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"Improving the odds with your X-ray and neutron diffraction data : freely available state-of-the-art crystallographic software for mineralogists via the internet"

by Lachlan M. D. Cranswick (CCP14 Project Secretary, UK)

For presentation at AGU 2002 workshop - National Museum of Natural History, Smithsonian Institution, Washington D.C., USA, Thursday 30th May 2002; 1:00PM

[AGU 2002, Washington D.C., USA]

This page is located at http://www.ccp14.ac.uk/poster-talks/aca_2002a/


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Table of Contents

Improving the odds with your X-ray and neutron diffraction data : freely available state-of-the-art crystallographic software for mineralogists via the internet

Notes Free Zone - they are on the web http://www.ccp14.ac.uk/poster-talks/agu_2002a/

Talk Aims

For those new to Crystallography

Using the right crystallographic method can make the difference!

Le Bail fitting: results of the volume of Oxygen and the earthís other core

The risks of not knowing what you donít know

Why bother knowing about a variety of modern software? (1 of 2)

Why bother knowing about freely available software? (2 of 2)

Single Crystal vs Powder diffraction (1 of 8)

Single Crystal vs Powder diffraction (2 of 8)

Single Crystal vs Powder diffraction (3 of 8)

Single Crystal vs Powder diffraction (4 of 8)

Single Crystal vs Powder diffraction (5 of 8)

Single Crystal vs Powder diffraction (6 of 8)

Single Crystal vs Powder diffraction (7 of 8)

Single Crystal vs Powder diffraction (8 of 8)

Talk Agenda

Sample Preparation and Data Collection

Variable Count Time data collection

VCT Literature References

VCT for Powder Indexing (1 of 4) Fixed Count Time data (data collected by Jeremy Cockcroft)

VCT for Powder Indexing (2 of 4) Variable Count Time data (normalized as FCT) (data collected by Jeremy Cockcroft)

VCT for Powder Indexing (3 of 4) Fixed Count Time data (zoomed) This peak position is not going to be very precise

VCT for Powder Indexing (3 of 4) Variable Count Time data (zoomed) This "trace" peak position will be more precise

VCT for Structure Solution and Refinement (1 of 4) Variable Count Time data (as collected)

VCT for Structure Solution and Refinement (2 of 4) Variable Count Time data (normalised as FCT)

VCT for Structure Solution and Refinement (3 of 4) Variable Count Time data (normalised as FCT)

VCT for Structure Solution and Refinement (4 of 4) Variable Count Time data (displayed as VCT)

Where is VCT Data Collection?

Phase Identification/Search Match for Powder Diffraction

Find out which software, databases and methods work the best: Search Match Round Robin (2nd May 2002 to 30th June 2002): http://sdpd.univ-lemans.fr/smrr/ and CCP14 mirrors

Has the structure been solved already? Crystallographic Structure Databases

ICSD via the Web

Powder Data Conversion / Importing Data

Structure Importing, Conversion and Transformation

Powder Diffraction Utility Software

Peak Profiling for Powder indexing

Fundamental Parameters Peak Profiling mode : fit to a low angle peak : Bragg-Brentano diffractometer data

Powder Indexing FOM Results XFIT Fundamental Parameters peak profiling compared to empirical Peak Fitting

Powder Indexing - a non trivial endeavour

Powder Indexing - the "Crysfire" suite

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

Chekcell : easy to see non-matching or impurity peaks

Chekcell : automatic cell and spacegroup searching

Chekcell: "integration" of Ton Spek and A. Meetsmaís Le Page

Chekcell: GUI Cell transformation

Chekcell: Density / Z / Molecular Volume Explorer

Chekcell: example of using Le Page

Why doesnít this powder sample index?

