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
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]
Notes Free Zone - they are on the web
http://www.ccp14.ac.uk/poster-talks/aca_2002b/
Slide 2
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
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
• Mmap with Crysfire 2002 (NEW!!!!)
• 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.
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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.
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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
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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
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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
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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
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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
Others (better with some user guidance): Scanix, Autox
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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:
Crysfire
Powder v2.00
PowderX
PROSZKI
WinPlotr
• and after primary indexing:
Chekcell
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Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - specialist programs
• Supercel is a specialised indexing program by Juan RodriguezCarvajal 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/
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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 16
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - the Crysfire suite (2)
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 17
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
New Release - Crysfire 2002
June 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
• Greater ease of use, especially for first-time users
• Better resilience, especially under the Windows/NT family
(master program totally rewritten)
Slide 18
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 19
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Routine Crysfire Example
Importing an XFIT peak file with xf2crys, to give a Crysfire CDT file
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Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Routine Crysfire Example
Run crysfire (giving the following screen)
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Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Routine Crysfire Example
“lo” to load a CDT file
Slide 22
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Routine Crysfire Example
“sa” to target an indexing program
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Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Routine Crysfire Example
target ITO with defaults
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Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Routine Crysfire Example
“in” to start the targetted program running ITO
Slide 25
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Powder Indexing - Routine Crysfire Example
ITO runs
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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 27
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 28
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 29
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 (dicvol, treor, taup, kolh, lzon)
– lo to load
– sa to save (to Q)
– in to launch indexing
– look at the output file
– look at the summary file
– look at the Le Page summary file of reduced cells
– repeat
Slide 30
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 31
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 32
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 sampledisplacement 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
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Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Crysfire Self Calibration
Example
• Self calibration output of an inorganic
Slide 34
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 35
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/
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Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Chekcell : easy to see non-matching or impurity peaks
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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 38
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 39
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 40
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 41
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Chekcell: example of it running
Load the raw diffraction data
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Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Chekcell: example of it running
Load the peak position file
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Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Chekcell: example of it running
Load the Crysfire summary file
Slide 44
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 45
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
high-resolution X-ray powder diffraction
data: a variant of T3R3 human insulinzinc complex produced by grinding",
Acta Cryst. (2000). D56, 1549-1553.
Slide 46
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 Rhombohedral
• 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 47
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 a particularly robust and flexible way to search for 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 48
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 49
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
MMAP
• But another use is for checking out trial solutions taken from the summary
lists generated by other indexing programs
• The usual guides to which solutions are the most promising are ones like
figures of merit, numbers of lines indexed, etc., but only at the position of
the refined cell in the map
• That’s like having a list of high points in a landscape, and trying to tell tall
buildings from natural features with only their heights to go on
• Knowing the surroundings of the high-point tells us which are man-made,
and similarly which Mmap peak corresponds to the physical solution
Slide 50
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
MMAP - which of these objects is man made?
Using peak height as the selection criteria.
Height of 80
Height of 80
Height of 78
Height of 65
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Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
MMAP - which of these peaks is man made? 2
• It’s obvious once you can see the landscape
Slide 52
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Analogous problem with powder indexing
• Traditional indexing only gives you the
numbers (and possibly a Chekcell style fit)
where a large number of trial cells can give
reasonable matches
• Mmap shows you the actual “landscape”
Slide 53
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
An Mmap landscape
• Quick scan of an alpha*/beta* section for some real data for a triclinic cell
(a finely-divided triclinic biological sample showing some line broadening)
• There are a number of high points scattered across the map
• Each of these peaks is a potential solution (+others others out of section)
Slide 54
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Mmap
• Let’s take some real data and see how figureof-merit lists can be illuminated by looking at
the landscapes that they come from.
Slide 55
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Mmap
• After refinement, though one peak has reached a figure of merit of 21,
it still has a long list of competitors - no one solution really stands out
• There are 48 peaks in the whole list, all non-equivalent
• 17 of these have M>10 and index all of the first 20 lines
Slide 56
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Mmap : Is the following a good solution?
Here is the traditional set of information that we have for
solution 1 from that list:
a = 10.631A
b = 10.212 A
c = 3.5704 A
alpha = 101.56 deg
beta = 93.80 deg
gamma = 112.24 deg
V = 347.152 A3
M20 = 21.02
Slide 57
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Mmap : Yes looks a good solution
• Here is a magnification of the region around map-peak 1 (M=21.0),
reloaded into Crysfire from the Mmap summary file using LC and then
selecting a cell.
• It’s relatively compact (though sitting on a lowish diagonal ridge)
Slide 58
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Mmap : Is the following a good solution?
Similarly for the solution that corresponds to map-peak 2:
a = 10.787 A
b = 10.470 A
c = 3.6227 A
alpha = 107.14 deg
beta = 79.52 deg
gamma = 115.47 deg
V = 352.236 A3
M20 = 16.05
Slide 59
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Mmap
• A similar magnified map around map-peak 2 (M=16.0)
• This is revealed to be less well defined as well as lower, with its central
region extending as a broad ridge right off the top of the map
Slide 60
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Mmap: Is the following a good solution?
And for map-peak 3:
a = 10.760 A
b = 10.170 A
c = 3.5307 A
alpha = 100.33 deg
beta = 80.33 deg
gamma = 114.75 deg
V = 343.288 A3
M20 = 14.57
Slide 61
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Mmap
• Map-peak 3 (M=14.6) is broader still, and also drifts off the top of the map
Slide 62
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk
Mmap
• We can also avoid wasting time on landscapes that are broad and featureless,
indicating data problems or wrong initial assumptions, and so not worth pursuing
Slide 63
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
 They’re both under continuing development
(Crysfire 2002 to be released this June)
• Relevant web links:
– Crysfire: http://www.ccp14.ac.uk/tutorial/crys/
– Chekcell: http://www.ccp14.ac.uk/tutorial/lmgp/
Slide 64
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk