Freely Available Software to Assist in Solving Structures from Powder Diffraction

Lachlan M.D. Cranswick

CCP14 (Collaborative Computation Project Number 14 for Single Crystal and Powder Diffraction)

CLRC Daresbury Synchrotron Laboratory, Warrington, Cheshire, WA4 4AD, UK

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

E-mail: [email protected]

Solving a structure from powder diffraction data normally requires starting from raw data conversion through to displaying a publication quality stucture model. To help make this type of endeavour a going concern, a large amount of crystallographic software is presently freely available via the Internet to academics and students (commercial users should contact the program authors to determine licence conditions). This ranges from data conversion, peak profiling, indexing, structure solution, crystal structure validation up to photo-realistic rendering of the final refined solution.

The following notes provide web links to most of the presently known and freely available software; and also tries to give a feel for what some of these programs look like. In the past few years there has been a trend for to put GUIs (Graphical User Interfaces) and advanced graphics onto freely available software to make them more powerful and friendly to use. These notes are as current as possible for August 2000.

Single crystal programs are also cited as presently they can be very useful in assisting in structure solution from powder diffraction. Users are advised that they can greatly enhance and improve the effectively of their crystallographic resources by investigating available and newly developed programs to build a software toolkit optimised to the phases systems and structures. The difference between an intractable or unsolvable structure and one that is relatively routine could purely be the difference in which software is applied to the problem. Many of the cited packages are under continual development; thus this document may quickly go out of with new functionality added to programs. Readers are encouraged to take nothing for granted and investigate for themselves the following mentioned programs in creating a robust tool set for the analysis of their crystallographic problems.

With regard to the web references provided in the following text. The Internet is presently very quite dynamic and unstable. Web and ftp sites that exist one month might disappear or move the next. Thus the reader should not consider these World Wide Web links to be written in stone. If a web site provided in the below text has ceased to exist, the keywords of the program name may allow convenient finding of this or related software by using the program title in a web search engine. Scientists can be most at risk at not knowing what they do not know. Thus much of this information is provided in helping keywords that have been found to work with World Wide Web search engines are also provided. Most of the below stated programs are also mirrored (with tutorials and hints for many of the programs) at the CCP14 website at http://www.ccp14.ac.uk.

 

Agenda

Has the structure been solved already?

Powder X-ray Diffraction Search Match and Phase Identification

Crystal Structure Databases

Powder Data Conversion

Structure Data Conversion and Transformation via Graphical User Interfaces

Powder Pattern Viewing and Processing

Peak Finding and Peak Profiling

Powder Indexing

Spacegroup Assignment

Unit Cell Refinement

Full Profile Fitting (Pawley, LeBail)

Texture analysis software

Single Crystal Suites

Structure Solution Specifically for Powder Diffraction

Structure Solution Using Single Crystal Software

2D to 3D molecular Model Generation

Single Crystal Refinement programs for assisting in building up the structure

Rietveld structure refinement

Rietveld structure refinement software that is Fourier Map/Q Peak Friendly

Hydrogen Placement Using Single Crystal Software

Free Standing Powder and Single Crystal Fourier Map software

Structure Validation including Platon/Addsym

Crystallographic Structure Visualisation: during structure solution and refinement

Powder Diffraction Pattern Calculation

Photo realistic rendering of crystal structures and Fourier contour maps

Miscellaneous Links

Setting up dual and multiboot PC computers containing Windows and UNIX

IUCr and ICSU sponsored Crystallographic Nexus CD-ROMs for academics and students isolated from the internet.

Useful Crystallographic Websites

On-line crystallographic web tutorials

Web Search Engines

 

Phase ID and Search Match from Powder Diffraction Data

Search Match Databases

1. ICDD (commercial at this time costing US$6,200 for a starting copy): http://www.icdd.com

3. Pauling Database (expected release 2007?)

2. Consider making your own up from synthesised phases and calculated powder patterns.

Search Match Software (as of August 2000) :

Summary list of search-match software at: http://www.ccp14.ac.uk/solution/search-match.htm

All search-match software should be considered commercial unless mentioned otherwise

AXES for DOS:

ftp://ftp.physic.ut.ee/pub/pc/axes/

Bede ZDS for Windows

http://www.bede.com/

Bruker "DIFFRACplus" for Windows

http://www.bruker-axs.com/

Crystallographica Search-Match" for Windows

http://www.crystallographica.co.uk

Diffraction Technology "Traces" for Windows

http://www.ozemail.com.au/~difftech/products/traces.htm

"DRXWin" for MS-Windows

http://icmuv.uv.es/drxwin/

Radicon "LookPDF" for Windows

http://www.radicon.xraysite.com/

Macdiff (freeware):

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

MacPDF for Mac

http://world.std.com/~crose/MacPDFWebSite/MacPDF_V3.html

MDI "Jade" for Windows

http://www.materialsdata.com/products.htm

MicroPDSM

?????

