dirdif routine structure solution using your chemical knowledge
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1
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?
3
INTRO DIRDIF LOGISTICS
DDSTART
DDMAIN
PATTY
PHASEX
TRACOR
ORIENT
TRAVEC
FOUR
NUTS
organizer
supervisor
utilities
DIRDIF finished
R2
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 !
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
4
PHASEX
TRACOR
ORIENT
TRAVEC
FOUR
summary
4vector search
ROT+
POSN
model
5 TRICKS and HELP
6 WHAT is NEXT?
23
(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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