Fast, Intuitive Structure Determination II: Crystal Indexing and Data Collection Strategy. April 2,

Transcription

1 Fast, Intuitive Structure Determination II: Crystal Indexing and Data Collection Strategy April 2,

2 Welcome I I 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 April 2,

3 Crystal indexing and Data collection strategy planning 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 April 2,

4 Harvesting reflections for indexing Select parameters to harvest reflections for crystal indexing Populate reflection array April 2,

5 Harvesting results 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 April 2,

6 April 2,

7 Indexing Select reflection array Choose output for cell parameters Choose methods April 2,

8 Indexing results Results from Difference Vectors FFT, and leastsquares methods Histograms and score indicate fit April 2,

9 Initial refinement Refine unit cell parameters against reflection array Improve fit of orientation matrix April 2,

10 Determination of Bravais class Orthorhombic P chosen Based solely on cell metrics April 2,

11 April 2,

12 Constrained unit cell refinement Fix lengths and angles as appropriate for lattice type April 2,

13 Manipulating reflection arrays using RLATT 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 April 2,

14 Reflection array in reciprocal space 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 April 2,

15 Visual cleanup of a reflection array Rotate array until looking along lattice planes Use the Lattice overlay tool with click and drag to select to lattice planes April 2,

16 Selecting lattice planes Use the + key to generate subdivisions - removes subdivisions April 2,

17 Selecting lattice planes 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 April 2,

18 Inverting the selection Click the invert selection button to keep the good reflection in the red group April 2,

19 Adding selected reflections to a different group Change the current group to the green group Click add to current group Red reflections are good Green reflections are bad April 2,

20 Cleanup in the second direction Change back to the rotation mode and look for the second direction Repeat the cleanup in the second direction April 2,

21 Cleanup in the third direction Repeat the cleanup in the third direction April 2,

22 Lattice cleanup Cleaned-up lattice with green reflections 564 red reflections 210 green reflections April 2,

23 Cleaned lattice Cleaned-up lattice without green reflections 564 red reflections Indexing and refining the red array will now yield much better results April 2,

24 RLATT help Click on the? symbol in the menu bar and then click into the dialog on the right for a list of RLATT keyboard commands April 2,

25 Indexing after cleanup April 2,

26 Indexing results Consistent results from 3 indexing methods April 2,

27 April 2,

28 Refinement results Good fit to indices Good agreement in reflection position April 2,

29 Constrained unit cell refinement Refine Bravaisconstrained cell against good reflections April 2,

30 Search known cells Search CellCheckCSD Local subset of CSD Cell dimensions Space group Formula Links to WebCSD Structure Reference April 2,

31 Data collection strategies 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 April 2,

32 Diffraction Geometry in 2D λ = 2d sin(θ) Source Ewald sphere X-ray detector Reciprocal lattice April 2,

33 Detection area in 3D, square detector The detection area of a detector is the projection of the (square) detector onto the surface of the Ewald sphere April 2,

34 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 April 2,

35 Cusp area 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 April 2,

36 You have done this before Relax! Some strategies are really not that difficult April 2,

37 Diffraction geometry in 3D Ewald sphere Chi at Omega plane Reciprocal space Incident beam April 2,

38 Omega scans Omega scans are geometrically very flexible A combination of omega scans can cover reciprocal space very effectively April 2,

39 Omega scans Omega scans are geometrically very flexible A combination of omega scans can cover reciprocal space very effectively April 2,

40 Phi scan Phi scans are always oriented along the phi spindle axis They are most efficient if they are perpendicular to the beam April 2,

41 Phi scan Phi scans are always oriented along the phi spindle axis They are most efficient if they are perpendicular to the beam April 2,

42 Calculating strategy with the QUEEN Communicates directly with instrument for limits Exploits symmetry of crystal to optimize strategy Input desired resolution and choose Laue symmetry, if desired April 2,

43 April 2,

44 Using the QUEEN strategy optimizer QUEEN recommends detector distance Choose scan constraints Choose target multiplicity April 2,

45 April 2,

46 Results from strategy calculation Window summarizes outcome Runs chosen Multiplicity Redundancy Missing reflections April 2,

47 April 2,

48 Extending the strategy Extend strategy for additional redundancy and to collect missing reflections April 2,

49 April 2,

50 Viewing coverage Reciprocal space viewer to show strategy and missing data April 2,

51 April 2,

52 Inputting scan parameters Dialog for frame width and scan time Calculator for targeted completion time April 2,

53 April 2,

54 Calculating experiment time Preset options Input desired completion time April 2,

55 April 2,

56 The Experiment plug-in Worksheet for inputting instrument operations Direct import from strategy plug-in April 2,

57 Setting up experiments Drop-down menu for operations Editable fields for parameters Controls include Position Omega/Phi scans Temperature Video Generator April 2,

58 April 2,

59 Adding temperature control Pull down to Thermostat operation Input target temperature Input ramp rate April 2,

60 Adding the strategy Click button Append Strategy Runs will be added below the last operation April 2,

61 Video for face-indexing Pull down to crystal video April 2,

62 Video for face-indexing Click Validate Useful for runs created outside the strategy planner Validation also performed on Execute April 2,

63 The measurement begins Screen shifts to Monitor tab Displays frames as collected April 2,

64 Monitoring the experiment Each frame presented as it is recorded Display with or without overlays Examine frame file header April 2,

65 Crystal indexing and data collection strategy planning 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 April 2,

66 Questions and Answers Any questions? Please type any questions you may have for our speakers in the Q&A panel and click Send. How did we do? When you exit the webinar, please fill out our evaluation survey to let us know. We appreciate your feedback. Thank you! April 2,

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