Portable Logic for UNIX (freeware)

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

PADS New Edition

E-mail: [email protected]

Philips Search-Match for MS-Windows

http://www-eu.analytical.philips.com/products/xrd/

Socabim

????

Siefert "RayfleX" Software for MS-Windows:

http://www.roentgenseifert.com/seif4.9.htm

Mark Raven - CSIRO, "XPLOT" for Windows:

http://www.clw.csiro.au/services/mineral/xplot.htm

"XPowder" for Windows

http://www.ugr.es/~jdmartin/

"ZDS" for DOS and Windows

http://krystal.karlov.mff.cuni.cz/xray/zds/zdscore.htm

 

 

Crystal Structure Databases (as of August 2000)

Database

Address

Specialisation

Global Free Access?

ICSD

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

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

Inorganic and Minerals

No

CCDC/Cambridge

http://www.ccdc.cam.ac.uk/

Organic and Organometallic

No

Crysmet

http://www.tothcanada.com

Metals and Alloys

No

MINCRYST

http://database.iem.ac.ru/mincryst/

http://database.iem.ac.ru/mincryst/s_full.php3

Minerals

Yes

Mineral Web

http://www.man.ac.uk/Geology/MineralWeb/Mineral_Web.html

Minerals

Yes

American Mineralogist

http://www.geo.arizona.edu/xtal-cgi/test/

Minerals

Yes

Lama Modulated Structures

http://www.cryst.ehu.es/icsdb/

Modulated Structures

Yes

(Academics and students may already have free access to many of these via national facilities.) e.g., EPSRC funded CDS (Chemical Database Service) for UK Students and Academics:

http://cds.dl.ac.uk/

Some single crystal suites have a point and click interface into the Cambridge database allowing connectivity checks, cell searches to be performed in an easy to do manner. Platon/System S is one of these style of programs which links into the CSD Quest program. While Crystals for Windows does dynamic bond-length and angle comparison of data from the Cambridge database.

Platon/System S/Pluton (by Ton Spek):

UNIX: http://www.cryst.chem.uu.nl/platon/ ftp://xraysoft.chem.uu.nl/pub/

Windows (ported by Louis Farrugia): http://www.chem.gla.ac.uk/~louis/software/

Crystals (D. Watkin, R. Cooper, et al):

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

 

 

Powder Data Conversion

Summary list at: http://www.ccp14.ac.uk/solution/powderdataconv/

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

Tutorial on techniques to convert X-ray powder diffraction (Debye-Scherrer) to a synthetic digital diffractogram.

http://www.indiana.edu/~xl10rd/XRDFilmTutorial.htm

   

ConvX Windows Mass Data Conversion

http://www.ceramics.irl.cri.nz/Convert.htm

Philips VAX RD, ASCII X-Y, Siemens/Bruker/DiffracPlus (RAW), Philips Binary (RD, SD),Sietronics (CPI), GSAS (DAT), DBWS Based (LHPM, RIET7, Fullprof) (DAT), ScanPI (INT)

Philips VAX RD, ASCII X-Y, Siemens/Bruker/DiffracPlus (RAW), Philips Binary (RD, SD) Sietronics (CPI), GSAS (DAT), DBWS Based (LHPM, RIET7, Fullprof) (DAT), ScanPI (INT)

DLConvert

http://www.ccp14.ac.uk/projects/dl-conv/index.htm

Daresbury Laboratory Beamlines: 9.1 angular dispersive, 2.3 angular dispersive, 16.4 Dispersive; Binary MCA Ortec CHN, Argonne Energy Dispersive Data; XT Data

XFIT Dat, CPI, GSAS, XY, linear interpolated data

Powder v2.00 for Windows

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

DBWS, GSAS CW, GSAS CW ESD, LHPM, Philips RD/SD binary, Philips UDF, MXP18 Binary, RIET7, Scintag, Siemens ASCII, Sietronics CPI, WPPF/Profit, Y free ascii, XY free ascii, free ascii. Line; X, XY, XYZ

DBWS, GSAS CW, GSAS CW ESD, LHPM, Philips RD/SD binary, Philips UDF, MXP18 Binary, RIET7, Scintag, Siemens ASCII, Sietronics CPI, WPPF/Profit, Y free ascii, XY free ascii, XYZ free ascii. Line; X, XY, XYZ

PowderX for Windows

http://www.ccp14.ac.uk/tutorial/powderx/index.htm

Mac Science ASCII, BD90 (Raw), X-Y, Rigaku (DAT), Sietronics (CPI), TsingHua Rigaku (USR) Siemens/Bruker ASCII (UXD), Siemens/Bruker Binary (RAW), Philips ASCII (UDF), Philips Binary (RD) Mac Science Binary, RIET7 (DAT), ORTEC Maestro (CHN)

ALLHKL (POW), Sietronics (CPI), FOURYA/ XFIT/ Koalariet (XDD), Fullprof (DAT), GSAS (DAT), Rietan (INT), Simpro (DUI), X-Y (XRD), DBWS (DAT), LHPM (DAT)

Winfit for Windows

http://www.geol.uni-erlangen.de/html/software/soft.html

Geol. Dept. Erlangen (DFA), Siemens/Bruker Diffrac V 2.1 (1 range) (RAW), (TRU), ASCII X-Y, ICDD Format (PD3), ZDS (ZDS), Software of F Nieto (CRI), Philips (UDF), Philips Binary (RD), STOE (RAW), JADE (MDI), MacDiff of Rainer Petschick (DIF), Converted RAW File (Bish, Eberl,..) (ASC), XDA Rietveld (XDA)

Siemens/Bruker Diffrac V 2.1 (1 range) (RAW), Philips Binary (RD), ASCII X-Y, XDA Rietveld (XDA)

ConvX Powder Diffraction Data Interconverter Interface

 

Structure Data Conversion and Transformation via Graphical User

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

Name

Web

Conversion?

Transform-ation

HKL data

Formats In

Formats Out

Cryscon

http://www.shapesoftware.com

Yes

Yes

Yes

Free Format, CCDC FDAT, Shelx, CIF, DBWS, LHPM, ICSD, ORTEP, XTLVIEW, ATOMS, RIETAN, GSAS, Am Mineral, Fullprof, Vibratz

Free Formation, CCDC FDAT, Shelx, CIF, DBWS, LHPM, ICSD, ORTEP, Rietan, GSAS, Fullprof

Ortep-3

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

Yes

No

No

Shelx, CIF, GX, SPF/Platon, ORTEP, CSD/CCDC FDAT, CSSR XR, Crystals, GSAS, Sybol MOL/MOL2, MDL MOL, XYZ file, Brookhaven PDB, Rietica-LHPM, Fullprof

ORTEP, Shelx, XYZ

WinGX

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

Yes

Yes

Yes

CSSR, Shelx, Cif, CSD/CCDC FDAT, GX

Shelx, CIF, GX, SPF/Platon, CACAO

Powder Cell

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

Yes

Yes (Int Tab)

No

Powder Cell (CEL), Shelx, ICSD

Powder Cell, BGMN, Shelx, Opal

ICSD Web

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

Yes

No

No

Inorganic Database

ICSD, Shelx, Fullprof, GSAS Macro, Powder Cell, Lazy Pulvarix

Structure transformation and inter-conversion using the shareware Cryscon program

 

Powder Diffraction Pattern Viewing and Processing

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

Program

Address

Windows

UNIX

Data Formats

CMPR

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

Yes

Yes

BT-1, DBWS, Fullprof, LHPM, GSAS, BNL X7A, XY Data

Powder Cell

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

Yes

No

Siemens RAW, Philips UDF, XY, CPI, Riet7, APX63

Powder v 2.00

http://www.ccp14.ac.uk/ccp/web-mirrors/ndragoe/appchem/labs/kitazawa/dragoe/html/software.html

Yes

No

DBWS, GSAS CW, GSAS CW ESD, LHPM, Philips RD/SD binary, Philips UDF, MXP18 Binary, RIET7, Scintag, Siemens ASCII, Sietronics CPI, WPPF/Profit, Y free ascii, XY free ascii, free ascii. Line; X, XY, XYZ

Powder X

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

Yes

No

Mac Science ASCII, BD90 (Raw), X-Y, Rigaku (DAT), Sietronics (CPI), TsingHua Rigaku (USR) Siemens/Bruker ASCII (UXD), Siemens/Bruker Binary (RAW), Philips ASCII (UDF), Philips Binary (RD) Mac Science Binary, RIET7 (DAT), ORTEC Maestro (CHN

Winfit

http://www.geol.uni-erlangen.de/html/software/winsoft.html

Yes

No

Geol. Dept. Erlangen (DFA), Siemens/Bruker Diffrac V 2.1 (1 range) (RAW), (TRU), ASCII X-Y, ICDD Format (PD3), ZDS (ZDS), Software of F Nieto (CRI), Philips (UDF), Philips Binary (RD), STOE (RAW), JADE (MDI), MacDiff of Rainer Petschick (DIF), Converted RAW File (Bish, Eberl,..) (ASC), XDA Rietveld (XDA)

Winplotr

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

ftp://bali.saclay.cea.fr/pub/divers/winplotr/

Yes

No

Fullprof, GSAS, XRFIT, HRMPD G42, 6TI, G41/G61, RX, DMC/PSI, XY

XFIT/Koalariet

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

Yes

No

Riet7 DAT, CPI, XDD, XDA, XY, SCN

The CMPR Powder Diffraction Toolkit for UNIX and Windows

 

Peak Finding and Peak Profiling (As of August 2000)

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

Program

Address

Peak Finding

Peak Profiling

Data Formats

CMPR

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

No

Yes

BT-1, DBWS, Fullprof, LHPM, GSAS, BNL X7A, XY Data

GSAS RAWPLOT

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

No

Yes

GSAS Format

Powder v 2.00

http://www.ccp14.ac.uk/ccp/web-mirrors/ndragoe/appchem/labs/kitazawa/dragoe/html/software.html

Yes

No

DBWS, GSAS CW, GSAS CW ESD, LHPM, Philips RD/SD binary, Philips UDF, MXP18 Binary, RIET7, Scintag, Siemens ASCII, Sietronics CPI, WPPF/Profit, Y free ascii, XY free ascii, free ascii. Line; X, XY, XYZ

Powder X

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

Yes

No

Mac Science ASCII, BD90 (Raw), X-Y, Rigaku (DAT), Sietronics (CPI), TsingHua Rigaku (USR) Siemens/Bruker ASCII (UXD), Siemens/Bruker Binary (RAW), Philips ASCII (UDF), Philips Binary (RD) Mac Science Binary, RIET7 (DAT), ORTEC Maestro (CHN

Winfit

http://www.geol.uni-erlangen.de/html/software/winsoft.html

No

Yes

Geol. Dept. Erlangen (DFA), Siemens/Bruker Diffrac V 2.1 (1 range) (RAW), (TRU), ASCII X-Y, ICDD Format (PD3), ZDS (ZDS), Software of F Nieto (CRI), Philips (UDF), Philips Binary (RD), STOE (RAW), JADE (MDI), MacDiff of Rainer Petschick (DIF), Converted RAW File (Bish, Eberl,..) (ASC), XDA Rietveld (XDA)

Winplotr

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

ftp://bali.saclay.cea.fr/pub/divers/winplotr/

Yes

Yes

Fullprof, GSAS, XRFIT, HRMPD G42, 6TI, G41/G61, RX, DMC/PSI, XY

XFIT/Koalariet

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

No

Yes

Riet7 DAT, CPI, XDD, XDA, XY, SCN

a) Peak finding in PowderX for Windows and b) peak profiling in XFIT for Windows

 

 

 

Powder Indexing

Programs such as Ito, Dicvol and Treor have multiple downloads via the Internet. Armel Le Bail's site is given as the cited download site.

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

Indexing Programs

Download

Within Suites

Dicvol

http://sdpd.univ-lemans.fr/ftp/dicvol91.zip

Crysfire, Powder v 2.0, Winplotr

Eflech/Index

http://www.bgmn.de/related.html

 

Fjzn

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

Crysfire

Ito

http://sdpd.univ-lemans.fr/ftp/ito13.zip

Crysfire, Powder v 2.0

Kohl

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

Crysfire

Lzon

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

Crysfire

Losh

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

Crysfire

Supercel

http://www-llb.cea.fr/winplotr/winplotr.htm ftp://bali.saclay.cea.fr/pub/divers/winplotr/

Winplotr

Taup/Powder

ftp://hprib.lps.u-psud.fr/pub/powder/

http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/taupin-indexing/pub/powder/

Crysfire

Treor

http://sdpd.univ-lemans.fr/ftp/treor90.zip

Crysfire, Powder v 2.0, Powder X, Winplotr

Xray Scan

http://phyhp.phy.ncku.edu.tw/~hjs/hjseng.html

http://www.ccp14.ac.uk/ccp/web-mirrors/xrayscan-indexing/~hjs/hjseng.html

 

Suites that link into Indexing Programs

Program

Address

Indexing Programs Linked (August 2000)

CMPR

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

Manual Indexing via interactive slide bars

Crysfire

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

Ito, Dicvol, Treor, Losh, Lzon, Kolh, Taup/Powder

Powder X

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

Treor, Manual Indexing

Powder V 2.00

http://www.ccp14.ac.uk/ccp/web-mirrors/ndragoe/appchem/labs/kitazawa/dragoe/html/software.html

Ito, Dicvol, Treor

Winplotr

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

ftp://bali.saclay.cea.fr/pub/divers/winplotr/

Dicvol, Treor, Supercell

Chekcell

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

Crysfire suite, Manual Indexing

Example of Chekcell for Graphically Finding the Best Cell/Spacegroup Combination.

