DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE

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DIRDIFROUTINE 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

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DIRDIF DEMO NANCY 2006 INTRO

PATTY

PHASEX

TRACOR

ORIENT

TRAVEC

FOUR

summary

2R2 AUTO

recycling

4vector search

ROT+

POSN

model

3H.A.

Patterson

1DIR meth. >

DIF struct.

5 TRICKS and HELP

6 WHAT is NEXT?

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INTRO DIRDIF LOGISTICS

DDSTART

DDMAIN

PATTY

PHASEX

TRACOR

ORIENT

TRAVEC

FOUR

NUTS

organizer

supervisor

utilities

DIRDIF finished

R2

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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 !

runDD FOUR NORECY

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the problem starting phases?

sigma-2 or result

tangent formula

AB INITIO DIRECT METHODS

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DIRECT METHODSapplied to

DIFFERENCE STRUCTURE FACTORS

Fp part.str.f.known

Fr part.str.f. unnkown

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DIRDIF

FOUR

NUTS

DIRDIF finished

DDSTART

DDMAIN

MONOS

DEMO 4 S only with PHASEX

runDD PHASEX NORECY

PHASEX

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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 with999 known phases + 10 unknown lettersymbols

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ENANTIOMORPH PROBLEM

FOUR

NUTS

DIRDIF finished

DDSTART

DDMAIN

MONOS

DEMO 5 S misplaced 0.135 A centric!runDD PHASEX NORECY[ repeat!]

PHASEX

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H.A. PSEUDOSYMMETRY

SbS4.....

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1963 DIRECTE METHODEN

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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

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2

R2 AUTO recycling

PATTY

PHASEX

TRACOR

ORIENT

TRAVEC

FOUR

summary

2R2 AUTO

recycling

4vector search

ROT+

POSN

model

3H.A.

Patterson

5 TRICKS and HELP

6 WHAT is NEXT?

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R2-driven AUTOMATIC RECYCLING

remove one atom: R2 = lower? atom gone!R2 = higher? get it back!

reciprocal spacedirect methodsR2-criterion

MONOS DEMO 6

S only

6a: correct6b: misplaced

run DD PHASEX

direct spaceelectron density interpreationchemical knowledgecell contents, H.A., geometry

1969 DUAL SPACE recycling

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partial structure expansion byDIRDIF

DDSTART

DDMAIN

PHASEX

FOUR

NUTS

DIRDIF finished

CAROL 3 mol/cell

CAROL DEMO

DD FOUR NORECYnot good

DD PHASEX NORECY DD ,, ,, DD ,, ,, going better

DD PHASEXperfect

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Patterson programs inDIRDIF

PATTY

TRACOR

ORIENT

TRAVEC

DIRDIF finished

R2

molecular

fragments

heavyatoms

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3

H.A. Patterson

PATTY

PHASEX

TRACOR

ORIENT

TRAVEC

FOUR

summary

4vector search

ROT+

POSN

model

3H.A.

Patterson

5 TRICKS and HELP

6 WHAT is NEXT?

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HEAVY ATOM PATTERSON

PROGRAM PATTYsolves crystal structures fasterthan the chemists can make crystals

FOM = < P (vij ) >vij = rj(s) – ri(s’)

i, j = atom s, s’ = symmetryr = tentative atomic position from the minimum functionv = interatomic vector (based on tentative positions)P = observed Patterson (function value for a vector)FOM = figure of merit using Nordman weights

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heavy atom structures withDIRDIF

PATTY

PHASEX

FOUR

NUTS

DIRDIF finished

DDMAIN

DDSTART

DEMOMONOS

run DD PATTY

DEMOKAP2

run DD PATTY

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origin problem (superstructure)

symbolic addition on REAL part

symbolic addition on IMAGINAIRY part

origin and

enantiomorph

NGUY

PBAG

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OXATON - what to do ?

3 independent molecules

3 [ S O5 C19]

PATTY: S ?

ORIENT: SC7 ?

or: OC8 ?

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vector searchAnd rec. space correlation functions

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PHASEX

TRACOR

ORIENT

TRAVEC

FOUR

summary

4vector search

ROT+

POSN

model

5 TRICKS and HELP

6 WHAT is NEXT?

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(r)

vector search withDIRDIF

TRACOR

ORIENT

TRAVEC

DIRDIF finished

t

(r) (r)

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ORBASE and ORUSER

ACKNORT

WRONG MODEL ?

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MODELS FROM YOUR OWN WORK !

model BASKET

JOOST1

2007VECTOR SEARCH AS FIT AS A FIDDLE

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HUMMEL

USING THE CAMBR. CRYST. DATA BASE

NOT OK USE NEXT MODEL

MUEN

1976

VECTOR

SEARCH

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5 TRICKS and HELP

summary

5 TRICKS and HELP

6 WHAT is NEXT?

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6 WHAT is NEXT?

summary

6 WHAT is NEXT?

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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

forPATTYTRACORORIENTsimilar

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TRANSLATION SEARCH

some peaks

must be wrong

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DIRDIF DEMO NANCY 2006

PATTY

PHASEX

TRACOR

ORIENT

TRAVEC

FOUR

summary

R2

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DIRDIF DEMO NANCY 2006

PTB

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DIRDIF DEMO NANCY 2006

DIRDIF unified 2006

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