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DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE

DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE. Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould Jan M.M. Smits and others

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DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE

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  1. DIRDIFROUTINE STRUCTURE SOLUTION USINGYOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould Jan M.M. Smits and others Marieken van Nieumeghen DIRDIF computer program for crystal structure determination by Patterson methods and direct methods applied to difference structure factors

  2. DIRDIF DEMO NANCY 2006 INTRO 4 vector search ROT+ POSN model 3 H.A. Patterson PATTY ORIENT TRACOR 1 DIR meth. > DIF struct. TRAVEC PHASEX 2 R2 AUTO recycling 5TRICKS and HELP FOUR 6WHAT is NEXT? summary

  3. INTRO DIRDIF LOGISTICS organizer DDSTART supervisor DDMAIN PATTY ORIENT TRACOR TRAVEC PHASEX R2 FOUR utilities NUTS DIRDIF finished

  4. MONOS: DIRDIF TEST STR. DDSTART MONOS DEMO 1 full structure DEMO 2 S only DEMO 3 S misplaced 0.125A centric ! run DD FOUR NORECY DDMAIN FOUR NUTS DIRDIF finished

  5. AB INITIO DIRECTMETHODS the problem starting phases? sigma-2 or result tangent formula

  6. DIRECT METHODSapplied to DIFFERENCE STRUCTURE FACTORS Fp part.str.f. known Fr part.str.f. unnkown

  7. DIRDIF DDSTART DDMAIN MONOS DEMO 4 S only with PHASEX run DD PHASEX NORECY PHASEX FOUR NUTS DIRDIF finished

  8. program PHASEX delta F = conventional Fourier coeff. = starting for tangent formula Fr = PHASEX-refined str.f. of the remainder of the structure enantiomorph problem symbolic addition with 999 known phases + 10 unknown lettersymbols

  9. ENANTIOMORPH PROBLEM DDSTART DDMAIN MONOS DEMO 5 S misplaced 0.135 A centric! run DD PHASEX NORECY [ repeat!] PHASEX FOUR NUTS DIRDIF finished

  10. H.A. PSEUDOSYMMETRY SbS4.....

  11. 1963 DIRECTE METHODEN

  12. advantage of PHASEX direct methods the known part of the structure is subtracted from the observed data • many phases known strong starting set • number of atoms reduced • heavy atoms subtracted • the cause of problems in conventional direct methods is subtracted from the structure: • -- heavy Patterson overlap usually comes from a fragment of the molecule that can be used as a partial structure • -- strong pseudo-symmetry is subtracted

  13. 2 R2 AUTO recycling 4 vector search ROT+ POSN model 3 H.A. Patterson PATTY ORIENT TRACOR TRAVEC PHASEX 2 R2 AUTO recycling 5TRICKS and HELP FOUR 6WHAT is NEXT? summary

  14. R2-driven AUTOMATIC RECYCLING remove one atom: R2 = lower? atom gone! R2 = higher? get it back! 1969 DUAL SPACE recycling direct space electron density interpreation chemical knowledge cell contents, H.A., geometry reciprocal space direct methods R2-criterion MONOS DEMO 6 S only 6a: correct 6b: misplaced run DD PHASEX

  15. partial structure expansion by DIRDIF CAROL 3 mol/cell DDSTART DDMAIN CAROL DEMO DD FOUR NORECY not good DD PHASEX NORECY DD ,, ,, DD ,, ,, going better DD PHASEX perfect PHASEX FOUR NUTS DIRDIF finished

  16. Patterson programs in DIRDIF PATTY ORIENT heavy atoms molecular fragments TRACOR TRAVEC R2 DIRDIF finished

  17. 3 H.A. Patterson 4 vector search ROT+ POSN model 3 H.A. Patterson PATTY ORIENT TRACOR TRAVEC PHASEX 5TRICKS and HELP FOUR 6WHAT is NEXT? summary

  18. HEAVY ATOM PATTERSON PROGRAM PATTY solves crystal structures faster than the chemists can make crystals FOM = < P (vij ) > vij = rj(s) – ri(s’) i, j = atom s, s’ = symmetry r = tentative atomic position from the minimum function v = interatomic vector (based on tentative positions) P = observed Patterson (function value for a vector) FOM = figure of merit using Nordman weights

  19. heavy atom structures with DIRDIF DDSTART DDMAIN DEMO MONOS run DD PATTY PATTY PHASEX FOUR DEMO KAP2 run DD PATTY NUTS DIRDIF finished

  20. origin problem (superstructure) symbolic addition on REAL part symbolic addition on IMAGINAIRY part NGUY origin and enantiomorph PBAG

  21. OXATON - what to do ? 3 independent molecules 3 [ S O5 C19] PATTY: S ? ORIENT: SC7 ? or: OC8 ?

  22. vector search And rec. space correlation functions 4 4 vector search ROT+ POSN model ORIENT TRACOR TRAVEC PHASEX 5TRICKS and HELP FOUR 6WHAT is NEXT? summary

  23. vector search with DIRDIF t (r) (r) (r) ORIENT TRACOR TRAVEC DIRDIF finished

  24. ORBASE and ORUSER ACKNORT WRONG MODEL ?

  25. MODELS FROM YOUR OWN WORK ! 2007 VECTOR SEARCH AS FIT AS A FIDDLE JOOST1 flexible model BASKET

  26. USING THE CAMBR. CRYST. DATA BASE 1976 VECTOR SEARCH HUMMEL MUEN ? ! NOT OK USE NEXT MODEL

  27. 5 TRICKS and HELP 5TRICKS and HELP 6WHAT is NEXT? summary

  28. 6 WHAT is NEXT? 6WHAT is NEXT? summary

  29. MULTISOLUTIONS EB2207 Combine PATTY and R2 results QFOM = SQRT( PFOM * R2expect ) / R2 PATTY-nr PFOM R2exp R2 # QFOM # best output 1 1.000 .422 .616 5 1.055 4 - PFOM OK 2 .948 .422 .626 6 1.010 5 + OK 3 .913 .422 .557 2 1.114 2 + OK 4 .891 .562 .608 3 1.163 1 + QFOM yes 5 .866 .422 .610 4 0.991 6 - OK 6 .842 .422 .556 1 1.072 3 + R2 7 .795 .422 .769 7 0.753 7 - MARS for PATTY TRACOR ORIENT similar

  30. TRANSLATION SEARCH some peaks must be wrong

  31. DIRDIF DEMO NANCY 2006 PATTY ORIENT TRACOR TRAVEC PHASEX R2 FOUR summary

  32. DIRDIF DEMO NANCY 2006 Thank you for your attention PTB

  33. DIRDIF DEMO NANCY 2006 DIRDIF unified 2006

  34. marieken300 300x300 dpi 122 kb

  35. archief kristalman.jpg

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