 

Spacegroup Assignment

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

Non Whole Profile Fitting (based on HKLs)

Program

Address

Method

Chekcell

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

Graphically and automatic determination using peak list file and powder data

Platon

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

HKL File

Absen

(within ORTEX and WinGX)

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

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

HKL File

International Tables

http://www.iucr.org/iucr-top/it/

Manually from HKLs

Whole Profile Lebail/Pawley methods (being guided by R factors).

Refer to Le Bail and Pawley fitting programs.

Example of running Chekcell for automatic determining optimum cell and spacegroup combinations.

Example of running Absen spacegroup assignment software within WinGX

 

Unit Cell Refinement

Summary list at: http://www.ccp14.ac.uk/solution/unitcellrefine/

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

Program

Address

Can overlay Raw diffraction data

Can use Internal Standard

Celref

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

Yes

No

Eracel

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

No

No

LAPOD

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

No

No

LAPODS

http://www.ccp14.ac.uk/solution/ccp/web-mirrors/powderx/lapod/

No

No

Powder v2.00

http://www.ccp14.ac.uk/ccp/web-mirrors/ndragoe/appchem/labs/kitazawa/dragoe/html/software.html

No

Yes

Refcel

ftp://img.cryst.bbk.ac.uk/pdpl/ http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/profil/PDPL/

No

No

UNITCELL

http://www.esc.cam.ac.uk/astaff/holland/

No

No

Wincell

http://fazil.rajabalee.free.fr/delphi_an.htm

No

No

XLAT

ftp://jgiqc.llnl.gov/

No

Yes

Example of running Celref for Windows

Example of running UNITCELL for Windows (Mac and UNIX versions available)

 

Full Profile Fitting (Pawley, LeBail)

Summary lists at:

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

Pawley http://www.ccp14.ac.uk/solution/pawley/

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

Overlap by Armel Le bail can take Le Bail extracted intensity files in Shelx, Sirpow and EXPO format converting them to F, Fsq and Intensity files in Shelx format http://sdpd.univ-lemans.fr/ftp/overlap.zip

Le Bail Extraction Programs

Program

Address

Known to recycle Intensities

ARIT

http:// sdpd.univ-lemans.fr/arit.html

 

BGMN

http://www.bgmn.de

 

EXPO

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

 

EXTRACT

(part of XRS-82)

http://www.kristall.ethz.ch/LFK/software/xrs/

 

Fullprof

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

Yes

GSAS

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

Yes

LHPM-Rietica

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

Yes

Powder Cell

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

Yes

Mprofil

http://www.dl.ac.uk/CCP/CCP14/ccp/ccp14/ccp14-by-program/mprep5-mprofil5/

 

RIETAN 2000

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

 

WinMprof

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

Yes

XND

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

 

Pawley Extraction Programs

Program

Address

Known to recycle Intensities

Simpro

http://www.uni-tuebingen.de/uni/pki/simref/simpro.html

 

WPPF

ftp://ftp.ccp14.dl.ac.uk/wdpp/WinNT/Table12b/Wppf/ ftp://ftp.ccp14.dl.ac.uk/wdpp/Win95/Table12b/Wppf/ ftp://ftp.ccp14.dl.ac.uk/wdpp/VaxVMS/Table12b/Wppf/ ftp://ftp.ccp14.dl.ac.uk/wdpp/MS-DOS/Table12b/Wppf/ ftp://ftp.ccp14.dl.ac.uk/wdpp/AlphaVMS/Table12b/Wppf/

 

 

 

Texture analysis software

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

Program

Address

BEARTEX

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

GSAS

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

MAUD for Java (GPL'd)

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

POFINT

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

popLA

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

Symmet

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

Examples of the MAUD for Java Graphical User Interface

 

Single Crystal Suites

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

Program

Address

Linked Solution Software

Refinement

Crystals

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

Sir, Shelxs

Crystals

NRCVAX

Contact Peter White: [email protected]

Solver

NRCVAX

ORTEX

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

Shelxs

Shelxl 97

Platon / System S

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

Sir, Shelxs, Crunch, Dirdif

Shelxl 97

WinGX

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

Sir, Shelxs, Dirdif, Patsee

Shelxl 97

Xtal (GPL'd)

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

Crisp, Patsee

Xtal (3 different programs)

 

Examples of the WinGX graphical user interface

The SXGRAPH Graphical User Interface over Shelxl97 provided with WinGX.

