Transcript Re-stating the obvious: To solve structures from powder

Re-stating the obvious: To solve
structures from powder diffraction,
first they must be indexed!
Lachlan M. D. Cranswick
CCP14 (Collaborative Computation Project No 14 for
Single Crystal and Powder Diffraction)
Department of Crystallography;
Birkbeck College, University of London,
Malet Street, Bloomsbury, London, WC1E 7HX, UK.
E-mail: [email protected]
WWW: http://www.ccp14.ac.uk
Based on a co-authored presentation
at the ACA 2002 conference in SanAntonio, Texas, USA
Lachlan M. D. Cranswick
Robin Shirley
CCP14 (Collaborative Computation Project No 14 for
Single Crystal and Powder Diffraction)
Department of Crystallography;
Birkbeck College, University of London,
Malet Street, Bloomsbury, London, WC1E 7HX, UK.
E-mail: [email protected]
WWW: http://www.ccp14.ac.uk
School of Human Sciences
University of Surrey
Guildford, Surrey, GU2 7XH, U.K.
Tel: (+44) 01483 686864
Fax: (+44) 01483 259553
E-mail: [email protected]
Talk Aims
• Some history of Indexing of Powder Diffraction Data
• Peak finding and peak profiling software
• Fundamental Parameters Peak Fitting
• Available powder indexing software and indexing suites
• Crysfire in action
• Chekcell in action
• MCMaille by Armel Le Bail (released Sep 2002)
• Possibilities for the future and conclusion
Slide 3
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Some History of Powder Indexing
• First published manual powder indexing method:
– Runge, C. (1917), "Die Bestimmung eines Kristallsystems durch
Rontgenstrahlen", Physik. Z., 18, 509-515.
• Candidates for first published computer based powder indexing
– Haendler, H. M. & Cooney, W. A. (1963), "Computer Determination of Unit-Cell
from Powder-Diffraction Data", Acta Cryst., 16, 1243-1248.
– Lefker, R. (1964), "Indexing of tetragonal and hexagonal X-ray powder
photographs with the aid of a small computer", Anal. Chem., 36, 332-334.
Slide 4
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Some History of Powder Indexing - 2
•Candidates for first published publicly available powder-indexing
program
– Haendler, H. M. & Cooney, W. A. (1963), "Computer Determination of Unit-Cell
from Powder-Diffraction Data", Acta Cryst., 16, 1243-1248.
– Lefker, R. (1964), "Indexing of tetragonal and hexagonal X-ray powder photographs
with the aid of a small computer", Anal. Chem., 36, 332-334.
– Werner, P.-E. (1964), "Trial and error computer methods for the indexing of
unknown powder patterns", Z. Krist., 120, 375-387.
– Hoff, W. D. & Kitchingman, W. J. (1966), "Computer indexing of x-ray powder
patterns from crystals of unknown structures", J. Sci. Instrum., 43, 952-953.
Slide 5
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Some History of Powder Indexing - 3
•Candidates for first publically available general indexing program
– Ishida, T & Watanabe, Y. (1967), "Probability Computer Method of Determining the
Lattice Parameters from Powder Diffraction Data", J. Phys. Soc. Japan, 23, 556-565.
– Roof, R. B. (1968), "INDX: A Computer Program to Aid in the Indexing of X-Ray
Powder Patterns of Crystal Structures of Unknown Symmetry", Los Alamos
Laboratory, University of California, Report LA-3920.
– Taupin, D. (1968), "Une Methode Generale pour l'Indexation des Diagrammes de
Poudres", J. Appl. Cryst., 1, 178-181.
– Visser, J. W. (1969), "A Fully Automatic Program for Finding the Unit Cell from
Powder Data", J. Appl. Cryst., 2, 89-95.
Slide 6
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Checking Sample Purity
• Powder indexing requires line-position data of the highest available
quality
• An important aspect of this is purity, since indexing programs don’t like
to struggle with impurity lines, and several will not accept them at all.
