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

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