Some Alternatives to Crysfire: Winplotr, PowderX

Unit Cell Refinement (powders)

CELREF for Unit Cell Refinement

Full Profile Fitting (Powder)

Le Bail full profile fitting - Rietica Rietveld

Le Bail full profile fitting - Rietica Rietveld - 2 of 2

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

Materials Analysis Rietveld/Texture Software

Single Crystal Absorption Correction Options

Platon options for absorption correction

Single Crystal Indexing / Twinning

ROTAX Single Crystal Twinning Software

"Generic" structure solution from powder diffraction data

"Specialised and Commercial" Structure Solution Programs

EXPO direct methods in Action (1 of 4) Edit the input / control file - inorganic

EXPO direct methods in action (2 of 4) Click on the OK button to start

EXPO direct methods in action (3 of 4) Le Bail fitting of the powder pattern (not the full range of data as high angle data can be just noise and spoil the direct methods)

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

Important with realspace programs to input good starting information (too much bad or too little good can put you in a world of not getting anywhere fast)

New FOX real space structure solution by Vincent Favre-Nicolin and Radovan Cerny

Adding polyhedra in Fox - 1 of 5

Adding polyhedra in Fox - 2 of 5

Adding polyhedra in Fox - 3 of 5

Adding polyhedra in Fox - 4 of 5

Adding polyhedra in Fox - 5 of 5

Single Crystal Structure Solution

Single Crystal Structure Solution (Whatís it like to use the software?)

Shelxs direct methods (Cesium Titanium Silicate) via WinGX as an interface

Sir97 direct methods with auto-building (Cesium Titanium Silicate) via WinGX as an interface (in this case - first try does not solve - just leave Sir97 to automatically continue on)

Dirdif automatic Patterson methods (Cesium Titanium Silicate) via WinGX as an interface (solves and auto-builds in default mode - all atoms correctly found and labelled)

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

Single Crystal Structure Refinement Software JANA Single Crystal and Powder Diffraction Refinement

Structure Refinement using Powder Diffraction Data (Rietveld Refinement)

Rietveld Program Interfaces

Rietveld Programs - Rietica by Brett Hunter

Mentioning GSAS Rietveld: Some Relevant Background

Brian Tobyís EXPGUI Interface for GSAS

Restrained Rietveld structure refinement of organics

Fourier capability in Rietveld Software

Single Crystal Suites (applicable to powder diffraction)

WinGX for Windows single crystal suite Louis Farrugia: http://www.chem.gla.ac.uk/~louis/software/

WinGX for Windows single crystal suite Families of programs included/linkable with WinGX

WinGX for Windows single crystal suite Viewing the raw CCD frames and raw profile data

WinGX for Windows single crystal suite Structure Solution

WinGX for Windows single crystal suite Absorption Correction

WinGX for Windows single crystal suite Refinement - Shelxl 97 (WinGX now links to Crystals as well)

WinGX for Windows single crystal suite Fourier Electron Density Contour Maps

WinGX for Windows single crystal suite Easy Interlinking with Ton Spekís Platon

WinGX for Windows single crystal suite Structure Plotting

WinGX for Windows single crystal suite Validation and Structure Checking

Graphically interacting with the structure

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

Some Specialist Applications

Platon: Validation - why taking an interest?

Structure validation and quality checking

WinGX for Windows single crystal suite Validation and Structure Checking

Platonís Addsym (by Ton Spek) (finding missing symmetry): Structure Published in 1997 P1 - Triclinic: 42 non-H atoms

Platonís Addsym: Correction Published in 1999: C2 - Monoclinic: 22 non-H atoms

Platonís Addsym: Press of a button: 2000: FDD2 - Orthorhombic: 11 non-H atoms (Short Communication Abstract: "P1 or P-1? Corrigendum", Acta Cryst B56 (2000) 744 from Richard E. Marsh)

Platonís Addsym - finding extra symmetry in inorganics and minerals - P1 triclinic starting structure

Platonís Addsym: for powders

Powder diffraction pattern calculation Powder Cell for Windows

Powder diffraction pattern calculation Poudrix for Windows

Photorealistic hardcopy output of structures

Photorealistic hardcopy output of structures GUI WinORTEP / GUI Struplo / WinGX

Photorealistic hardcopy output of structures Balls and Sticks - Polyhedral, etc

Photorealistic hardcopy output of Fourier Maps Marching Cubes by Michal Husak (http://www.ccp14.ac.uk/tutorial/marchingcube/)

Dual Boot UNIX / Windows PC and Crystallographic Nexus CD-ROMs for those isolated from the internet

Summary

Author: Lachlan Cranswick

Email: l.m.d.cranswick@dl.ac.uk

Home Page: http://www.ccp14.ac.uk

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