 

Structure Solution Software Specifically for Powder Diffraction

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

Freely Available Software

Program

Address

Method

EXPO 2000

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

Direct Methods and Real Space

ESPOIR (GPL'd)

http://sdpd.univ-lemans.fr/sdpd/espoir/

Real Space

Focus

http://www.kristall.ethz.ch/LFK/software/

Chemical Information, Zeolites

ZEFSA II (GPL'd)

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

Real Space, Zeolites

Commercially Available Software

Program

Address

Method

Cerius 2

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

Real Space

WinCSD/CSD

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

 

DIFFRACplus TOPAS

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

Real Space

Endeavour

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

Real Space

Dash mentioned here(?)

(Druid and Mystic of old)

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

Real Space

Example of automatic Le Bail fitting within EXPO

Example of EXPO completing the Fourier cycling to give a solve structure

 

Structure Solution Using Single Crystal Software

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

Program

Address

Method

CAOS

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

Patterson

Crisp

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

Direct Methods

Crunch

http://chemb0b.leidenuniv.nl:80/~rag//

Direct Methods

Dirdif

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

Patterson, Fragment

Patsee

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

Fragment

Shake’n’Bake (SnB)

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

SnB

Shelxs 86/97/d

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

Direct Methods, Patterson, SnB style

Sir92/97/2000

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

Direct Methods, SnB style

Solver

Contact Peter White ([email protected])

Direct Methods

XFPA

Contact Frantisek Pavelcik ([email protected])

Patterson

Screen images of a) Dirdif for Windows and b) Sir97 solving structures

 

 

2D to 3D molecular Model Generation

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/)

These can be helpful for fragment based search methods for real space and reciprocal space methods. Some 2D to 3D model builders are better than others. Three freely available ones are listed. Corina via a web interface is the easiest to start with.

Summary List at: http://www.ccp14.ac.uk/solution/2d_3d_model_builders/

Program

Address

Caveates

CORINA

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

Web Based

Momo

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

From the makers of Patsee

Dirdif

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

Can generate 3D models with hydrogens from 2D models

Screen Images showing a) Generating a 2D Fragment in Corina via a Java Applet and b) viewing the resulting 3D optimised fragment in PDB format in Platon

 

 

Single Crystal Refinement programs for assisting in building up the structure

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/)

Program

Address

CAOS

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

Crystals

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

NRCVAX

Contact Peter White ([email protected])

Shelxl

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

Xtal (GPL’d)

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

WinGX,

GUI CalcOH,

GUI Xhydex

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

 

Screen Image of Crystals for Windows

 

 

Rietveld structure refinement

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

Program

Address

Advertised Specialisations

ARITVE

http://sdpd.univ-lemans.fr/aritve.html

Glasses

BGMN

http://www.bgmn.de

Fundamental Parameters

DBWS

Contact Ray Young ([email protected])

 

DEBVIN

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

Polymers

EXPO

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

 

Fullprof

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

General, Incommensurate, Magnetic, Combined Neutron/X-ray/Single Crystal, TOF, Fourier Map Facility via GFOUR

GSAS

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

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

General, Magnetic, Combined Neutron/X-ray/Single Crystal, Texture, TOF, Fourier Map facility

Koalariet

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

Fundamental Parameters

LHPM/Rietica

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

Full GUI Interface. Has in built Bond Valence software.

MAUD for Java (GPL'd)

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

Materials Analysis, Texture

PREMOS/REMOS

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

Modulated Structures

ProDD

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

TOF

Profil

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

 

Riet7/SR5

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

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

Variable Count Time

RIETAN-2000 (GPL’d)

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

TOF, maximum-entropy method (MEM)

Rietquan

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

Quantitative Analysis

Simref

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

Incommensurate, High temperature multiple dataset refinement

WinMprof

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

Le Bail fitting, In built Fourier peak finding for building up structures.

XND

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

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

Incommensurate, High temperature multiple datasets refinement

XRS-82/DLS-76

http://www.kristall.ethz.ch/LFK/software/

Zeolites

Screen Image of a) part of the EXPGUI Interface of GSAS and b) Rietica-LHPM Graphical User Interface

 

 

Hydrogen Placement Using Single Crystal Software

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

Important to try and place hydrogens if they are present in the structure during final stages of refinement.

Program

Address

CAOS

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

Crystals

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

Dirdif

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

Shelxl

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

Xtal (GPL’d)

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

Screen Images of a) GUI XHYDEX and b) GUI CALC-OH Provided within the WinGX Single Crystal Suite for finding of Hydrogens

 

 

Rietveld structure refinement software that is Fourier Map/Q peak Friendly

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

Summary list at: http://www.ccp14.ac.uk/solution/rietveld_fourier_maps/

Program

Address

Advertised Specialisations

BGMN

http://www.bgmn.de

Outputs Shelx FCF files that can be read by various single crystal suites

EXPO

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

Has in built Fourier Map capability

Fullprof

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

Links into the GFOUR program

GSAS

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

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

In built Fourier including the ability to output VRML based Fourier Maps.