• Some suggestions from Robin for checking sample purity:
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Optical (polarising) microscope
Density analysis in a gradient column
Electron microscopy and diffraction of selected crystallites
And, if time permits, see whether properties are changing with time
Slide 7
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Peak Profiling Software
•For Overall Summary of available peak profiling software refer to:
http://www.ccp14.ac.uk/solution/peakprofiling/
•Some of the available freeware includes:
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CMPR
DRXWin
EFLECH
GPLSFT
pearson.xls
Rawplot (with GSAS)
SHADOW
Powder v2.00
PowderX
Winfit
Winplotr (with Fullprof)
XFIT
Slide 8
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Empirical peak fitting :
Some tricks may be required for stability and reasonable results
• Peaks over small ranges may
have to be linked to have the
same shape and width
• Usually fit small ranges of data
- groups of peaks
• Might have to fit large and
medium peaks first, followed
by trace peaks
Slide 9
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Peak Profiling: high accuracy peak positions using Fundamental
Parameters peak profiling
•Example of Fundamental parameters (convoluting in the geometry elements of the
diffractometer) that can provide accurate peak positions as though your sample was
being run on an “ideal” diffractometer.
•Tutorial at:
– http://www.ccp14.ac.uk/tutorial/xfit-95/fun1.htm
•Available Fundamental Parameters Peak Profiling and Rietveld software:
•XFIT (no longer maintained)
– http://www.ccp14.ac.uk/tutorial/xfit-95/xfit.htm
•Topas (Commercial - sequel to XFIT)
– http://www.bruker.com
•BGMN (Commercial - academic demonstration version is freely downloadable)
– http://www.bgmn.de
•EFLECH/Index freeware from BGMN website
– http://www.bgmn.de/related.html
Slide 10
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
XFIT Fundamental Parameters Peak Profiling mode :
fit to a low angle peak on a Bragg-Brentano diffractometer
Slide 11
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing FOM Results
XFIT Fundamental Parameters peak profiling compared to
empirical Peak Fitting
Slide 12
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - indexing programs
• Overall Summary of available powder indexing software refer to:
http://www.ccp14.ac.uk/solution/indexing/
• Powder Indexing:
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Classic (widely used): Ito, Dicvol, Treor
High symmetry (exhaustive): Taup (=Powder), Dicvol
Other powerful (general symmetry): Lzon, Kohl (=TMO), Fjzn
Dominant-zone cases: Lzon, Losh, Mmap
Semi-automatic (via SIW basis set): Losh, Mmap
Fundamental parameters & covariance matrix: EFLECH/Index
Incommensurate, etc: Supercell
Monte Carlo / Random search: EFLECH/Index, McMaille
Others (better with some user guidance): Scanix, Autox
Slide 13
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - indexing suites
• Overall Summary of available powder indexing software refer to:
http://www.ccp14.ac.uk/solution/indexing/
• Integrated Suites:
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Crysfire
Powder v2.00
PowderX
PROSZKI
WinPlotr
• and after primary indexing:
– Chekcell
Slide 14
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - specialist programs
• Supercel is a specialised indexing program by Juan Rodriguez-Carvajal for
tackling incommensurate cells and super/sub-cell relationships. (available
within Winplotr/Fullprof)
Web: http://www-llb.cea.fr/winplotr/winplotr.htm
FTP: ftp://bali.saclay.cea.fr/pub/divers/fullprof.2k/
Slide 15
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - specialist programs
• McMaille reconstitutes a peak listing into a full profile and performs
monte carlo based searching for good cells. Because it is Monte Carlo
based it can be very slow, but due to it being whole profile, can be
insensitive to trace impurity peaks.
