Table of Contents
Re-stating the obvious: To solve structures from powder diffraction, first they must be indexed!
Based on a co-authored presentation at the ACA 2002 conference in San-Antonio, Texas, USA
Notes Free Zone - they are on the web
Talk Aims
Some History of Powder Indexing
Some History of Powder Indexing - 2
Some History of Powder Indexing - 3
Checking Sample Purity
Peak Profiling Software
Empirical peak fitting : Some tricks may be required for stability and reasonable results
Peak Profiling: high accuracy peak positions using Fundamental Parameters peak profiling
XFIT Fundamental Parameters Peak Profiling mode : fit to a low angle peak on a Bragg-Brentano diffractometer
Powder Indexing FOM Results XFIT Fundamental Parameters peak profiling compared to empirical Peak Fitting
Powder Indexing - indexing programs
Powder Indexing - indexing suites
Powder Indexing - specialist programs
Powder Indexing - specialist programs
Powder Indexing - Using PowderX
Powder Indexing - Using Winplotr
Powder Indexing - the Crysfire suite (1)
Powder Indexing - the Crysfire suite (2)
Powder Indexing - the Crysfire suite (3)
New Release - Crysfire 2002
Why bother running more than one powder indexing program?
Powder Indexing - Routine Crysfire Example Run crysfire
Powder Indexing - Routine Crysfire Example Importing an XFIT peak file using the IM (Import command)
Powder Indexing - Routine Crysfire Example “lo” to load a CDT file estimate of expected unit cell volume is given
Powder Indexing - Routine Crysfire Example “in” to target an indexing program
Powder Indexing - Routine Crysfire Example target ITO with defaults
Powder Indexing - Routine Crysfire Example ITO runs
Powder Indexing - Routine Crysfire Example After Ito completes, press enter to see output file
Powder Indexing - Routine Crysfire Example Then “enter” again to see “one solution per line” summary
Powder Indexing - Routine Crysfire Example “Enter” again to see Le Page summary of reduced cells
Powder Indexing - Routine Crysfire Example
Powder Indexing - Routine Crysfire Example Finally: the complete summary file - 3332 trial solutions
Powder Indexing - Routine Crysfire Example Complete Le Page summary file of reduced cells - 3332 trial solutions
Crysfire Self Calibration Bragg-Bretano Data
Crysfire Self Calibration Example
Crysfire Rescaling
Crysfire Re-scaling Protein Data (from Bob von Dreele)
Crysfire Rescaling example Inorganic - on opening : Crysfire suggests rescaling
Ignoring the rescaling suggestion No obvious solutions
RS is the Rescale Command Crysfire will automatically change the filename and title
After running the indexing programs: MS, then U to unscale the summary file
Indexing using the suggested rescaling of 0.5 An obvious cubic (23.923 A) solution found by Taup
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 (Crysfire 2001 now also provides a reduced-cell summary)
Chekcell: GUI Cell transformation
Chekcell: Density / Z/ Mol. Vol explorer
Chekcell: example of it running Load the raw diffraction data
Chekcell: example of it running Load the peak position file
Chekcell: example of it running Load the Crysfire summary file
Chekcell: example of it running Use the tools to evaluate the trial cells
Crysfire / Chekcell: indexing powder Protein data
Crysfire / Chekcell: indexing powder Protein data
MMAP
MMAP - what does the output look like?
MMAP - what does the output look like?
MMAP
MMAP - which of these objects is man made? Using peak height as the selection criteria.
MMAP - which of these peaks is man made? 2
Analogous problem with powder indexing
An Mmap landscape
Mmap
Mmap
Mmap : Is the following a good solution?
Mmap : Yes looks a good solution
Mmap : Is the following a good solution?
Mmap
Mmap: Is the following a good solution?
Mmap
Mmap
MCMaile by Armel Le Bail
A MCMaile ASCII input file
MCMaile is running
MCMaile output files
MCMaile : on large cubic
MCMaile : on large cubic
SDPDRR-II (Structure Determination by Powder Diffractometry Round Robin - 2 )
SDPDRR-II - Indexing Results
SDPDRR-II - Sample 1
SDPDRR-II - Sample 2
SDPDRR-II - Sample 3
SDPDRR-II - Sample 3 Tetragonal or Cubic?
SDPDRR-II - Sample 3: Tetragonal: 1 peak unmatched - 46 hkl’s (P42MC et al) to match 25 reflections
SDPDRR-II - Sample 3: Tetragonal: Running LePage shows a cubic cell (18.885Å)
SDPDRR-II - Sample 3: Visual inspection of cubic cell implies “bad”peak could still be an impurity
SDPDRR-II - Sample 3: Cubic: 37 hkl’s to match 25 reflections (I23 et al) (vs 46 hkl’s in tetragonal)
SDPDRR-II - Samples 4 to 8
Be on the lookout for bugs in the Software! Found in LePage - within Chekcell
The Future
Conclusion
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