1. 1 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 Marieken van Nieumeghen DIRDIF computer program for crystal structure determination by Patterson methods and direct methods applied to difference structure factors

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

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

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

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

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

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

8. 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. 9 ENANTIOMORPH PROBLEM FOUR NUTS DIRDIF finished DDSTART DDMAIN MONOS DEMO 5 S misplaced 0.135 A centric! run DD PHASEX NORECY [ repeat!] PHASEX

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

11. 11 1963 DIRECTE METHODEN

12. 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. 13 2 R2 AUTO recycling PATTY PHASEX TRACOR ORIENT TRAVEC FOUR summary 2 R2 AUTO recycling 4 vector search ROT+ POSN model 3 H.A. Patterson 5 TRICKS and HELP 6 WHAT is NEXT?

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

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

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

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

18. 18 HEAVY ATOM PATTERSON PROGRAM PATTY solves crystal structures faster than the chemists can make crystals FOM = 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. 19 heavy atom structures with DIRDIF PATTY PHASEX FOUR NUTS DIRDIF finished DDMAIN DDSTART DEMO MONOS run DD PATTY DEMO KAP2 run DD PATTY

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

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

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

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

24. 24 ORBASE and ORUSER ACKNORT WRONG MODEL ?

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

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

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

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

29. 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. 30 TRANSLATION SEARCH some peaks must be wrong

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

32. 32 DIRDIF DEMO NANCY 2006 PTB

33. 33 DIRDIF DEMO NANCY 2006 DIRDIF unified 2006

34. 34 marieken300 300x300 dpi 122 kb

35. 35 archief kristalman.jpg