After running auto generated

scripts through quest:

Red bonds imply bonds are

too short for this geometry

Bonds now within what is

expected from the CSD

Though in the above validation case (to a novice crystallographer) the thermal from the incorrect atom may not be so obvious.

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/

Context for Windows (freeware) can do column mode editing:

(toggle Control L for normal and column editing mode)

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

Refer: Data Conversion/Importing data/structures

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

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

Structure Importing, Conversion and Transformation

Be careful with these and check the results.

Best program at the moment is the shareware program CRYSCON

http://www.shapesoftware.com

Powder Diffraction Utility Software

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

Example of PowderX for Windows

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.

For Overall Summary of available powder indexing software refer to:

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

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. Latest beta version comes with Le Page and GUI Cell Transformation.

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

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

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

Unexpected Cell and Spacegroup

(though visually very compelling)

Validated after the event from a single crystal

Crysfire/Chekcell for Indexing and Spacegroup Assignment

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

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

1 impurity peak on the best data files

Crysfire/Chekcell for Indexing and Spacegroup Assignment

Why Isn’t this cell solving

(Organometallic)

From Armel Le Bail’s site: ESRF Powder Data as well

(very difficult problems can still be difficult on any available software program)

Manual Single Crystal Indexing/Spacegroup Assignment

Single Crystal Absorption Correction Options

Ortex, Crystals, WinGX and Platon give access to a variety of Absorption correction options.

Viewing or HKL Profiles

Blessing DREAR Software

Numerical:

Semi-Empirical:

Psi-scans, Camel-Jockey, Multiscan

RefDelF:

Difabs, XABS2, Shelxa

Platon

(Viewing the Crystal Habit and multiple absorption correction options)

Single Crystal Indexing/Spacegroup Assignment

(some of which is also applicable to powder diffraction)

Twinning Resources: http://www.ccp14.ac.uk/solution/twinning/

Most hardware vendors provide options for indexing but there are free-standing programs that can provide other options.

DIRAX for difficult Indexing problems.

ftp://ftp.chem.uu.nl/pub/dirax/

Twindex.

ftp://laue.chem.ncsu.edu/pub/X-ray/twindex/

The Merohedral Crystal Twinning Server

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

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])

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 (or where unit weighting of each reflection is important).

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:

Mass unit cell refinement using Le Bail fitting

In this case using the Rietica for Windows Rietveld:

(multply the following by a few more 100 to 1000 powder patterns)

http://www.rietica.org/

Materials Analysis Rietveld/Texture Software

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

Materials Analysis Rietveld

MAUD (for Java PC/Mac/UNIX)

Crystallite size and shape

Pole figure/Refinement wizard

MAUD Quantitative Phase Analysis Tutorial:

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

"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/

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/

"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/

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 :

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):

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)

Range of programs to choose from:

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

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.

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

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 ([email protected])

XFPA – Frantisek Pavelcik

Patterson Methods and automatic structure building

E-mail: [email protected]

Single Crystal Examples. Summary:

1) Push the button,

2) Structure solves

Shelxs97 direct methods:

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

Resulting structure ready for building up:

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

http://www.ccp14.ac.uk/tutorial/sir97/

Here Sir97 is just at the point of automatically assigning atom types during the automatic building up of a structure:

After Completion (just have to rename 3 atoms):

Dirdif solving a Structure. Program of choice for heavy atom problems.

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

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/

Resulting structure with every assigned non-Hydrogen atom correctly placed and named:

(New December 2000 version 1.1)

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

Structure solved (in this cases via the Platon/System S suite) and built to near completion (though this is really a heavy atom problem). One missing Carbon atom and various atom reassignments to be done.

(Linux, SGI, IBM AIX, and Alpha Executables available at present)

Information and Install Tutorials for Linux:

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

Java GUI Interface will then take you through setting up SnB up to visualising resulting structures. Is not for those who like speedy results.

Two new packages for large structures:

On a new Cyclodextrin structure (Expected > 1000 atoms in the asymmetric unit). Was in the "unsolvable bin" prior to being passed on to the Sirware Group and George Sheldrick): Both Sir2000 and ShelxD programs solved the Cyclodextrin in default modes:

(times are not directly comparable as are different computers)

2D-3D Model Building Software

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

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

Getting Fragments intoDirdif/Dirdif for Windows.

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

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, a Cyclodextrin Fragment)

Single Crystal Structure Refinement

(Applicable to powder diffraction for helping build up the structure)

Range of programs to choose from:

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

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/

DS*SYSTEM/LSBF Refinement

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

NRCVAX

Contact: [email protected]

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

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

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

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

Single Crystal Structure Refinement:

GUI CRYSTALS for Windows:

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

cp_ring <defines and regularized the rigid body>

end

Refine selected atoms as a rigid body.

#list 12

end

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

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)

• Lack of easy to use Fourier Map Generation and viewing using appropriate algorithms such as maximum entropy to clear up the electron density contour maps.

Restrained Rietveld Structure Refinement

(Organics)

Software not as powerful as single crystal but there are some tutorials with tricks on the CCP14 web site:

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

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.

Range of programs to choose from:

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

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/

DS*SYSTEM

ShakePSD, ShakePSDL, Multan for Structure Solution

LSBF for refinement

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

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

Single Crystal Suites (Cont’d)

(Applicable to Powder Diffraction)

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

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/

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: [email protected]

Single Crystal Suite Examples

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.

Multiple Pathways for Structure Solving

Solving in one program – automatic building in another: via Platon/System S

(Cesium Titanium Silicate)

Solve in Shelx86

Use the System S/Platon EXOR function to build up the structure

(also have the other options of using Crunch, Sir and Dirdif to build up the structure).

One oxygen atom left to find (after refining heavy atoms anisotropically). Purple Q peak stands out quite clearly.

Transparently Running the Squeeze Option (that comes with Platon) within WinGX

http://www.cryst.chem.uu.nl/platon/pl000303.html

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.

Graphically Interacting with the Structure

Graphically Interacting with the Structure

Graphically Interacting with the Structure

Graphically Interacting with the Structure

Summary List at:

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

Examples:

(including

VRML output)

WinMPROF (Q peak location)

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:

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)

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:

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

Is trivial to run Addsym routinely via Platon

Another Example of Platon/Addsym

http://www.cryst.chem.uu.nl/platon/pl000401.html

PLATON/ADDSYM analysis of all 1970 Cc structures in the CSD (Apr 1999):

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

PLATON/ADDSYM analysis of all 1848 P1 structures in the CSD (Oct 1999):

http://www.cryst.chem.uu.nl/platon/p1.mis

A Case of subcell symmetry

Originally in P1:

(96 independent Carbon atoms)

9.74832 12.74268 15.70341 99.506 77.047 92.504

Using < 20th Nov 2000 Platon/Addsym

(24 independent Carbon atoms)

7.8517 9.7483 12.7427 87.496 80.494 77.047

Using => 20th Nov 2000 Platon/Addsym

(3 independent Carbon atoms)

5.5375 5.5660 8.0032 90.000 108.177 90.000

Specialist Applications

(Single Crystal and Powder Diffraction)

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

List of Software:

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

Quantitative Phase Analysis

Non-trivial and in many cases, custom solutions may be required. (a complete symposium in itself)Rietveld programs are commonly used for Quantitative Analysis (refer above list).

Maud for Java Quantitative Analysis Tutorial:

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

Refer to non-Rietveld references cited in:

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

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

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/

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

Free UNIX Operating Systems (install off the internet)

Linux

FreeBSD (can run linux binaries)

(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):

(Commercial software)

Freely Available Compilers, GUI Building Kits and Source Code

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)

Summary

E-mail: [email protected]