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Developments in xia2

Developments in xia2. Graeme Winter CCP4 Dev Meeting 2008. What is xia2?. Automated robust data reduction and analysis Thorough – takes additional steps when many users wouldn’t bother In: images from e.g. synchrotron beamline

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Developments in xia2

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  1. Developments in xia2 Graeme Winter CCP4 Dev Meeting 2008

  2. What is xia2? • Automated robust data reduction and analysis • Thorough – takes additional steps when many users wouldn’t bother • In: images from e.g. synchrotron beamline • Out: measurements for downstream phasing via e.g. HAPPy, Mr BUMP, Phenix…

  3. Recent changes • Inclusion in CCP4 6.1 • Many command line options • Integrated with AutoRickshaw (EMBL H) • Robust lattice determination • Support for Q270, Pilatus • Zero input option

  4. 3 Month plans • BioXHit ends in June => so does xia2 development • Include robust system to decide resolution limits etc (next slides) • Finish release 0.3.0 to go with release version of CCP4 6.1

  5. Chef Let’s cook them books!

  6. What is chef? • A tool to help you use the best of the reflections you have • Uses unmerged intensities • Uses robust statistics to decide: • d*min for different functions (resolution) • Dmax for different functions (dose) • Additional program “doser” to add dose information to unmerged MTZ files

  7. In • MTZ files from scala with “output unmerged” set • DOSE / TIME information for doser: • BATCH 1 DOSE 2.5 TIME 2.5 • BATCH 2 DOSE 7.5 TIME 8.2 • …

  8. Running doser hklin TS03_12287_chef_INFL.mtz hklout infl.mtz < doser.in doser hklin TS03_12287_chef_LREM.mtz hklout lrem.mtz < doser.in doser hklin TS03_12287_chef_PEAK.mtz hklout peak.mtz < doser.in chef hklin1 infl.mtz hklin2 lrem.mtz hklin3 peak.mtz << eof isigma 2.0 resolution 1.65 range width 30 max 1500 print comp rd rdcu anomalous on labin BASE=DOSE eof

  9. Output • Resolution vs. dose • Completeness vs. dose for each data set

  10. Methods • Based on “new” cumulative-pairwise R factor RCP: • Inspired by Rd in Diederichs (2006)

  11. And RCP means..? • How well do the measurements up to dose D agree? • Closely related to I/σ • Reasonably robust as it does not depend on sigma estimates or means • Gets bigger when systematic variation contributes to spread

  12. Requirements • Radiation damaged MAD data – what do I want for: • Substructure determination – big anomalous / dispersive signal • Phase calculation – well measured ΔF • Phase extension & improvement – good F • Refinement – good F • 85% Limit RCP < R(I/σ) + S(I/σ, Nm, Nu)

  13. Example • JCSG TB0541 – heavily radiation damaged… • 3 wavelength MAD – INFL + LREM, PEAK • Massive signal • P43212, 90 degrees * 3 => plenty of data • Chef says “use data to 1.65A, D=~600s”

  14. Before (INFL) For TS03/12287/INFL High resolution limit 1.66 7.41 1.66 Low resolution limit 52.7 52.7 1.7 Completeness 95.8 98.4 72.5 Multiplicity 6.4 5.1 4.2 I/sigma 13.1 25.6 2.2 Rmerge 0.085 0.045 0.654 Rmeas(I) 0.117 0.077 0.808 Rmeas(I+/-) 0.099 0.054 0.816 Rpim(I) 0.045 0.032 0.374 Rpim(I+/-) 0.051 0.029 0.478 Wilson B factor 19.372 Anomalous completeness 95.5 100.0 72.3 Anomalous multiplicity 3.4 3.5 2.1 Anomalous correlation 0.546 0.695 0.032

  15. After (INFL – first 60 degrees) For TEST001/12287/LREM High resolution limit 1.63 7.3 1.63 Low resolution limit 52.56 52.56 1.68 Completeness 92.6 98.3 62.9 Multiplicity 4.1 3.3 2.4 I/sigma 13.6 26.2 2.1 Rmerge 0.052 0.033 0.317 Rmeas(I) 0.065 0.041 0.504 Rmeas(I+/-) 0.066 0.043 0.445 Rpim(I) 0.031 0.021 0.306 Rpim(I+/-) 0.041 0.027 0.311 Wilson B factor 18.731 Anomalous completeness 91.8 99.4 59.4 Anomalous multiplicity 2.2 2.2 1.3 Anomalous correlation -0.227 0.071 0.01

  16. Why improvement? • Limit radiation damage => σF more meaningful • Limit damage => ΔF better • Without systematic damage get higher resolution for given I/σ

  17. However… • Pipe MTZ through scaleit / solve / cad / resolve / Arp/Warp and get very similar results – slight improvement though • This is most interesting, because it means that 55% of the “data” did not add to the quality of the result

  18. Plans • Currently writing this up for J. Appl. Cryst • Chef will be included in CCP4 6.1 • Next: include this as part of xia2 (makes 0.3.0) • Extend chef to make decisions about anomalous / dispersive differences

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