Data Reduction in CrysAlis Pro

Transcription

1 Data Reduction in CrysAlis Pro Daniel Baker Agilent Technologies UK Mathias Meyer Agilent Technologies Poland Oliver Presly Agilent Technologies UK

2 Layout Introduction: CrysAlis Pro overview Part I: Automatic data reduction Part II: Manual data reduction Part III: Refinalisation Part IV: Twin data reduction Part V: Protein data reduction Part VI: Advanced features (Incommensurate, HP, batch processing, synchrotron, external formats) Conclusion: Summary 2

3 Layout Introduction: CrysAlis Pro overview Part I: Automatic data reduction Part II: Manual data reduction Part III: Refinalisation Part IV: Twin data reduction Part V: Protein data reduction Part VI: Advanced features (Incommensurate, HP, batch processing, synchrotron, external formats) Conclusion: Summary 3

4 X-ray Product Configurations Modular Products - Tuned to Application 4-circle Goniometer X-ray Sources CCD Detectors 4

5 Crystallographic Software: CrysAlis Pro CrysAlis Pro has been designed to be as simple to use as possible: User friendly GUI Simple workflow Fully integrated platform Supporting SM and PX Highly automated......but full of manual features for those who want them SM PX 5

6 A Perfect Tool from Crystal to Structure! Mounting Screen/Pre Strategy Experiment Structure 6

7 Layout Introduction: CrysAlis Pro overview Part I: Automatic data reduction Part II: Manual data reduction Part III: Refinalisation Part IV: Twin data reduction Part V: Protein data reduction Part VI: Advanced features (Incommensurate, HP, batch processing, synchrotron, external formats) Conclusion: Summary 7

8 Automatic Data Reduction How it works Turns raw experimental data into a format that allows for structure solution and refinement Requires unit cell Produces reflection file (*.hkl), processing information file (*.lst) and crystal summary info file (*.sum) Uses unit cell to predict where peaks should appear on each frame Automatic profiling calculation followed by masking of peaks to collect intensity for.hkl file h k l F 2 obs sf 2 obs

9 Automatic Data Reduction Example Sucrose crystal 13 minute experiment Every 25 frames data reduction takes place AutoChem gets structure before experiment has finished (if installed) Excellent R int and R 1 with zero user intervention 9

10 Automatic Data Reduction Example Automatic data reduction and structure solution R 1 = 2.86% R int = 1.40% R int = 1.48% R 1 = 2.22% I/s =

11 Automatic vs. Manual Data Reduction Why do a manual data reduction? Can do concurrent automatic processing of twins or incommensurate structures Can visually analyse any diffuse scatter present Can apply additional corrections to improve data Presence of weakly-diffracting peaks may make automatic selection of space group difficult e.g. weak superstructure reflections Sometimes the user knows best! 11

12 Layout Introduction: CrysAlis Pro overview Part I: Automatic data reduction Part II: Manual data reduction Part III: Refinalisation Part IV: Twin data reduction Part V: Protein data reduction Part VI: Advanced features (Incommensurate, HP, batch processing, synchrotron, external formats) Conclusion: Summary 12

13 Manual Data Reduction Introduction CrysAlis Pro allows the user full control of the data reduction procedure Data reduction wizard steps the user through the various steps 13

14 Manual Data Reduction Inputs View orientation matrix for unit cell to be used Twin/incommensurate features Quasi-crystals 14

15 Manual Data Reduction Inputs Choose which runs to use for data reduction 15

16 Manual Data Reduction Reflection model & special options Automatic model refinement Sample wobbling (cold stream) Sample slippage Access to special parameters 16

17 Manual Data Reduction Model refinement options No need to decide now program does it for you! PROFFIT For every run Global cell & model refinement Per-run refinement Per-frame refinement Model 1 Model 2 Prediction accuracy evaluation Prediction accuracy evaluation Choose more accurate approach Integration Frame1 Frame2 17

18 Manual Data Reduction Sample slippage example Superficially gives impression of twin Twin indexing matches 96.8% of reflections but twin integration doesn t help 18 7/4/2013

19 Manual Data Reduction Sample slippage example 19 7/4/2013

20 Manual Data Reduction Sample slippage example 20 7/4/2013

21 Manual Data Reduction Sample slippage example No slip Intentional sample slip Reference data Slip Data (Pre-Treatment) Slip Data (Post-Treatment) R int (%) I/σ R 1 (%) Comp (%) % 98.4% 21 7/4/2013

22 Manual Data Reduction Reflection model & special options Several special features for: Weak samples adjust masks according to prediction uncertainty Twin data Increase/decrease mask size Protein Single wavelength only integration High pressure Bad profile rejection Also useful for twins, multicrystals, iced samples, SM/PX etc. 22

23 Manual Data Reduction Background correction Choice of background correction: Average background Define range and frequency Smart background Combination of local and average background Improves statistics (I/s) for samples with varying background features Can t be used for twin data (yet ) 23

24 Manual Data Reduction Background correction example 100μm Well-mounted sample Standard peak-hunting produces many non-lattice peaks. 100μm Intentionally badly-mounted sample 24 7/4/2013

25 Manual Data Reduction Background correction example Well-mounted Badly-mounted Reference Data Auto analysis Smart Background Time 3h 8m 16h 18m 16h 18m Diff. Limit R int (%) I/σ R 1 (%) Comp (%) /4/2013

26 Space Group Determination (GRAL) Monoclinic cell choices Automatic selection from 3 possible cell choices for particular monoclinic space groups (GRAL) - In Auto mode, a setting with β angle closest to 90 is selected - In Interactive mode, all 3 choices are presented with the same default as in Auto mode 26

27 Data Reduction Tab Summary of information regarding the data reduction process Shortcuts to Frame/run list, absorption options window, and space group options Information updates after every automatic data reduction cycle during experiment, or after any manual re-finalisation 27

28 Data Reduction Output 28

29 Data Reduction Output graphs Scale factor Sample temperature 29

30 Layout Introduction: CrysAlis Pro overview Part I: Automatic data reduction Part II: Manual data reduction Part III: Refinalisation Part IV: Twin data reduction Part V: Protein data reduction Part VI: Advanced features (Incommensurate, HP, batch processing, synchrotron, external formats) Conclusion: Summary 30

31 Refinalisation Introduction Refinalisation is a repeat of the finalisation step of the data reduction Able to apply several additional corrections Absorption Filters Resolution Space group change 31

32 Refinalisation Face-indexing Two different methods (point or drag) to quickly draw shape of crystal Video guide coming soon on user forum 32

33 Refinalisation Absorption correction No problem running large crystal with micro-focus source 33

34 Refinalisation ABSPACK 34

35 Refinalisation Filters Main filters: R int / d-spacing / I/s Used to remove outliers and improve data 35

36 Refinalisation New window teaser 36

37 Layout Introduction: CrysAlis Pro overview Part I: Automatic data reduction Part II: Manual data reduction Part III: Refinalisation Part IV: Twin data reduction Part V: Protein data reduction Part VI: Advanced features (Incommensurate, HP, batch processing, synchrotron, external formats) Conclusion: Summary 37

38 Twin Data Reduction Introduction 53% indexed as single crystal 91% indexed as twin Software recognises that sample is modelled as twin 38

39 Twin Data Refinalisation Example HKLF4 no twin modelling R int = 4.15% R 1 = 14.29% HKLF5 twin data reduction R int = 3.9% R 1 = 4.52% I/s = 11.1 I/s =

40 Twinning and Incommensurate Data Processing in CrysAlis Pro Dr Fraser White Agilent Technologies UK September 18 th :00 am ET (Americas) 4:00 pm CET (Europe)

41 Layout Introduction: CrysAlis Pro overview Part I: Automatic data reduction Part II: Manual data reduction Part III: Refinalisation Part IV: Twin data reduction Part V: Protein data reduction Part VI: Advanced features (Incommensurate, HP, batch processing, synchrotron, external formats) Conclusion: Summary 41

42 Protein Data Reduction CrysAlis Pro has a dedicated PX mode for running protein experiments Extra features specifically for protein samples.mtz files A/B scale factors Import/export of data 42

43 Protein Data Reduction A/B-factor refinement F2 New correction in ABSPACK Designed for correcting crystal decay in time Added extra factor to ABSPACK scaling model: Theta CrysAlis Pro only! 43

44 Protein Data Reduction A/B-factor refinement A/B-coefficients plots show decay of the sample Example from beamline protein data B A No decay correction With decay correction 44

45 Protein Data Reduction A/B-factor refinement Unexpected usefulness for some high theta small molecule data: can correct for some resolution-dependent effects, e.g. prediction uncertainty at high angle Without B-factor With B-factor R % 3.77% R int 7.5% 7.2% 45

46 Layout Introduction: CrysAlis Pro overview Part I: Automatic data reduction Part II: Manual data reduction Part III: Refinalisation Part IV: Twin data reduction Part V: Protein data reduction Part VI: Advanced features (Incommensurate, HP, batch processing, synchrotron, external formats) Conclusion: Summary 46

47 Advanced Features Incommensurates Output a.hklmno file for structure solution in external programs More in the next webinar! 47

48 Advanced Features High pressure Designed primarily for high-pressure data for filtering out reflections overlapped by diamond diffraction spots 48

49 Advanced Features High pressure Example HP data: Structure unsolvable although data seem to be of sufficient quality (R int ) After filtering structure solved no. of reflections No filtering With filtering R int 6.4% 10% R 1 34% (no structure) 9% Profile agreement No filter Profile agreement = 0.8 I/s= 10 With filter Higher value for R int after filtering! Diamond reflections are symmetrically equivalent and falsify R int value. Standard outlier rejection filter fails. 49

50 Bad Profile Rejection SM example Simulation of cryo-failure (shield flow turned off) 50 7/4/2013

51 Bad Profile Rejection SM example No ice Large ice build-up Reference Data Auto analysis d range and run Filtering Bad profile filtering R int (%) I/σ R 1 (%) Comp (%) /4/2013

52 Advanced Features Batch processing Multi-temperature experiments problem there are many data sets to process 52

53 Advanced Features Batch processing XX PROFFITBATCH Browse for the folder Set PROFFIT parameters Click Finish A script proffitbatch.mac gets created in the directory selected at the start You can edit it or run as is using SCRIPT command 53

54 Advanced Features Synchrotron/External frame formats Massive dataset from synchrotron: 4 runs of 10,000 images each; making a total of 40,000 images Possible to read in a large variety of external frame formats into CrysAlis Pro Full auto-analysis on protein sample successful even with very small diffraction spots More details on Protein Webinar and future applications note! 54

55 Layout Introduction: CrysAlis Pro overview Part I: Automatic data reduction Part II: Manual data reduction Part III: Refinalisation Part IV: Twin data reduction Part V: Protein data reduction Part VI: Advanced features (Incommensurate, HP, batch processing, synchrotron, external formats) Conclusion: Summary 55

56 Summary Automatic data reduction during experiment Full override control in manual mode Fully accessible statistics from tables and graphs Easy-to-use face-indexing tool Many options in data reduction and re-finalisation to improve data quality Can handle twins, incommensurates, HP data, SM, PX, synchrotron etc. Outputs everything you need for structure solution/refinement Read in many external formats Come along to the Agilent booth at the ACA in Hawaii we can process your data for you with our software Constantly being updated and improved 56

57 Software Updates CrysAlis Pro is frequently updated with fixes for known problems New features are introduced in annual major updates All updates are Free and available from our user forum, Free multi-user, multi-site license 57

58 Q&A New applications note on data recovery Go to and click on the Library tab, and the Literature link. Search for CrysAlisPro to find relevant app notes Please type your question into the chat box. Send a direct chat to the Host which is private, or a chat to All Participants which is public 58

59 Thank you for listening! All feedback and comments are welcome The live CrysAlis Pro Webinar series continues on September 18 th 2013 Register at: 59