factors affecting data quality - university of california,...
TRANSCRIPT
![Page 1: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/1.jpg)
Factors affecting data quality
Simon J. Teat
Advanced Light Source
21th April 2015
![Page 2: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/2.jpg)
Scattering Efficiency
• Scattering Efficiency = f2 Vcrystal
V2cell
• where:-
• f = number of electrons per atom
• Vcrystal = volume of the crystal
• Vcell = volume of the unit cell
M.M.Harding J. Synchrotron Radiation, 250-259 1996
![Page 3: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/3.jpg)
Effect of disorder
![Page 4: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/4.jpg)
Other factors
• Wavelength
– modify strong of interaction
• Rocking width/Mosaicity and size
broadening
– Signal to noise
• Intensity of incident beam
![Page 5: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/5.jpg)
Data: What do you want from it?
• Connectivity
• Hydrogen position
• Accurate bond lengths and angles
• Absolute configuration
![Page 6: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/6.jpg)
Data: Any good?
• What does the diffraction look like?
• How well does it index?
• What does the reciprocal lattice look like?
• How well does it integrate?
• Space group determination ease?
• Structure solves easily?
• Structure refines well?
![Page 7: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/7.jpg)
Look at the Diffraction Pattern
![Page 8: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/8.jpg)
Fobs Map at 2.50Å
![Page 9: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/9.jpg)
Fobs Map at 2.0Å
![Page 10: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/10.jpg)
Fobs Map at 1.75Å
![Page 11: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/11.jpg)
Fobs Map at 1.50Å
![Page 12: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/12.jpg)
Fobs Map at 1.25Å
![Page 13: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/13.jpg)
Fobs Map at 1.00Å
![Page 14: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/14.jpg)
Fobs Map at 0.75Å
![Page 15: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/15.jpg)
0.50Å
![Page 16: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/16.jpg)
Fobs and Difference Map 0.5Å
![Page 17: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/17.jpg)
Indexing
![Page 18: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/18.jpg)
Cell Refinement
![Page 19: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/19.jpg)
View the lattice
![Page 20: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/20.jpg)
Lattice and Integration Resolution
![Page 21: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/21.jpg)
Integration
![Page 22: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/22.jpg)
Sadabs
![Page 23: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/23.jpg)
XPREP
![Page 24: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/24.jpg)
XPREP
![Page 25: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/25.jpg)
XPREP
![Page 26: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/26.jpg)
Monoclinic
![Page 27: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/27.jpg)
Indexing
![Page 28: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/28.jpg)
Cell Refinement
![Page 29: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/29.jpg)
Lattice Choice
![Page 30: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/30.jpg)
View of the Reciprocal Space
![Page 31: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/31.jpg)
![Page 32: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/32.jpg)
![Page 33: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/33.jpg)
Both Orientations
![Page 34: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/34.jpg)
The Crystal is a Reticular Twin
• Integrate both components
• TWINABS- HKLF 4 and 5
![Page 35: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/35.jpg)
The Crystal is a Reticular Twin
• HKLF 4 data through XPREP
• Potentially go back to TWINABS and
XPREP
• Solve on HKLF 4 data
• Refine with both HKLF 4 and 5 data
![Page 36: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/36.jpg)
Types of Twinning – Merohedral
• The twinning operator is part of the Laue Class not the point group
– Racemic twinning e.g looks like 2/m but is 2
– Tetrahedral, Trigonal/hexagonal, Cubic e.g. looks like 4/mmm but is 4/m
– Pseudo-merohedral • The twinning operator is part of the symmetry of the higher cell
e.g. look orthorhombic but is monoclinic.
– Reticular • e.g obverse/reverse twinning, false centred cell.
– Non-Merohedral • The twinning operator transforms between the two orientations
can be anything but commonly 180º
![Page 37: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/37.jpg)
Indication of twinning
• Multiple diffraction patterns
• |E*E-1| smaller than would be expected
• Problems choosing spacegroup
• Problems solving structure
• Large residual peak in non-sensible places
• K-values for weak data
• Disagreement reflects Fobs >> Fcalc
• Weighting scheme large
• Poor refinement R1 high than expected
![Page 38: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/38.jpg)
Not Twinned?
![Page 39: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/39.jpg)
|E*E-1|
![Page 40: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/40.jpg)
LST file indications
![Page 41: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/41.jpg)
INS format for TWIN
![Page 42: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/42.jpg)
![Page 43: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/43.jpg)
![Page 44: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/44.jpg)
![Page 45: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/45.jpg)
![Page 46: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/46.jpg)
![Page 47: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/47.jpg)
![Page 48: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/48.jpg)
![Page 49: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/49.jpg)
Supercells
Attfield et al
Al(O3PCH2CH2PO3)(OH)
(H3NCH2CH2NH3)
Monoclinic P21/m
a = 8.052 = 90
b = 7.029 = 98.441
c = 8.977 = 90
Volume = 503.2
![Page 50: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/50.jpg)
![Page 51: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/51.jpg)
Supercells
Synchrotron Cell
Monoclinic P21/n
a = 11.142 = 90
b = 7.008 = 96.24
c = 12.903 = 90
Volume = 1001.50
Lab Cell
Monoclinic P21/m
a = 8.052 = 90
b = 7.029 = 98.441
c = 8.977 = 90
Volume = 503.2
Al(O3PCH2CH2PO3)(OH)(H3NCH2CH2NH3)
![Page 52: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/52.jpg)
Supercells
Lattice exceptions: P A B C I F Obv Rev All
N (total) = 0 2987 2979 2982 2987 4474 3965 3964 5956
N (int>3sigma) = 0 1639 1233 1592 1583 2232 2163 2171 3233
Mean intensity = 0.0 22.2 8.3 22.1 19.3 17.5 21.2 20.7 20.9
Mean int/sigma = 0.0 6.0 3.9 5.9 5.8 5.3 6.0 5.9 5.9
![Page 53: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/53.jpg)
Supercells
![Page 54: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/54.jpg)
Rosseinsky et al
NiC28H14O7N2
Trigonal P3
a = 19.285 = 90
b = 19.285 = 90
c = 11.270 = 120
Volume = 3665.9
Rosseinsky et al
![Page 55: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/55.jpg)
Supercells
![Page 56: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/56.jpg)
Supercells
![Page 57: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/57.jpg)
Supercells
NiC28H14O7N2
Trigonal P3
a = 33.521 = 90
b = 33.521 = 90
c = 11.302 = 120
Volume = 10998
NiC28H14O7N2
Trigonal P3
a = 19.285 = 90
b = 19.285 = 90
c = 11.270 = 120
Volume = 3665.9
![Page 58: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/58.jpg)
Supercells
![Page 59: Factors affecting data quality - University of California, Berkeleyyaghi.berkeley.edu/research-news/Lecture_2_SJT_factors.pdfTypes of Twinning –Merohedral • The twinning operator](https://reader033.vdocument.in/reader033/viewer/2022060822/609b5df63df668061d33bda8/html5/thumbnails/59.jpg)
Supercells