Table of Contents
An overview of available software for solving crystal structures from powder diffraction
Talk Aims
Notes Free Zone - they are on the web http://www.ccp14.ac.uk/poster-talks/aca_2002a/
The risks of not knowing what you don’t know
Why bother knowing about a variety of crystallographic software
Single Crystal vs Powder diffraction (1 of 6)
Single Crystal vs Powder diffraction (2 of 6)
Single Crystal vs Powder diffraction (2a 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
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 (normalized as FCT)
VCT for Structure Solution and Refinement (3 of 4) Variable Count Time data (normalized 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
Phase Identification/Search Match for Powder Diffraction 2 of 3 - Identifying an organic - DL-Valine
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
Crystallography Suites that link into the structure databases
Powder Data Conversion / Importing Data
Powder Diffraction Utility Software
Peak Profiling for Powder indexing
Peak Profiling: high accuracy peak positions using Fundamental Parameters peak profiling in XFIT
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/ Mol. Vol explorer
Crysfire / Chekcell: indexing powder Protein data
Full Profile Fitting (Powder)
Le Bail full profile fitting - Rietica Rietveld
Materials Analysis Rietveld/Texture Software
"Generic" structure solution from powder diffraction data
"Specialised and Commercial" Structure Solution Programs
Important with realspace programs to input good starting information (too much bad or too little good can put your in a world of "not getting anywhere")
Single Crystal Structure Solution
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)
Using Crystals to help add hydrogens Automatic Hydrogen Addition
Crystals : Manual Hydrogen Addition - 1 of 2
Crystals : Manual Hydrogen Addition - 2 of 2
Structure Refinement using Powder Diffraction Data (Rietveld Refinement)
Rietveld Program Interfaces
Rietveld Programs - Rietica by Brett Hunter
Mentioning GSAS Rietveld: Some Relevant Background
GSAS scales : 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 (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 Structure Solution
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
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)
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) (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 (by Ton Spek): 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 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
Dual Boot UNIX / Windows PC and Crystallographic Nexus CD-ROMs for those isolated from the internet
Summary
|