Table of Contents
Freely available crystallographic software for powder diffraction.
Notes Free Zone - they are on the web
Talk Aims
For those new to Crystallography
Using the right crystallographic method can make the difference!
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 9)
Single Crystal vs Powder diffraction (2 of 9)
Single Crystal vs Powder diffraction (3 of 9)
Single Crystal vs Powder diffraction (4 of 9)
Single Crystal vs Powder diffraction (5 of 9)
Single Crystal vs Powder diffraction (6 of 9)
Single Crystal vs Powder diffraction (7 of 9)
Single Crystal vs Powder diffraction (8 of 9)
Single Crystal vs Powder diffraction (9 of 9)
Talk Agenda
Phase Identification/Search Match for Powder Diffraction
Phase Identification/Search Match for Powder Diffraction 2 of 3 Identifying an organic – DL-Valine
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
A hopeful trend: Crystallography Suites that link directly into the crystal structure databases
Powder Data Conversion / Importing Data
Structure Importing, Conversion and Transformation
Powder Sample Preparation and Data Collection
Variable Count Time data collection
VCT Literature References
VCT for trace Phase ID (1 of x) Fixed Count Time data (data collected by Jeremy Cockcroft)
VCT for trace Phase ID (1 of x) Variable Count Time data (displayed as FCT) (data collected by Jeremy Cockcroft)
VCT for trace Phase ID (1 of x) Fixed Count Time data (zoomed)
VCT for trace Phase ID (1 of x) Variable Count Time data (displayed as FCT)
Variable Count Time applications
VCT to aid in phase ID and profile fitting (1 of 2) Fixed Count Time
VCT to aid in phase ID and profile fitting (2 of 2) Variable Count Time
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 (displayed as FCT)
VCT for Structure Solution and Refinement (3 of 4) Variable Count Time data (displayed as FCT)
VCT for Structure Solution and Refinement (4 of 4) Variable Count Time data (displayed as VCT)
Where is VCT Data Collection?
Powder Diffraction Utility Software
Peak Profiling (indexing, unit cell refinement, size/strain, etc)
Powder Indexing - a non trivial endeavour
Powder Indexing - the “Crysfire” suite
Chekcell: Interpreting Crysfire Summary Files: Powder Indexing and Spacegroup Assignment
Chekcell : automatic cell and spacegroup searching
Chekcell: “integration” of Ton Spek and A. Meetsma’s Le Page
Chekcell: example of using Le Page
Crysfire / Chekcell: indexing powder Protein data
Some Alternatives to Crysfire: Winplotr, PowderX
New MCMaille by Armel Le Bail (Sep 2002)
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
“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
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
EXPO direct methods in action (4 of 4) Structure after being solved and auto built
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
2D to 3D model building software
Getting fragments into Dirdif, Patsee for Windows
Single Crystal Structure Refinement Software (Applicable to powder diffraction for helping build up the structure)
Example of Crystals for Windows David Watkin, Richard Cooper, et al.
Guided structure refinement using Crystals
Interrupt the Guided Refinement in Crystals Manual Hydrogen Addition - 1 of 2
Interrupt the Guided Refinement in Crystals Manual Hydrogen Addition - 2 of 2
Structure refinement using Crystals New validation via CCDC Mogul program: local geometry checking
Validation using Crystals Cambridge database local geometry check (2 of 2)
Validation within Rietveld / powder Software
Structure Refinement using Powder Diffraction Data (Rietveld Refinement)
Rietveld Program Interfaces
Rietveld Programs - Rietica by Brett Hunter
Mentioning GSAS Rietveld: Some Relevant Background
GSAS : Solving and refining a protein from powder data
Brian Toby’s EXPGUI Interface for GSAS
Restrained Rietveld structure refinement of organics
Fourier capability in Rietveld Software
Single Crystal Suites (also applicable to powder diffraction)
WinGX for Windows single crystal suite Louis Farrugia
WinGX for Windows single crystal suite Structure Solution
WinGX for Windows single crystal suite Refinement - Shelxl 97 (WinGX now links to Crystals as well)
WinGX for Windows single crystal suite Hydrogen Addition options
WinGX for Windows single crystal suite Easy Interlinking with Ton Spek’s Platon
WinGX for Windows single crystal suite Structure Plotting
Some Specialist Applications
Quantitative Phase Analysis
MAUD for Java : GPL’d (you get the source code)
Quantitative Phase Analysis - is it routinely easy?
Graphically interacting with the structure
Graphically interacting with the structure (more examples)
Platon: Validation - why take an interest?
Structure validation and quality checking
WinGX for Windows single crystal suite Validation and Structure Checking
Platon’s Addsym (by Ton Spek): checking for extra symmetry : e.g., 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
Platon’s Addsym: for powders
Powder diffraction pattern calculation Powder Cell for Windows
owder 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 Using GRETEP by Jean Laugier and Bernard Bochu
Freeware for photorealistic hardcopy output of structures Balls and Sticks by Sung J. Kang & Tadashi C. Ozawa
Photorealistic hardcopy output of Fourier Maps Marching Cubes by Michal Husak
Dual Boot UNIX / Windows PC and Crystallographic Nexus CD-ROMs for those isolated from the internet
Don’t be a “passive kitten”
Summary
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