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 earth’s other core
The risks of not knowing what you don’t 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. Meetsma’s Le Page
Chekcell: GUI Cell transformation
Chekcell: Density / Z / Molecular Volume Explorer
Chekcell: example of using Le Page
Why doesn’t 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 (What’s 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 Toby’s 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 Spek’s 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
Platon’s Addsym (by Ton Spek) (finding missing symmetry): Structure Published in 1997 P1 - Triclinic: 42 non-H atoms
Platon’s Addsym: Correction Published in 1999: C2 - Monoclinic: 22 non-H atoms
Platon’s Addsym: Press of a button: 2000: FDD2 - Orthorhombic: 11 non-H atoms (Short Communication Abstract: "P1 or P-1? Corrigendum", Acta Cryst B56 (2000) 744 from Richard E. Marsh)
Platon’s Addsym - finding extra symmetry in inorganics and minerals - P1 triclinic starting structure
Platon’s 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
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