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Extending the limits of the SHELXCDE->ARP/wARP pipeline

Progress report on Crank: Model building Biophysical Structural Chemistry Leiden University, The Netherlands. Extending the limits of the SHELXCDE->ARP/wARP pipeline. Earlier tests on Crank. Pavol’s talk/results: all SAD examples can be automatically built (apart for SAD gere with peak).

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Extending the limits of the SHELXCDE->ARP/wARP pipeline

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  1. Progress report on Crank:Model buildingBiophysical Structural ChemistryLeiden University, The Netherlands

  2. Extending the limits of the SHELXCDE->ARP/wARP pipeline

  3. Earlier tests on Crank • Pavol’s talk/results: all SAD examples can be automatically built (apart for SAD gere with peak). • 33 test cases for SAD/MAD/SIRAS starting from substructure detection to model building: http://www.bfsc.leidenuniv.nl/software/crank/ (follow test link)

  4. Preliminary results on JCSG with the CRANK in CCP4 6.1 • Started with known heavy atom substructure, but unknown number of monomers/solvent content • Using only default values: sequence, mtz, f’, f” only input • First sets of jobs run: before substructure detection results (so, more input errors…) • DISCLAIMER: analyzed last night after dinner until 3:30 a.m.!

  5. Crank interfaces: UNIX script

  6. Results from “CCP4” pipelineBP3->SOLOMON->PIRATE->BUCCANEER

  7. Results from “CCP4” pipelineBP3->SOLOMON->ARP/wARP

  8. Issues to be addressed • Used default number of building cycles: In some cases more of the model could be built with more cycles (i.e. flex-WARP) • Hand determination failed a bit too many times (about 15). In my unsystematic analysis, SHELXE was better than SOLOMON.

  9. Future work • Getting windows version of crank • Opening up Crank web server • Feature freeze on crank and concentrate more on algorithmic developments: • AFRO Fa’s for SAD/MAD/unmerged data • BP3/Refmac phasing – expand multivariate approach (SIRAS/MAD – Pavol’s talk) • Refmac model building: Pavol’s talk

  10. Crank Interfaces: web interface for Crank server (48 nodes)

  11. Acknowledgements • Program authors: G. Sheldrick, G. Murshudov, V. Lamzin, A. Perrakis, K. Cowtan, P. Emsley and co-workers. • R.A.G. de Graaff, I. Sikharulidze, P. Skubak, J.P. Abrahams, JCSG staff, Z. Dauter, and M. Weiss. • Debugging/suggestions: CCP4 staff, Auto-Rickshaw guys, users. Cyttron

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