LHPM/Rietica

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

In built Fourier Map display

RIETAN-2000 (GPL’d)

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

Maximum-entropy method (MEM) for generating Fourier Maps

WinMprof

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

In built Fourier peak finding for building up structures.

Screen Image of GFOUR for Windows which interlinks with Fullprof Rietveld

 

Free Standing Powder and Single Crystal Fourier Map software

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

Summary list at: http://www.ccp14.ac.uk/solution/rietveld_fourier_maps/

Program

Address

Caveates

GFOUR for Windows

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

Wants Fullprof/GFOUR happy files to generate Maps

Platon for UNIX/Windows

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

Wants Shelx format FCF format files to generate Maps

WinGX for Windows. Also has Map viewing via Contour and Mapview

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

Wants Shelx format FCF files to generate the Fourier Map; or a WinGX format MAP file

Marching Cubes 3D Fourier Map viewer

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

Views WinGX, Crystals or Project XD map files

FOUE (GPL'd)

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

Converts GSAS Binary Fourier Map files into WinGX, Crystals, Project XD and ASCII formats

Screen Image of the Mapview Fourier Map Viewing Software Provided with the WinGX Single Crystal Suite

 

Structure Validation (including Platon/Addsym)

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

Most of these programs are made for single crystal applications but are very applicable to powder diffraction problems.

Program

Address

Caveates

Valist for Windows

ftp://ftp.ill.fr/pub/dif/valist/

Bond Valence Checking. Can read common file formats

Valence

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

Bond Valence Checking

Platon for UNIX/Windows

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

Includes Addsym. Mandatory software to check for Missing Symmetry as well as other common problems!

WinGX for Windows

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

Links to a variety of validation packages including Platon

ORTEX

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

GUI based Void finding

Crystals

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

Bond length and angle checking with the Cambridge database

Example of Addsym finding better symmetry based on "Short Communication: "P1 or P-1? Corrigendum", Acta Cryst B56 (2000) 744 from Richard E. Marsh"

1. Original Structure was published in P1 Triclinic in 1997

2. Reinterpreted by March as C2 Monoclinic in 1999

3. Found by a click of a button with Addsym to be Fdd2 Orthorhombic

Screen Image of a) original P1 Triclinic structure and b) resulting Fdd2 structure in Platon after analysis with Addsym

 

 

Crystallographic Structure Visualisation: during structure solution and refinement

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

Most of these programs are made for single crystal applications but are very applicable to powder diffraction problems. They also can generate information on bond lengths, angles and local co-ordination at the click of a button.

Program

Address

Compatible File Formats

Platon for UNIX/Windows

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

Cif, Platon SPF, Shelx INS / RES, PDB

Ortep-3 / GUI WinStruplo/ WinGX for Windows

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

Shelx, CIF, GX, SPF/Platon, ORTEP, CSD/CCDC FDAT, CSSR XR, Crystals, GSAS, Sybol MOL/MOL2, MDL MOL, XYZ file, Brookhaven PDB, Rietica-LHPM, Fullprof

ORTEX

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

Shelx INS/RES

Crystals, Cameron

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

Shelx INS/RES, Crystals

Gretep

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

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

Shelx INS/RES, Gretep, Powder Cell, Lazy Pulvarix

Structure Viewing in Gretep (can handle inorganics and alloys as well):

Structure Viewing in Ortep-3 (reads many file formats including LHPM, Fullprof and GSAS files)

 

Powder Diffraction Pattern Calculation

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

Pretty much every Rietveld program can calculate powder patterns but specialised programs may be of benefit.

Program

Address

Compatible File Formats and major features

GUI Powder Cell for Windows

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

Powder Cell (CEL), Shelx, ICSD. Structure transformation options.

Lazy Pulvarix for Windows within WinGX

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

Formats importable into GUI WinOPTEP, then saved as Shelx. Shelx, CIF, GX, SPF/Platon, ORTEP, CSD/CCDC FDAT, CSSR XR, Crystals, GSAS, Sybol MOL/MOL2, MDL MOL, XYZ file, Brookhaven PDB, Rietica-LHPM, Fullprof

Powdis and Powutl / ORTEX Suite

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

Shelx INS/RES, CIF

GUI Poudrix for Windows

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

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

Shelx INS/RES, Poudrix, Powder Cell, Lazy Pulvarix. Calculates anomolous dispersion correctly for synchrotron wavelengths.

Lazy Pulvarix from the author, Prof. Erwin Parthe

E-mail to [email protected]

Lazy Pulvarix

Lazy Pulvarix via the ICSD web

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

 

Examples of the a) Powder Cell Interface and b) Poudrix GUI Interface

 

 

Photo realistic rendering of crystal structures and Fourier contour maps

(If links are broken, refer to the CCP14 Mirrors area: http://www.ccp14.ac.uk/mirror/ or the IUCr's Sincris software list at http://www.iucr.org/sincris-top/logiciel/)

This is trivial to perform and is available via a wide variety of software. For most programs you will need the freely available Povray software (http://www.povray.org)

Program

Address

Rendering engine

Compatible File Formats

GUI Powder Cell for Windows

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

Povray

Powder Cell (CEL), Shelx, ICSD..

Ortep-3, GUI WinStruplo, WinGX

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

Raster3D and Povray

Formats importable into GUI WinOPTEP and GUI WinStruplo. Shelx, CIF, GX, SPF/Platon, ORTEP, CSD/CCDC FDAT, CSSR XR, Crystals, GSAS, Sybol MOL/MOL2, MDL MOL, XYZ file, Brookhaven PDB, Rietica-LHPM, Fullprof. Anisotropic atoms.

ORTEX

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

Raster3D

Shelx INS/RES, CIF. Rendering of Movies. Anisotropic atoms.

Platon

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

Raster3D and Povray

Shelx INS/RES, Poudrix, Powder Cell, Lazy Pulvarix. Calculates anomolous dispersion correctly for synchrotron wavelengths. Anisotropic atoms.

Xtal

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

 

Lazy Pulvarix

Marching Cubes

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

Povray

Fourier Maps: Crystals, WinGX, Project XD. Refer also to FOUE for converting GSAS Fourier Maps into Marching Cubes format

 

Photorealistic Rendering a) Structures using Platon via Povray and b) Fourier Maps using Marching Cubes 3D via Povray

 

 

 

Miscellaneous Links

Site

Address

Crystallographic Nexus CD-ROM for crystallographers isolated from the internet

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

FreeBSD and Windows Multiboot Tutorial

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

Linux and Windows Multiboot Tutorial

http://www.ccp14.ac.uk/solution/linux/linwin95a.html

Linux for Crystallography

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

IUCr Website and mirrors

Including Crystallography World Wide and Sincris Crystallographic Software Library

http://www.iucr.org/iucr-top/

http://www.us.iucr.org/iucr-top/

http://www.ch.iucr.org/iucr-top/

http://www.se.iucr.org/iucr-top/

http://www.ru.iucr.org/iucr-top/

http://www.fr.iucr.org/iucr-top/

http://www.il.iucr.org/iucr-top/

http://www.au.iucr.org/iucr-top/

http://www.jp.iucr.org/iucr-top/

http://www.za.iucr.org/iucr-top/

Crystallography World Wide Educational Resources (and Mirrors)

http://www.iucr.org/cww-top/edu.index.html

http://www.us.iucr.org/cww-top/edu.index.html

http://www.ch.iucr.org/cww-top/edu.index.html

http://www.se.iucr.org/cww-top/edu.index.html

http://www.ru.iucr.org/cww-top/edu.index.html

http://www.fr.iucr.org/cww-top/edu.index.html

http://www.il.iucr.org/cww-top/edu.index.html

http://www.au.iucr.org/cww-top/edu.index.html

http://www.jp.iucr.org/cww-top/edu.index.html

http://www.za.iucr.org/cww-top/edu.index.html

Advanced Certificate in Powder Diffraction on the Web: Birkbeck College, University of London

http://pd.cryst.bbk.ac.uk/pd/

Internet course: Learn how to succeed in a Structure Determination by Powder Diffractometry (SDPD) with the help of experts by the University of Maine (France)

http://sdpd.univ-lemans.fr/course/

QTA Internet Course Learn how to Quantitatively Determine the Crystallographic Texture of materials using x-ray and neutron diffraction by D. Chateigner and A. Jouanneaux

http://pecdc.univ-lemans.fr/qta/

Strategies in Structure Determination from Powder Data by A. Le Bail

http://sdpd.univ-lemans.fr/iniref/tutorial/indexa.html

Web Search Engines

Web Search Engine

Address

Google

http://www.google.com

Altavista

http://www.altavista.com

Links2Go Crystallography

http://www.links2go.com/topic/Crystallography

Inference Find

http://www.infind.com/

EZResult

http://www.easyresults.com/

Hotbot Web Search

http://www.hotbot.com

Multicrawl

http://www.multicrawl.com/

Meta Crawler

http://www.metacrawler.com/

All The Web

http://www.alltheweb.com/