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Fast, Intuitive Structure Determination II: Crystal Indexing and Data Collection Strategy
April 2, 2013 1
Welcome
Dr. Michael Ruf Product Manager – Crystallography Bruker AXS Inc. Madison, WI, USA
Bruce C. Noll, Ph.D. Sr. Applications Scientist – Crystallography Bruker AXS Inc. Madison, WI, USA
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Crystal indexing and Data collection strategy planning
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• Indexing provides unit cell information • Is this a known cell? • Is this a single crystal? • What is the Bravais class?
• Strategy planning • Efficient data collection • Unique data • Well-distributed redundancy • Scheduling instrument usage
• Select parameters to harvest reflections for crystal indexing
• Populate reflection array
Harvesting reflections for indexing
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• 774 reflections harvested from 2 sets of 12 frames
• Reflections selected at I ≥ 10σ(I)
• Indicators for data collection: • Resolution
versus scan speed
• Crystal mosaicity
Harvesting results
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• Select reflection array
• Choose output for cell parameters
• Choose methods
Indexing
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• Results from Difference Vectors FFT, and least-squares methods
• Histograms and score indicate fit
Indexing results
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• Refine unit cell parameters against reflection array
• Improve fit of orientation matrix
Initial refinement
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• Orthorhombic P chosen
• Based solely on cell metrics
Determination of Bravais class
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• Fix lengths and angles as appropriate for lattice type
Constrained unit cell refinement
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• RLATT – The reciprocal lattice viewer provides many tools to visualize and manipulate reflections arrays in reciprocal space
• This example will show how to remove spurious reflections from a diffraction pattern that is contaminated by small crystallites attached to the crystal investigated
Manipulating reflection arrays using RLATT
• Random orientation of reflections from 24 scans from 2 runs
• 774 reflections • By default the
editing tool “rotate” is active
• Use “click and drag” to rotate the array
Reflection array in reciprocal space
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• Rotate array until looking along lattice planes
• Use the “Lattice overlay” tool with “click and drag” to select to lattice planes
Visual cleanup of a reflection array
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• Use the “+” key to generate subdivisions
• “-” removes subdivisions
Selecting lattice planes
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• Continue to add selection lines until all lattice lines are selected
• The “page up” key will add lines to the top and bottom
• The “page down” key will remove lines
Selecting lattice planes
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• Click the “invert selection” button to keep the “good” reflection in the red group
Inverting the selection
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• Change the “current” group to the green group
• Click add to current group
• Red reflections are “good”
• Green reflections are “bad”
Adding selected reflections to a different group
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• Change back to the “rotation mode” and look for the second direction
• Repeat the cleanup in the second direction
Cleanup in the second direction
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• Repeat the cleanup in the third direction
Cleanup in the third direction
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• Cleaned-up lattice with green reflections
• 564 red reflections • 210 green
reflections
Lattice cleanup
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• Cleaned-up lattice without green reflections
• 564 red reflections • Indexing and
refining the red array will now yield much better results
Cleaned lattice
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• Click on the ? symbol in the menu bar and then click into the dialog on the right for a list of RLATT keyboard commands
RLATT help
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Indexing after cleanup
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• Consistent results from 3 indexing methods
Indexing results
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• Good fit to indices • Good agreement
in reflection position
Refinement results
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• Refine Bravais-constrained cell against good reflections
Constrained unit cell refinement
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• Search CellCheckCSD • Local subset of
CSD • Cell dimensions • Space group • Formula • Links to
WebCSD • Structure • Reference
Search known cells
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• A successful structure determination requires acquisition of complete data to atomic resolution
• Adequate multiplicity is needed for meaningful scaling and absorption correction and improves the overall quality of the data
Data collection strategies
Diffraction Geometry in 2D
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Source
X-ray detector Ewald sphere
Reciprocal lattice
λ = 2d sin(θ)
Detection area in 3D, square detector
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• The detection area of a detector is the projection of the (square) detector onto the surface of the Ewald sphere
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Detection area in 3D, square detector
• The size of the detection area depends on the detector’s size and its distance from the sample
• The position of detection area depends on the 2Θ swing angle of the detector
Cusp area
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• One single scan will miss the cusp and will not be sufficient to collect true multiplicity
• Changing the crystal’s orientation using one axis and scanning using another axis will allow the acquisition of missing data and
• Provide redundant data
• Relax! Some strategies are really not that difficult…
You have done this before
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Diffraction geometry in 3D
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Ewald sphere
Incident beam Omega plane Reciprocal space
Chi at 54.74
Omega scans
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• Omega scans are geometrically very flexible
• A combination of omega scans can cover reciprocal space very effectively
Omega scans
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• Omega scans are geometrically very flexible
• A combination of omega scans can cover reciprocal space very effectively
Phi scan
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• Phi scans are always oriented along the phi spindle axis
• They are most efficient if they are perpendicular to the beam
Phi scan
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• Phi scans are always oriented along the phi spindle axis
• They are most efficient if they are perpendicular to the beam
• Communicates directly with instrument for limits
• Exploits symmetry of crystal to optimize strategy
• Input desired resolution and choose Laue symmetry, if desired
Calculating strategy with the QUEEN
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• QUEEN recommends detector distance
• Choose scan constraints
• Choose target multiplicity
Using the QUEEN strategy optimizer
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• Window summarizes outcome • Runs chosen • Multiplicity • Redundancy • Missing
reflections
Results from strategy calculation
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• Extend strategy for additional redundancy and to collect missing reflections
Extending the strategy
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• Reciprocal space viewer to show strategy and missing data
Viewing coverage
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• Dialog for frame width and scan time
• Calculator for targeted completion time
Inputting scan parameters
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• Preset options • Input desired
completion time
Calculating experiment time
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• Worksheet for inputting instrument operations
• Direct import from strategy plug-in
The Experiment plug-in
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• Drop-down menu for operations
• Editable fields for parameters
• Controls include • Position • Omega/Phi
scans • Temperature • Video • Generator
Setting up experiments
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• Pull down to Thermostat operation
• Input target temperature
• Input ramp rate
Adding temperature control
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• Click button “Append Strategy”
• Runs will be added below the last operation
Adding the strategy
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• Pull down to crystal video
Video for face-indexing
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• Click “Validate” • Useful for runs
created outside the strategy planner
• Validation also performed on “Execute”
Video for face-indexing
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• Screen shifts to Monitor tab
• Displays frames as collected
The measurement begins
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• Each frame presented as it is recorded
• Display with or without overlays
• Examine frame file header
Monitoring the experiment
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• Indexing provides wealth of information in short period of time • Unit cell dimensions • Unit cell volume • Unit cell symmetry (Bravais class) • Estimate of unit cell contents • Indication of crystal quality
• Strategy planning • Efficient collection of data
• Coverage • Redundancy • Time
Crystal indexing and data collection strategy planning
Questions and Answers
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Thank you!
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