http://shelx.uni-ac.gwdg.de/SHELX/index.html

Single Crystal Data: Tetracycline

Solved ready for building up:

Powder Diffraction Data: Tetracycline

 

Sir97 direct methods:

http://www.ba.cnr.it/IRMEC/SirWare_main.html

http://www.ccp14.ac.uk/ccp/web-mirrors/sirware/IRMEC/SirWare_main.html

Single Crystal Data: Tetracycline

Solved and auto-built to near completion:

Powder Diffraction Data: Tetracycline

 

Dirdif (Patterson and fragment searching).

(Program of choice for heavy atom problems)

http://www-xtal.sci.kun.nl/xtal/documents/software/dirdif.html

http://www.ccp14.ac.uk/ccp/web-mirrors/dirdif/xtal/documents/software/dirdif.html

Single Crystal Data: Tetracycline

Solved and non-H atoms auto-built to completion:

Powder Diffraction Data: Tetracycline

 

2D-3D Model Building Software

(Applicable for Generating 3D fragments for Patsee/Dirdif Orient – Patterson methods)

Refer:

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 the following 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/Dirdif for Windows.

One of the User Friendliest methods is to use is WinGX’s "SXGRAPH" GUI Shelx INS/RES file Editor

(includes ability to manipulate structures for Dirdif fragment searching)

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)

(In the following case, Tetracycline)

Every attempted Structure Solution from Powder Diffraction Data can be a different Adventure requiring different techniques and pathways to succeed.

From the Personal Travel Log

(peripheral involvement in most of the following)

Inorganic: Lithium Titanate:

Peaks profiled with Philips PC-APD; Cell with treor; spacegroup from International Tables; manually extracted intensity with Philips PC-APD; solved with manual interpretation of Patterson Map from Shelx 76; building the structure with Shelxl93; Rietveld refinement with X-ray and Neutron data to obtain Li positions.

An Organic:

Cell/Spacegroup in Crysfire/Chekcell. Solved in default EXPO

 

 

Inorganic Intergrowth structure:

(Poorly Crystalline, multi-phase and Massive Peak-anisotropy)

Cell and spacegroup from TEM Electron Diffraction, Structure from 3.5 years of part time model building with bits of paper and comparing with direct space TEM and powder diffraction simulations.

Framework Structure

Routine indexing but 4 possible spacegroups. Peak anisotropy so Le Bail fitting in LHPM-Rietica; Solved in EXPO by breaking the recycling at the right moment. Refinement and location of template in GSAS using Fourier Options.

High Pressure Phase Transition:

Cell by Kohl/Crysfire. Solved by using powder cell’s phase transition option.

Alloy at High Pressure

Possible Orthorhombic Cell. Energy minimisation and simulated annearling in P1 using Bruker Topas and finding the correct spacegroup using Platon’s Addsym (monoclinic)

Organic Pharmaceutical:

Unconvincing Cells. Data diffracts down to poor resolution.

Eventual solution was for chemist to conclude they could probably get single crystals if they changed their experimental conditions.

Potential Road-Kill

(literature can give a very false impression as only successfully solved structures are published)

At least half dozen non-solved structures still on the Adventure highway.

 

Single Crystal Structure Refinement

(because of present capabilities of Rietveld software: can also be very useful for "building up structures; visualising the structure, helping out with generating restraints; hydrogen placement, etc)

CAOS (freestanding and also available inside Sir97)

http://www.isc.mlib.cnr.it/caos/

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

http://www.ba.cnr.it/IRMEC/SirWare_main.html

http://www.ccp14.ac.uk/ccp/web-mirrors/sirware/IRMEC/SirWare_main.html

Crystals

http://www.xtl.ox.ac.uk/

http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/crystals/pub/crystals/

NRCVAX

Contact: pwhite@pyrite.chem.unc.edu

Shelxl (refinement program for System S/ORTEX/WinGX)

http://shelx.uni-ac.gwdg.de/SHELX/index.html

The following freely available single crystal suites are based around Shelx for Refinement:

Platon/System S http://www.cryst.chem.uu.nl/platon/

ORTEX http://www.nuigalway.ie/cryst/software.htm

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

Xtal (GPL’d)

http://xtal.crystal.uwa.edu.au/

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

 

 

Single Crystal Structure Refinement:

Example of Sir97/CAOS:

By default, CAOS is used via a powerful scripting language. Is inside Sir97 (point and click mode) - thus the following screen dumps are from Sir97

Adding Hydrogens

Automatic Addition of Carbon and Nitrogen bonded hydrogens at the click of a button:

 

Single Crystal Structure Refinement:

GUI CRYSTALS for Windows:

Adding Hydrogens

 

Single Crystal Structure Refinement:

Controlling a Shelx refinement via WINGX using the SXGRAPH GUI for Windows:

Adding Hydrogens

Single Crystal Structure Refinement:

CRYSTALS for Windows:

Creating and Refining Rigid Bodies

(all done in Crystallographic space)

(The "Crystals" code has been redone in "CAOS"(?))

The following is peformed using the Crystals script interface. (The new version will be full GUI based as well as traditional scripts)

Convert 5 atoms into a regularized 5 membered ring

#regu replace

group 5 {name or point and click on atoms}

cp_ring <defines and regularized the rigid body>

end

Refine selected atoms as a rigid body.

#list 12

group {name or point and click on atoms}

end

ALL DONE. HERE ENDETH the LESSON!

 

Structure Refinement using Powder Diffraction Data

(Rietveld Refinement)

Large range of programs to choose from:

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

Freely Available Rietveld Software

(Contact Names are provided)

ARITVE

Armel Le Bail - armel@fluo.univ-lemans.fr

Refinement of Glasses, ASCII Control file

http://fluo.univ-lemans.fr:8001/aritve.html

http://www.cristal.org/aritve.html

http://www.ccp14.ac.uk/ccp/web-mirrors/armel/aritve.html

ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/web-mirrors/armel/aritve.html

BGMN

Joerg Bergmann - support@bgmn.de

Fundamental Parameters Rietveld

http://www.bgmn.de

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

ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/web-mirrors/bgmn/index.html

DBWS

Ray Young - r.young@physics.gatech.edu

DBWS Style Control File, Includes a DB2dI program for converting a Rietveld output into an appropriate D/I format suitable for submission to the ICDD.

Contact the author on the above E-mail address.

DEBVIN

Sergio Bruckner - sergio.bruckner@dstc.uniud.it

Rietveld refinement with generalized coordinates subjected to geometrical restraints. Applications in refinement of polymers.

ftp://ftp.cc.uniud.it/DEBVIN/

http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/debvin/DEBVIN/

ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/ccp14/ftp-mirror/debvin/DEBVIN/

EXPO

Sirware Group - cryst@area.ba.cnr.it

While mainly for Structure Solution, also has menu driven Rietveld.

http://www.ba.cnr.it/IRMEC/SirWare_main.html

http://www.ccp14.ac.uk/ccp/web-mirrors/sirware/IRMEC/SirWare_main.html

 

Fullprof for UNIX and PC

Juan Rodriguez-Carvajal - juan@bali.saclay.cea.fr

DBWS Style ASCII Control file with large variety of functionality.

ftp://charybde.saclay.cea.fr/pub/divers/

http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/fullprof/pub/divers/

ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/ccp14/ftp-mirror/fullprof/pub/divers/

WinPlotr Graphics link into Fullprof with enhanced functionality:

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

http://www.ccp14.ac.uk/ccp/web-mirrors/plotr/winplotr/winplotr.htm

GSAS for UNIX and PC

Bob Von Dreele - vondreele@lanl.gov

Menu driven interface with large vareity of functionality including Fourier map generation and viewing, ORTEP, Texture Analysis

ftp://ftp.lanl.gov/public/gsas/

http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/gsas/public/gsas/

EXP Tcl/Tk GUI - new GUI replacement of expedit being developed by Brain Toby:

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

http://www.ccp14.ac.uk/ccp/web-mirrors/briantoby/programs/crystallography/software/expgui/expgui_intro.html

Koalariet

Alan Coelho - CCP14 Contact - L. Cranswick (l.cranswick@dl.ac.uk)

Fundamental Parameters Rietveld - sequel is called "TOPAS" by Bruker

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

LHPM/Rietica for Win95/NT

Brett Hunter - bah@ansto.gov.au

Full GUI and/or DBWS ASCII file driven, Fourier Maps, I.D. Brown bond-valence analysis.

ftp://ftp.ansto.gov.au/pub/physics/neutron/rietveld/Rietica_LHPM95/

http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/ansto/pub/physics/neutron/rietveld/Rietica_LHPM95/

MAUD for Java

Luca Lutterotti - Luca.Lutterotti@ing.unitn.it

Sequel to Rietquan and all menu driven; concentrating on size/strain/stress analysis

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

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

ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/web-mirrors/lutterotti/~luttero/index.html

PREMOS/REMOS

Akiji Yamamoto - yamamoto@nirim.go.jp

Modulated Structure Refinement

http://www.nirim.go.jp/~yamamoto/

http://www.ccp14.ac.uk/ccp/web-mirrors/remos/~yamamoto/

ProDD

Jon Wright - jpw22@cam.ac.uk

Based on the CCSL profile refinement routines

http://www.cus.cam.ac.uk/~jpw22/

Profil

Jeremy Cockcroft - cockroft@gordon.cryst.bbk.ac.uk

Part of the PDPL Powder Diffraction Suite

ftp://img.cryst.bbk.ac.uk/pdpl/

http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/profil/PDPL/

 

Riet7/SR5

Ian Madsen - ian.madsen@minerals.csiro.au

DBWS Style Control File, Variable Count Time Data

ftp://ftp.minerals.csiro.au/pub/xtallography/

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

RIETAN-2000 (GPL’d)

Fujio Izumi - izumi@nirim.go.jp

Whole-pattern fitting based on the maximum-entropy method (MEM)

http://www.nirim.go.jp/~izumi/rietan/angle_dispersive/angle_dispersive.html

http://www.ccp14.ac.uk/ccp/web-mirrors/rietan/~izumi/rietan/angle_dispersive/angle_dispersive.html

ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/web-mirrors/rietan/~izumi/rietan/angle_dispersive/angle_dispersive.html

Rietquan for Windows

Luca Lutterotti - Luca.Lutterotti@ing.unitn.it

Menu driven; concentrating on size/strain/stress analysis. Superceded by MAUD for Java.

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

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

ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/web-mirrors/lutterotti/~luttero/index.html

Simref

Harold Ritter - harald.ritter@uni-tuebingen.de

Simultaneous Rietveld Refinement with Multible Powder Datasets High temperature experiment; Incommensurate structure refinement

Simpro Pawley software and MEED Maximum entropy also available.

http://www.uni-tuebingen.de/uni/pki/

http://www.ccp14.ac.uk/ccp/web-mirrors/pki/uni/pki/index.html

ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/web-mirrors/pki/uni/pki/index.html

WinMprof for Windows

Alain Jouanneaux - jouanneaux@univ-lemans.fr

Le Bail fitting. Has in built Fourier Q peak finding for building up structures.

http://pecdc.univ-lemans.fr/WinMProf/WinMProf.htm

http://www.ccp14.ac.uk/ccp/web-mirrors/winmprof/WinMProf/WinMProf.htm/

ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/web-mirrors/winmprof/WinMProf/WinMProf.htm

XND

Jean-Francois Berar - berar@polycnrs-gre.fr

Simultaneous Rietveld Refinement with Multible Powder Datasets High temperature experiment; Incommensurate structure refinement, Can handle "parasitic emission lines" such as CukB, Tungsten

http://RX-Crg1.polycnrs-gre.fr/public/xnd/xnd.html

ftp://labs.polycnrs-gre.fr/pub/xnd/

http://www.ccp14.ac.uk/ccp/web-mirrors/xnd/public/xnd/xnd.html

http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/xnd/pub/xnd/

ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/web-mirrors/xnd/public/xnd/xnd.html

ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/ccp14/ftp-mirror/xnd/pub/xnd/

XRS-82/DLS-76

Christian Baerlocher - baerlocher@kristall.erdw.ethz.ch

Structure Refinement, ASCII Control Files

http://kristall.erdw.ethz.ch/software/soft.html

http://www.ccp14.ac.uk/ccp/web-mirrors/ethz/software/soft.html

ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/web-mirrors/ethz/software/soft.html

 

Rietveld Program Interfaces

Interfaces into Rietveld programs vary from GUIs to direct editing of ASCII files.

 

 

GUI LHPM/Rietica for Windows

 

 

 

 

EXPGUI for GSAS:

 

 

 

 

 

Fullprof

 

 

Where Rietveld programs are "behind" compared to Single Crystal Refinement Suites.

(focussing on organic structures)

 

Single Crystal Suites

(Applicable to Powder Diffraction: validation, etc )

Single crystal suites can be very powerful as they allow users to quickly pick and mix a variety of programs at the click of a button.

ORTEX - Patrick McArdle

Shelx86/Shelx97 for Structure Solution

Shelxl for refinement

http://www.nuigalway.ie/cryst/software.htm

CCP14 Mirror: http://www.ccp14.ac.uk/ccp/web-mirrors/ortex/cryst/software.htm

WinGX - Louis Farrugia

Shelx86/Shelx97, Sir92/Sir97, Dirdif, Patsee for Structure Solution

Shelxl for refinement

Fourier Map Calculation and Viewing

Links to very large array of programs.

http://www.chem.gla.ac.uk/~louis/wingx/

CCP14 Mirror: http://www.ccp14.ac.uk/ccp/web-mirrors/farrugia/~louis/wingx/

System S/Platon - Ton Spek

Shelx86/Shelx97, Sir97, Dirdif, Crunch Structure Solution

(Crunch, EXOR, Sir97 and Dirdif for auto-building)

Shelxl for refinement

Fourier Map Calculation and Viewing

Fully automatic Structure solution and refinement

http://www.cryst.chem.uu.nl/platon/

CCP14 Mirror: http://www.ccp14.ac.uk/ccp/web-mirrors/platon-spek/software.html

 

 

Single Crystal Suites (Cont’d)

(Applicable to Powder Diffraction)

 

Crystals –Watkin, Prout, Carruthers, Betteridge, R.I. Cooper

Shelxs and Sir for Structure Solution

Crystals for refinement

Fourier Map Calculation and Viewing

Guided refinement for students and chemists.

http://www.xtl.ox.ac.uk/

CCP14 Mirror: http://www.ccp14.ac.uk/ccp/web-mirrors/crystals/

Xtal (GPL’d)

Crisp and Patsee for Structure Solution

Xtal for refinement

Fourier Map Calculation and Viewing

http://xtal.crystal.uwa.edu.au/

CCP14 Mirror: http://www.ccp14.ac.uk/ccp/web-mirrors/xtal/

NRCVAX

Solver for Structure Solution

NCVAX for refinement

Contact: pwhite@pyrite.chem.unc.edu

 

Single Crystal Suite Examples

Note: it is almost impossible to do justice to any of these single crystal suites withing the time allowed. Allow access large range of functionality at the click of a button.

ORTEX Menu System

Examining a structure in ORTEX

 

WinGX menu system:

E.g., Links to Shelxs 86/97, Sir 92/97, Dirdif, Patsee and major number of other programs and utilities including Platon.

Platon/System S menu system for UNIX:

E.g., Links to Shelxs 86/97, Sir97, Crunch and Dirdif and multiple internal applications

 

Graphically Interacting with the Structure

 

Most freely available programs and suites now have the ability to interact directly with a graphical representation of the structure during solving and refining.

For routine and not so routine refinements, point and click interfaces are now available, complementing the ASCII file or command line interfaces.

3rd party programs can be useful: e.g., Ortep-3 by Louis Farrugia will also read Fullprof, Rietica and GSAS Rietveld structure files.

 

ORTEX / WinGX / Crystals/ CAOS-Sir97/ Platon-System S/ GNU Xtal Suite / Gretep

Fourier Capability in Rietveld Software (ability to effectively refine structures is falling behind abilty to solve– not making use of optimal algorithms such as Maximum Entropy )

Summary List at:

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

Examples:

Fullprof/GFOUR

 

 

 

GSAS

(including

VRML output)

 

 

 

WinMPROF (Q peak location)

 

Maximum Entropy Derived Fourier Capability in available Rietveld Software

Rietan2000 (GPL’d – can freely modify the source code and redistribute under the GNU Public Licence)

Rietan2000 by Fujio Izumi

http://www.nirim.go.jp/~izumi/rietan/angle_dispersive/angle_dispersive.html

MEED max ent software and Mevius Fourier Viewer

http://www.bk.tsukuba.ac.jp/~kumazawa/Software/Software.html

MEED Manual in English:

http://www.bk.tsukuba.ac.jp/~kumazawa/Software/meedman.html

Mevius Fourier Viewer page (Linux):

http://www.bk.tsukuba.ac.jp/~kumazawa/Software/mevius.html

 

Single Crystal Suite Fourier Map Generators and Viewers

(applicable for Powder Diffraction)

Foue (GPL’d) by Scott Belmonte can convert GSAS Fourier Maps into WinGX/Crystals and Project XD format)

http://www.ccp14.ac.uk/ccp/web-mirrors/scott-belmonte-software/

Example of WinGX fourier map animating through a zeolite with disordered template.

Fourier Maps – Single Crystal Suites

Crystals – Slant Plane Fourier Map:

Define the Slant Plane by selecting 3 atoms then right click to go into the Fourier Map option.

 

 

 

 

 

Examine slant plane difference map looking at hydrogen positions – via the Marching Cubes 3D Fourier Map viewer by Michal Husak (also linked into)

http://mysak.umbr.cas.cz/~husakm/Public/MarchingCubeELD/MarchingCubeELD.htm

http://www.ccp14.ac.uk/ccp/web-mirrors/marchingcube-fourierviewer/~husakm/Public/MarchingCubeELD/MarchingCubeELD.htm

Platon/System S Fourier Map:

Examining slant plane difference map looking at hydrogen positions.

 

 

Using WinGX MapView:

(Can be run as a freestanding program linked into any program that will output a Mapview friendly format)

Examining slant plane difference map looking at hydrogen positions

Using the 2D Bitmap Mode of MapView:

 

Structure Quality Checking

(Applicable to Powder Diffraction)

(Each suite can offer different features)

ORTEX:

Example of the Void Finding and graphical viewing within ORTEX (including estimate of time to completion)

Structure Quality Checking

WinGX:

Has GUIs linking to a wide variety of Structure Checking, Analysis Options and Utilities (including a Windows version of Platon).

 

GUI XHYDEX (GUI over code by G. Orpen): Searching for Likely hydrogen positions. GUI CALC-OH (Nardelli 1999) GUI Parst, GUI Model and Data Transformation, SG Info, etc, etc.

Platon (including Addsym - a mandatory program for all crystallographers!):

(links into WinGX and Crystals suite for Windows)

Addsym: check for missing symmetry. Will display or output a modified Shelx file with the updated structure if it finds a higher symmetry spacegroup. Will report miss-fitting atoms.

Refer: Short Communication: "P1 or P-1? Corrigendum", Acta Cryst B56 (2000) 744 from Richard E. Marsh

Original Structure Published in 1997 Triclinic, P1

 

Reinterpretation by Marsh in 1999

Gives: Monoclinic C2

 

 

Press of a button in Platon/Addsym

(on either structure) gives:

Orthorhombic Fdd2

(with the option of generating a new Shelx *.RES file)

Is trivial to run Addsym routinely via Platon

 

Powder Diffraction Pattern Calculation

 

Most Rietveld Programs can calculate powder patterns but may not be all that friendly to use compared to the following dedicated software:

Powder Cell

http://www.bam.de/a_v/v_1/powder/e_cell.html

Imports common file formats and GUI based editing of structure:

GUI based manipulation of structure as well as powder pattern.

 

 

Poudrix

http://www.ccp14.ac.uk/ccp/web-mirrors/lmgp-laugier-bochu/

 

 

Imports common file formats and GUI based editing of structure:

Can accurately model Anomalous Dispersion for Synchrotron X-rays.

 

 

Structure Visualisation and Photorealistic Hardcopy Output

Examples of Software that can do this:

(problem can be that or having a high enough quality printer)

ORTEX (Images and Movie Animations):

http://www.nuigalway.ie/cryst/

http://www.ccp14.ac.uk/ccp/web-mirrors/ortex/cryst/

Just open up a Shelx format *.INS/*.RES file and go for it

 

 

Movie Making in ORTEX

Open a Shelx File and optimise the view in ORTEX

Start the RASMOV Movie Generator

 

Set the Options you Desire:

 

Web Ready Animated GIF will be generated:

 

GUI WinOrtep 3/WUI WinStruplo/WinGX

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

http://www.ccp14.ac.uk/ccp/web-mirrors/farrugia/~louis/software/

Can load a variety of structure formats including some Rietveld formats such as GSAS, LHPM, Fullprof, Rietan.

 

 

 

 

Platon/Pluton/System S

http://www.cryst.chem.uu.nl/platon/

http://www.ccp14.ac.uk/ccp/web-mirrors/platon-spek/platon/

 

GNU Xtal Suite

http://xtal.crystal.uwa.edu.au/

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

 

Marching Cubes 3D Fourier Map Viewer

(links into Crystals and WinGX. GSAS via FOUE) –

outputs Povray files

http://mysak.umbr.cas.cz/~husakm/Public/MarchingCubeELD/MarchingCubeELD.htm

http://www.ccp14.ac.uk/ccp/web-mirrors/marchingcube-fourierviewer/~husakm/Public/MarchingCubeELD/MarchingCubeELD.htm

Dual Boot UNIX/Windows PCs

Obtain the ability to run a very wide range of crystallographic software on cheap, powerful commodity PCs.

Tutorials exist for helping you do this:

CCP14 based tutorials on installing multi-boot

A local UNIX advocate would be quite happy to get a dual boot system going for you.

Free UNIX Operating Systems (install off the internet)

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)

VMWARE (simultaneously run of Windows and Linux):

http://www.vmware.com/

(Commercial software)

Freely Available Compilers, GUI Building Kits and Source Code

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

 

If Isolated from the Internet (or on very slow links)

Free Xtal Nexus CD-ROMs for academics and students

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

(Supported & Sponsored by the IUCr, ICSU and CCP14)

 

Contact: Lachlan Cranswick

CCP14

CLRC Daresbury Synchrotron Laboratory,

Warrington, Cheshire, WA4 4AD U.K

E-mail: l.cranswick@dl.ac.uk

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

 

 

Where does the future lie for "routine" structure solution and refinement from powder diffraction data?

What does the word "routine" mean in the single crystal diffraction world?

If time permits.

Single Crystal System S/Platon demonstration:

Freely Available Software for academics and students

System S/Platon "intelligent" automated control.

Multiple "Structure Solution" programs

Shelx97/86, Sir97, Dirdif, Crunch

Multiple "Structure Building" options

EXOR, Sir97, Dirdif, Crunch

Shelxl97 for structure refinement

 

Summary and Acknowledgements

Downloadable via the EPSRC funded CCP14 website:

http://www.ccp14.ac.uk

ccp14@dl.ac.uk

Acknowledgements to:

BASF for funding my conference expenses

Conference organisers.