1 dirdif routine structure solution using your chemical knowledge paul t. beurskens gezina beurskens...
TRANSCRIPT
![Page 1: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/1.jpg)
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
![Page 2: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/2.jpg)
2
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?
![Page 3: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/3.jpg)
3
INTRO DIRDIF LOGISTICS
DDSTART
DDMAIN
PATTY
PHASEX
TRACOR
ORIENT
TRAVEC
FOUR
NUTS
organizer
supervisor
utilities
DIRDIF finished
R2
![Page 4: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/4.jpg)
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
![Page 5: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/5.jpg)
5
the problem starting phases?
sigma-2 or result
tangent formula
AB INITIO DIRECT METHODS
![Page 6: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/6.jpg)
6
DIRECT METHODSapplied to
DIFFERENCE STRUCTURE FACTORS
Fp part.str.f.known
Fr part.str.f. unnkown
![Page 7: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/7.jpg)
7
DIRDIF
FOUR
NUTS
DIRDIF finished
DDSTART
DDMAIN
MONOS
DEMO 4 S only with PHASEX
runDD PHASEX NORECY
PHASEX
![Page 8: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/8.jpg)
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 with999 known phases + 10 unknown lettersymbols
![Page 9: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/9.jpg)
9
ENANTIOMORPH PROBLEM
FOUR
NUTS
DIRDIF finished
DDSTART
DDMAIN
MONOS
DEMO 5 S misplaced 0.135 A centric!runDD PHASEX NORECY[ repeat!]
PHASEX
![Page 10: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/10.jpg)
10
H.A. PSEUDOSYMMETRY
SbS4.....
![Page 11: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/11.jpg)
11
1963 DIRECTE METHODEN
![Page 12: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/12.jpg)
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
![Page 13: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/13.jpg)
13
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?
![Page 14: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/14.jpg)
14
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
![Page 15: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/15.jpg)
15
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
![Page 16: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/16.jpg)
16
Patterson programs inDIRDIF
PATTY
TRACOR
ORIENT
TRAVEC
DIRDIF finished
R2
molecular
fragments
heavyatoms
![Page 17: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/17.jpg)
17
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?
![Page 18: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/18.jpg)
18
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
![Page 19: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/19.jpg)
19
heavy atom structures withDIRDIF
PATTY
PHASEX
FOUR
NUTS
DIRDIF finished
DDMAIN
DDSTART
DEMOMONOS
run DD PATTY
DEMOKAP2
run DD PATTY
![Page 20: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/20.jpg)
20
origin problem (superstructure)
symbolic addition on REAL part
symbolic addition on IMAGINAIRY part
origin and
enantiomorph
NGUY
PBAG
![Page 21: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/21.jpg)
21
OXATON - what to do ?
3 independent molecules
3 [ S O5 C19]
PATTY: S ?
ORIENT: SC7 ?
or: OC8 ?
![Page 22: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/22.jpg)
22
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?
![Page 23: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/23.jpg)
23
(r)
vector search withDIRDIF
TRACOR
ORIENT
TRAVEC
DIRDIF finished
t
(r) (r)
![Page 24: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/24.jpg)
24
ORBASE and ORUSER
ACKNORT
WRONG MODEL ?
![Page 25: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/25.jpg)
25
MODELS FROM YOUR OWN WORK !
model BASKET
JOOST1
2007VECTOR SEARCH AS FIT AS A FIDDLE
![Page 26: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/26.jpg)
26
HUMMEL
USING THE CAMBR. CRYST. DATA BASE
NOT OK USE NEXT MODEL
MUEN
1976
VECTOR
SEARCH
![Page 27: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/27.jpg)
27
5 TRICKS and HELP
summary
5 TRICKS and HELP
6 WHAT is NEXT?
![Page 28: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/28.jpg)
28
6 WHAT is NEXT?
summary
6 WHAT is NEXT?
![Page 29: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/29.jpg)
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
forPATTYTRACORORIENTsimilar
![Page 30: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/30.jpg)
30
TRANSLATION SEARCH
some peaks
must be wrong
![Page 31: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/31.jpg)
31
DIRDIF DEMO NANCY 2006
PATTY
PHASEX
TRACOR
ORIENT
TRAVEC
FOUR
summary
R2
![Page 32: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/32.jpg)
32
DIRDIF DEMO NANCY 2006
PTB
![Page 33: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/33.jpg)
33
DIRDIF DEMO NANCY 2006
DIRDIF unified 2006
![Page 34: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/34.jpg)
34
marieken300
300x300 dpi
122 kb
![Page 35: 1 DIRDIF ROUTINE STRUCTURE SOLUTION USING YOUR CHEMICAL KNOWLEDGE Paul T. Beurskens Gezina Beurskens Rene de Gelder Santiago Garcia-Granda Robert O. Gould](https://reader030.vdocuments.us/reader030/viewer/2022032606/56649eab5503460f94bb0e64/html5/thumbnails/35.jpg)
35
archiefkristalman.jpg