Web: http://www.cristal.org/McMaille/
Slide 16
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Using PowderX
– by Cheng Dong
– http://www.ccp14.ac.uk/tutorial/powderx/
• Peak finding
• Links to Treor
Slide 17
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Using Winplotr
– by Juan Rodriguez-Carvajal and T. Roisnel http://wwwllb.cea.fr/fullweb/powder.htm
• Peak finding / profiling
• Links to
– WinTreor,
– Windicvol,
– Winito and
– supercell
Slide 18
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - the Crysfire suite (1)
– by Robin Shirley (+ many contributing authors)
– http://www.ccp14.ac.uk/tutorial/crys/
• Intelligent defaults for control-parameters when launching
each indexing program
• Data rescaling for tackling high-volume cells from
macromolecular samples and zeolites
• Integrated under a common interface for use by nonspecialists
Slide 19
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - the Crysfire suite (2)
• Principal Contributors:
• Franz Kohlbeck (Kohl [=TMO])
• Daniel Louër (Dicvol, Lzon, Losh)
• Robin Shirley (Overall + Mmap, Lzon, Losh, Fjzn, etc)
• Ton Spek & A.Meetsma (Lepage)
• Daniel Taupin (Taup [=Powder])
• Jan Visser (Ito, Fjzn, Lzon, etc)
• Per-Eric Werner (Treor)
Slide 20
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - the Crysfire suite (3)
Crysfire 2000: 8 different indexing programs
(Ito, Dicvol, Treor, Taup, Kohl, Lzon, Fjzn, Losh)
• It’s good to have a wide variety of methods available:
– to cater for different types of problem
– to give a feel for the range of solutions out there
– and see which ones turn up repeatedly using different methods,
either identically or as derivative cells
Slide 21
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
New Release - Crysfire 2002
August 2002
Now 9 indexing programs:
Ito, Dicvol, Treor, Taup, Kohl, Lzon, Fjzn, Losh, Mmap
• New features:
• Mmap for exploring solution-space and evaluating trial cells
• Le Page/Niggli reduced-cell summary
• Greater ease of use, especially for first-time users
• Better resilience, especially under the Windows/NT family
(master program totally rewritten)
Slide 22
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Why bother running more than one powder
indexing program?
• Maximize the possibility of indexing unknowns by
taking advantage of different algorithms and different
program implementations.
Slide 23
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Routine Crysfire Example
Run crysfire (giving the following screen)
Slide 24
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Routine Crysfire Example
Importing an XFIT peak file using the IM (Import command)
Slide 25
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Routine Crysfire Example
“lo” to load a CDT file
estimate of expected unit cell volume is given
Slide 26
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Routine Crysfire Example
“in” to target an indexing program
Slide 27
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Routine Crysfire Example
target ITO with defaults
Slide 28
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Routine Crysfire Example
ITO runs
Slide 29
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Routine Crysfire Example
After Ito completes, press enter to see output file
Slide 30
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Routine Crysfire Example
Then “enter” again to see “one solution per line” summary
Slide 31
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Routine Crysfire Example
“Enter” again to see Le Page summary of reduced cells
Slide 32
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Routine Crysfire Example
•Repeat the sequence to run the remaining relevant indexing
programs. Recommended sequence is actually:
– Taup, Dicvol high sym, Ito, FJZN, Treor, Kohl, Dicvol low sym, Lzon
– in to select and launch an indexing program
– look at the output file
– look at the summary file
– look at the Le Page summary file of reduced cells
– repeat
Slide 33
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Routine Crysfire Example
Finally: the complete summary file - 3332 trial solutions
Slide 34
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Routine Crysfire Example
Complete Le Page summary file of reduced cells - 3332 trial solutions
Slide 35
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Crysfire Self Calibration
Bragg-Bretano Data
• Sometimes it’s hard to be sure how far the beam is penetrating
into the sample, giving an unknown sample-displacement error
• This can be addressed by trying self-calibration (SC)
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If indexing the uncorrected data has failed, try SC
Select T (for specimen-displacement correction ratio)
A list of candidates for T will be displayed, based on 1st/2nd-order line pairs
If a particular ratio comes up several times and looks plausible, adopt it
