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CCP4 from a user perspective

CCP4 from a user perspective. Johan P. Turkenburg York Structural Biology Laboratory University of York York, United Kingdom. York & York Structural Biology Laboratory. Overview. File formats CCP4 Website CCP4 Help CCP4BB CCP4 Program Suite CCP4 Interface

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CCP4 from a user perspective

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  1. CCP4 from a user perspective Johan P. Turkenburg York Structural Biology Laboratory University of York York, United Kingdom ACA Meeting 2005 Johan P. Turkenburg

  2. York & York Structural Biology Laboratory ACA Meeting 2005 Johan P. Turkenburg

  3. Overview • File formats • CCP4 Website • CCP4 Help • CCP4BB • CCP4 Program Suite • CCP4 Interface • Interaction with other programs • Example(s) of Use ACA Meeting 2005 Johan P. Turkenburg

  4. File formats • Reflection files (mtz format) • Coordinate files (pdb format) Provide ways in and out of CCP4 Suite ACA Meeting 2005 Johan P. Turkenburg

  5. MTZ files • Columns, columns, columns • Labels • Types • Non-ascii • Viewers PDB files • ‘standard’ • Ascii • Widely used ACA Meeting 2005 Johan P. Turkenburg

  6. CCP4 Website • http://www.ccp4.ac.uk • Downloads • Problem pages • Documentation • Meetings • Jobs ACA Meeting 2005 Johan P. Turkenburg

  7. CCP4 Help • Documentation • General crystallography • Help in interface ACA Meeting 2005 Johan P. Turkenburg

  8. CCP4BB • Members from all over the world • Fast, expert help from colleagues • Useful tips • Non-CCP4 topics • Heated (entertaining) discussions ACA Meeting 2005 Johan P. Turkenburg

  9. CCP4 Program Suite • Many programs from many authors • All aspects of crystallography ACA Meeting 2005 Johan P. Turkenburg

  10. Overview Data processing Molecular Replacement Experimental Phasing Density Improvement Model Building & Refinement Validation, Analysis, Deposition ACA Meeting 2005 Johan P. Turkenburg

  11. Interface • No more typos • Import/Export • Help • Defaults • Project Management !! • Tasks (logical sequence) • Graphs from log files ACA Meeting 2005 Johan P. Turkenburg

  12. Interface window ACA Meeting 2005 Johan P. Turkenburg

  13. Modules • Picture of task list in interface ACA Meeting 2005 Johan P. Turkenburg

  14. Data Reduction ACA Meeting 2005 Johan P. Turkenburg

  15. Two routes MOSFLM DENZO SCALA SCALEPACK TRUNCATE TRUNCATE MTZ file with structure factors etc. ACA Meeting 2005 Johan P. Turkenburg

  16. Experimental Phasing SHELXS and SHELXC/D/E CRANK & BP3 (Leiden) to come ACA Meeting 2005 Johan P. Turkenburg

  17. ACORN • Heavy atom substructures • Locating secondary structure elements • Density modification • At high resolution, complete ‘density’ determination Foadi,J., Woolfson,M.M., Dodson,E.J., Wilson,K.S., Yao Jia-xing and Zheng Chao-de (2000) Acta. Cryst.D56, 1137-1147. ACA Meeting 2005 Johan P. Turkenburg

  18. ACORN on a CBM • Data to 1.0A on Se form at l = 0.87Å (SRS) • Patterson shows Se very clearly • ACORN gave excellent map in 18 min on SGI Ab initio structure determination and functional characterization of CBM36: A new family of calcium-dependent carbohydrate binding modulesJamal-Talabani S, Boraston AB, Turkenburg JP, Tarbouriech N, Ducros VMA, Davies GJSTRUCTURE 12 (7): 1177-1187 JUL 2004 ACA Meeting 2005 Johan P. Turkenburg

  19. Patterson • Demo ACA Meeting 2005 Johan P. Turkenburg

  20. CBM ACORN map & final model ACA Meeting 2005 Johan P. Turkenburg

  21. Molecular Replacement ACA Meeting 2005 Johan P. Turkenburg

  22. MR programs • Molrep • AMoRe • Phaser (Randy Read, Tuesday morning) • Many utilities ACA Meeting 2005 Johan P. Turkenburg

  23. MR Utilities ACA Meeting 2005 Johan P. Turkenburg

  24. Density Improvement ACA Meeting 2005 Johan P. Turkenburg

  25. Model Building ACA Meeting 2005 Johan P. Turkenburg

  26. Refinement ACA Meeting 2005 Johan P. Turkenburg

  27. REFMAC • Algorithms • Scaling • Restraints (geometric & NCS) • TLS • Combines with ARP/wARP • Easy to use in interface ACA Meeting 2005 Johan P. Turkenburg

  28. Monomer library sketcher ACA Meeting 2005 Johan P. Turkenburg

  29. Structure Analysis ACA Meeting 2005 Johan P. Turkenburg

  30. Temperature factor analysis ACA Meeting 2005 Johan P. Turkenburg

  31. Validation & Deposition ACA Meeting 2005 Johan P. Turkenburg

  32. Map & Mask Utilities ACA Meeting 2005 Johan P. Turkenburg

  33. Reflection Data Utilities ACA Meeting 2005 Johan P. Turkenburg

  34. Convert from MTZ ACA Meeting 2005 Johan P. Turkenburg

  35. Coordinate Utilities ACA Meeting 2005 Johan P. Turkenburg

  36. Graphics & Viewing Utilities ACA Meeting 2005 Johan P. Turkenburg

  37. Program List ACA Meeting 2005 Johan P. Turkenburg

  38. ‘External’ Programs • Arp/warp • Shelx • Mosflm • Xtalview ACA Meeting 2005 Johan P. Turkenburg

  39. Example 1 Lyase • Space group H32, unit cell 58.8 58.8 588.5 • All programs used are runnable from interface • Se MAD Shelxd to find sites • MLPHARE, DM phasing/phase improvement • ARP/wARP, REFMAC model building/refinement • Input/output ‘chaining’ trivial (but not automatic) ACA Meeting 2005 Johan P. Turkenburg

  40. LYASE SHELXD ACA Meeting 2005 Johan P. Turkenburg

  41. LYASE SHELXE ACA Meeting 2005 Johan P. Turkenburg

  42. LYASE ARP/wARP ACA Meeting 2005 Johan P. Turkenburg

  43. Example 2 Two esterases • CE4 one crystal form (P41212 / P43212) • Cd SIRAS • SHELXD, MLPHARE, DM, ARP/WARP, REFMAC • AXA with 2 crystal forms (P21 / P212121) • Molecular Replacement ACA Meeting 2005 Johan P. Turkenburg

  44. CE4 SHELX C/D/E ACA Meeting 2005 Johan P. Turkenburg

  45. CE4 Phasing & Phase Improvement • MLPhare with site from SHELXD • DM ACA Meeting 2005 Johan P. Turkenburg

  46. AXA P21 AMoRe Rotation function ACA Meeting 2005 Johan P. Turkenburg

  47. AXA P212121 Analyse data ACA Meeting 2005 Johan P. Turkenburg

  48. AXA P212121 Analyse data Results ACA Meeting 2005 Johan P. Turkenburg

  49. AXA P212121 Solution MOLREP, two molecules Initial refinement REFMAC ACA Meeting 2005 Johan P. Turkenburg

  50. Acknowledgements • Eleanor Dodson • Keith Wilson • Gideon Davies • Ed Taylor • Sam Hart • Everyone else in YSBL ACA Meeting 2005 Johan P. Turkenburg

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