Table of Contents
Crunching problems into solutions: - freely available crystallographic software for single crystal and powder diffraction.
Aims of the EPSRC funded CCP14 Project
Talk Aims
Notes Free Zone - they are on the web - http://www.ccp14.ac.uk/poster-talks/thai_2002/
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 crystallographic software
Why bother knowing about a variety of modern software? (2 of 4) - Path of Most Resistance
Why bother knowing about freely available software? (4 of 4)
Single Crystal vs Powder diffraction (1 of 6)
Single Crystal vs Powder diffraction (2 of 6)
Single Crystal vs Powder diffraction (3 of 6)
Single Crystal vs Powder diffraction (4 of 6)
Single Crystal vs Powder diffraction (5 of 6)
Single Crystal vs Powder diffraction (6 of 6)
Talk Agenda
Phase Identification/Search Match for Powder Diffraction
Phase Identification/Search Match for Powder Diffraction 2 of 3 - Identifying an organic - DL-Valine
Phase Identification/Search Match for Powder Diffraction 3 of 3 - Multiphase mixture: Flourite, Corundum, Zincite
Has the structure been solved already? - Crystallographic Structure Databases
ICSD via the Web
A hopeful trend: Crystallography Suites that link into the 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
VCT for trace Phase ID (1 of x) Variable Count Time data (displayed as FCT)
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 3) Fixed Count Time
VCT to aid in phase ID and profile fitting (2 of 3) Variable Count Time
VCT to aid in phase ID and profile fitting (3 of 3) Overlaying VCT and FCT
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: GUI Cell transformation
Chekcell: Density / Z / Molecular Volume Explorer
Chekcell: example of using Le Page
Crysfire / Chekcell: indexing powder Protein data
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
Single Crystal Absorption Correction : WinGX
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
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
Single Crystal Structure Solution
Single Crystal Structure Solution - (What’s it like to use the software?)
Shelxs direct methods - (tetracycline hydrochloride) via WinGX as an interface
Sir direct methods and auto Fourier building - (tetracycline hydrochloride) via WinGX as an interface
Dirdif Patterson methods and auto Fourier building - (tetracycline hydrochloride) via WinGX as an interface
Crunch for UNIX direct methods and Fourier building - (tetracycline hydrochloride) via Platon/System S as an interface
2D to 3D model building software
Getting fragments into Dirdif and Patsee for Windows
Single Crystal Structure Refinement Software - (Applicable to powder diffraction for helping build up the structure)
Example of Crystals for Windows
Guided structure refinement using Crystals
Guided structure refinement using Crystals
Guided structure refinement using Crystals Have now refined atom positions Isotropically
Guided structure refinement using Crystals Have now refined atom positions anisotropically
Guided structure refinement using Crystals Automatic Hydrogen Addition
Interrupt the Guided Refinement in Crystals Manual Hydrogen Addition - 1 of 2
Interrupt the Guided Refinement in Crystals Manual Hydrogen Addition - 2 of 2
Interrupt the Guided Refinement in Crystals Generating Fourier maps and Marching Cubes for Windows
Structure refinement using Crystals Validation via Cambridge database: geometry checking
Validation using Crystals Cambridge database geometry check (1 of 4)
Validation using Crystals Cambridge database geometry check (2 of 4)
Validation using Crystals Cambridge database geometry check (3 of 4)
Validation using Crystals Cambridge database geometry check (4 of 4)
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
Rietveld: Rod Hill and Ian Madsen VCT data collection
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 - Families of programs included/linkable with WinGX
WinGX for Windows single crystal suite - Absorption Correction
WinGX for Windows single crystal suite - Structure Solution
WinGX for Windows single crystal suite - Refinement - Shelxl 97
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 - Fourier Electron Density Contour Maps
WinGX for Windows single crystal suite - Structure Plotting
WinGX for Windows single crystal suite - Validation and Structure Checking
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)
Crystal Structure validation - Why Bother?
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
Platon’s Addsym: Correction Published in 1999
Platon’s Addsym: Press of a button: 2000
Platon’s Addsym - (1 of 2) finding extra symmetry in inorganics and minerals - P1 triclinic starting structure.
Platon’s Addsym - (2 of 2) finding extra symmetry in inorganics and minerals - P1 triclinic starting structure.
Platon’s Addsym - - Be wary when using Addsym with Tilt Models
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 Fourier Maps - Marching Cubes by Michal Husak
Dual Boot UNIX / Windows PC and Crystallographic Nexus CD-ROMs for those isolated from the internet
Summary
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