Save it (SA) in Crysfire format under a new name, so that it can be reloaded
Do another cycle of indexing runs, this time with the “corrected” data
Slide 36
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Crysfire Self Calibration Example
• Self calibration output of an organometallic sample in
histogram format
Slide 37
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Crysfire Rescaling
• Most indexing program have evolved using a range of data
with solutions between 500 and 1500
• If you have cells outside this range, many indexing programs
can fail
• A possible solution to still index large cells it to rescale the
data by changing the wavelength
Slide 38
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Input for
RAWPLOT:
(1.15006 Å)
1.168100
1.656041
1.852174
1.918506
2.089703
2.345176
2.536523
2.623267
2.916919
2.992132
3.144491
3.319995
3.419907
3.458655
3.522905
3.564255
3.660448
3.712916
3.838720
3.933115
4.098415
4.151839
4.187484
4.234265
Crysfire Re-scaling
Protein Data (from Bob von Dreele)
Lysozyme – single peak fits for 24 reflections :
Rescale factor = 0.1
Rescaled cell = a of ~7.9Å and c of ~3.8Å
Unscaled cell = a of ~79Å and c of ~38Å
Slide 39
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Crysfire Rescaling example
Inorganic - on opening : Crysfire suggests rescaling
Slide 40
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Ignoring the rescaling suggestion
No obvious solutions
Slide 41
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
RS is the Rescale Command
Crysfire will automatically change the filename and title
Slide 42
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
After running the indexing programs:
MS, then U to unscale the summary file
Slide 43
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Indexing using the suggested rescaling of 0.5
An obvious cubic (23.923 A) solution found by Taup
Slide 44
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Chekcell: Interpreting Crysfire Summary Files:
Powder Indexing and Spacegroup Assignment
•Crysfire interlinks with Chekcell for Windows (part of the LMGP suite for Windows by Jean
Laugier and Bernard Bochu). Chekcell provides a graphical interface for manually and
automatically suggesting a best cell/spacegroup combination using both FOM and algorithms
relating to parsimony of superfluous HKLs.
http://www.ccp14.ac.uk/tutorial/lmgp/
Slide 45
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Chekcell : easy to see non-matching or impurity peaks
Slide 46
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Chekcell : automatic cell and spacegroup searching
can trudge through a
single selected unitcell;
or over 1000s of trial
cells looking for the
best cell and
spacegroup
combination based on
parsimony of extra
reflections criteria.
Slide 47
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Chekcell: “integration” of Ton Spek and A. Meetsma’s Le Page
(Crysfire 2001 now also provides a reduced-cell summary)
•Obtaining the Reduced Cell
– which in the past many powder indexing
programs have not determined either reliably
or at all
– Refer: "'Reduced Cells', M.J. Buerger,
(Zeitschift fur Kristallographie, BD 109, S.
42-60 (1957)”
– Crysfire 2001 gives a LePage overview
Chekcell displays a fuller analysis
•Efficient Sub-cell and super-cell
searching, then easy reviewing of
newly derived cells within the
Chekcell interface
Slide 48
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Chekcell: GUI Cell transformation
•Easily transform cells and test them withing Chekcell
•Knows about common transformations
•Can manually look at sub-cells and super-cells
Slide 49
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Chekcell: Density / Z/ Mol. Vol explorer
• Easily explore values of Z, density and estimated molecular volume - comparing
with your found trial cells.
Slide 50
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Chekcell: example of it running
Load the raw diffraction data
Slide 51
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Chekcell: example of it running
Load the peak position file
Slide 52
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Chekcell: example of it running
Load the Crysfire summary file
Slide 53
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Chekcell: example of it running
Use the tools to evaluate the trial cells
Slide 54
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Crysfire / Chekcell: indexing powder Protein data
Using the “Lepage”
feature in Chekcell
Can find the correct
rhombohedral cell as published
in:
•R. B. Von Dreele, P. W. Stephens, G. D.
Smith and R. H. Blessing, "The first protein
crystal structure determined from highresolution X-ray powder diffraction data: a
variant of T3R3 human insulin-zinc
complex produced by grinding", Acta Cryst.
(2000). D56, 1549-1553.
Slide 55
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Crysfire / Chekcell: indexing powder Protein data
Even on rescaled data, if Crysfire and the various indexing
programs do not find the “true cell”, Chekcell and possibly can
find a derivative cell which LePage (combined with Chekcell’s
“parsimony and superflous reflections” criteria), can find the true
cell. In the case of reindexing of the protein data:
– Crysfire and Dicvol finds
• 73.2645 70.5256 40.7430 90.000 90.000 90.000 Orthorhomic
– P222 or PMM2 or PMMM : 157 hkls to match 41 reflections
– LePage followed by Chekcell “parsimony check” then finds:
• 81.449 81.449 73.265 90 .000 90.000 120.00 Hexagonal setting
• 52.988 52.988 52.988 100.45 100.45 100.45 Rhombohedral
– R-3 or R3 etc : 60 hkls to match 41 reflections
Slide 56
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
MMAP
• Mmap explores sections of solution-space (e.g. sections with varying alpha* and
beta*, holding the other 4 parameters constant)
• The results are displayed as a map, with the high-ground colored
• It lists all the peaks in the map and refines them - each is a trial solution
• So it can act as an indexing program in its own right (taking the basis set
containing the first 4 constants from Lzon’s output)
• This offers another way to search for trial cells
• Use the new “LC” (Load a trial cell from the Crysfire summary file) to then run
MMAP (using the MM command) on it.
Slide 57
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
MMAP - what does the output look like?
Example MMap thumbnail output from a high FOM trial cell
Slide 58
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
MMAP - what does the output look like?
Example MMap output from a high FOM trial cell
Slide 59
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
MCMaile by Armel Le Bail
 Developed in September 2002 (on from the ESPOIR code)
 GPL’d (free and you get the source code)
 Whole profile Monte Carlo and Grid Search methods using a
pattern reconstituted from the peak list
 Columnar peak shape - can increase/decrease width
 Can make “important” trace peaks more likely to be part of a
solution by increasing their intensities.
 Insensitive to impurity peaks
 20,000 tests per second - but can still take many hours
 Thus a method of last resort
Slide 60
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
A MCMaile ASCII input file
Slide 61
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
MCMaile is running
Slide 62
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
MCMaile output files
 Chekcell *.ckm summary file of all trial cells and Fullprof
PRF profile file of top solution: viewable in Winplotr
Slide 63
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
MCMaile : on large cubic
 Finds cubic cell easily - even with trace “impurity” peaks
 Via outputted Chekcell *.ckm summary file. Top solution is
not correct solution (possible effect of impurity peaks)
Slide 64
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
MCMaile : on large cubic
 Finds cubic cell easily - even with trace “impurity” peaks
 Via outputted Chekcell *.ckm summary file. Second set of
solutions is correct
Slide 65
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
SDPDRR-II
(Structure Determination by Powder Diffractometry Round Robin - 2 )
 WWW: http://www.cristal.org/sdpdrr2/
 Started: Monday 9th September
 Part 1 (powder indexing):
 Start: Monday 9th September
 Finish: Sunday 13th October
 8 samples
 1 - 3 : Powder indexing and structure solution
 4 - 8 : Powder Indexing only
 > 100 downloads of the data (samples 1 to 3)
Slide 66
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
SDPDRR-II - Indexing Results
 WWW: http://sdpd.univ-lemans.fr/sdpdrr2/results/
 6 returns/100 downloads = 6% return rate
Slide 67
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
SDPDRR-II - Sample 1
 WWW: http://sdpd.univ-lemans.fr/sdpdrr2/results/
 Organisers: 10.323 7.395 8.535 90 91.29 90
 Reduced cell: 7.395 8.535 10.323 91.29 90.00 90.00
 P1:
 P2:
 P3:
10.318 7.393 8.527 90 91.3 90
10.321 7.392 13.236 90 139.90 90
10.322 14.787 8.529 90 91.35 90
 Reduced cell: 8.529 10.322 14.787 90.00 90.00 91.30
 P4:
 P5:
 P6:
No solution
8.523 10.327 7.397 90 90 91.34
8.525 7.394 13.230 90 128.748 90
Slide 68
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
SDPDRR-II - Sample 2
 WWW: http://sdpd.univ-lemans.fr/sdpdrr2/results/
 Organisers: 11.239 8.194 19.943 90 106.727 90
 Reduced cell: 8.194 11.239 19.875 106.06 90.00 90.00
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P1:
P2:
P3:
P4:
P5:
P6:
19.880 8.195 11.242 90 106.06 90
11.242 8.195 19.948 90 106.72 90
19.878 8.193 11.240 90 106.06 90
19.880 8.194 11.243 90 106.06 90
11.244 19.882 8.196 90 90 106.06
11.243 8.195 19.949 90 106.72 90
Slide 69
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
SDPDRR-II - Sample 3
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WWW: http://sdpd.univ-lemans.fr/sdpdrr2/results/
Organisers: 18.881 18.881 18.881 90 90 90 (vol 6734Å3)
P1:
13.349 13.349 9.439 90 90 90 (Tet - 1638Å3)
P2:
18.878 18.878 18.878 90 90 90
P3:
13.354 13.354 9.442 90 90 90 (Tet - 1638Å3)
P4:
No Solution
P5:
18.878 18.878 18.878 90 90 90
P6:
18.88 18.88 18.88 90 90 90
Slide 70
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
SDPDRR-II - Sample 3
Tetragonal or Cubic?
 2 participants (1 and 3) obtained the same tetragonal cell
instead of the correct cubic.
 Possibly due to default volume restrictions in the programs
used(?)
 What happens if you run LePage (via Chekcell) followed
by a “parsimony of extra reflections” check on the
tetragonal solution
Slide 71
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
SDPDRR-II - Sample 3: Tetragonal:
1 peak unmatched - 46 hkl’s (P42MC et al) to match 25 reflections
Slide 72
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
SDPDRR-II - Sample 3: Tetragonal:
Running LePage shows a cubic cell (18.885Å)
Slide 73
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
SDPDRR-II - Sample 3:
Visual inspection of cubic cell implies “bad”peak could still be an impurity
Slide 74
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
SDPDRR-II - Sample 3: Cubic:
37 hkl’s to match 25 reflections (I23 et al) (vs 46 hkl’s in tetragonal)
Slide 75
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
SDPDRR-II - Samples 4 to 8
 WWW: http://sdpd.univ-lemans.fr/sdpdrr2/results/
 Only one response - using the EFLECH/Index software of
Joerg Bergmann (http://www.bgmn.de/related.html)
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S4:
S5:
S6:
S7:
S8:
none suggested
6.011 16.937 18.229 90 90 92.19
none suggested
4.417 11.479 17.126 77.87 85.09 82.67
3.796 9.368 28.915 90 90 90
 Summary: Powder indexing is not easy and not routine!
Slide 76
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Be on the lookout for bugs in the Software!
Found in LePage - within Chekcell
Slide 77
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
The Future
 The message has got through that indexing has become a
bottleneck for solving structures from powder diffraction
data.
 New Indexing programs are being developed.
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MCMaille (Free GPL’d - get the source code as well)
Bruker SVD Indexing (commercial)
Accerlys Indexing program (commercial)
EFLECH/Index (new developments due to the SDPDRR-2)
Slide 78
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Conclusion
 Don’t give up if your lab’s favorite indexing program doesn’t
work on a particular dataset
 Suites like Crysfire offer a wide range of indexing tools
 Follow on with Chekcell to help pin down the correct
physical cell
 If that does not work - whole profile methods such as
MCMaille (still using Chekcell to evaluate trial solutions)
• Relevant web links:
• CCP14 Summary Page: http://www.ccp14.ac.uk/solution/indexing/
– Crysfire: http://www.ccp14.ac.uk/tutorial/crys/
– Chekcell: http://www.ccp14.ac.uk/tutorial/lmgp/
– McMaille: http://www.cristal.org/McMaille/
Slide 79
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk