Title How to read and understand…. Page Left system crystal system.
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Transcript of Title How to read and understand…. Page Left system crystal system.
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Title
How to read
and understand…
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Page
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Left system
crystal system
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Left point group
point group symbol
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Left space group1
space group symbol
international(Hermann-Mauguin) notation
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Left space group2
space group symbol
Schönflies notation
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Left symmetry diagram
diagram of symmetry operations
positions of symmetry operations
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Left positions diagram
diagram of equivalent positions
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Left origin
origin position vs. symmetry elements
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Left asymmetric
unit
definition of asymmetric unit (not unique)
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Left Patterson
Patterson symmetry
Patterson symmetry group is always primitive centrosymmetric without translational symmetry operations
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Right positions
equivalent positions
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Right special positions
special positions
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Right subgroups
subgroups
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Right absences
systematic absences
systematic absences result from translational symmetry elements
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Right generators
group generators
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Individual items
Interpretation of
individual items
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Left system
crystal system
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Systems
7 (6) Crystal systems
Triclinic a b c , , 90º
Monoclinic a b c 90º, 90º
Orthorhombic a b c 90º
Tetragonal a b c 90º
Rhombohedral a b c
Hexagonal a b c 90º , 120º
Cubic a b c 90º
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Left point group
point group symbol
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Point groups
Point groups describe symmetry of finite objects (at least one point invariant)
Set of symmetry operations:
rotations and rotoinversions
(or proper and improper rotations)
mirror = 2-fold rotation + inversion
Combination of two symmetry operations
gives another operation of the point group
(principle of group theory)
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Point groups general
Point groups describe symmetry of finite objects (at least one point invariant)
Schönflies International Examples
Cn N 1, 2, 4, 6
Cnv Nmm mm2, 4mm
Cnh N/m m, 2/m, 6/m
Cni , S2n N 1, 3, 4, 6
Dn N22 222, 622
Dnh N/mmm mmm, 4/mmm
Dnd N2m, Nm 3m, 42m, 62m
T , Th , Td 23, m3, 43m
O , Oh 432, m3m
Y , Yh 532, 53m
_ _ _ _ _
_ _ _ _ _
_
__
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Point groups crystallographi
c
32 crystallographic point groups (crystal classes) 11 noncentrosymmetric
Triclinic 1 1
Monoclinic 2 m, 2/m
Orthorhombic 222 mm2, mmm
Tetragonal 4, 422 4, 4/m, 4mm, 42m, 4/mmm
Trigonal 3, 32 3, 3m, 3m
Hexagonal 6, 622 6, 6/m, 6mm, 62m, 6/mmm
Cubic 23, 432 m3, 43m, m3m
_
_ _
_ _
_ _
_
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Trp
Trp RNA-binding protein 1QAW
11-foldNCS axis (C11)
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Xyl
Xylose isomerase 1BXB
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Xyl 222
Xylose isomerase 1BXB
Tetramer222 NCSsymmetry (D2)
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Left space group
space group symbols
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Space groups
Combination of point group symmetry with translations
- Bravais lattices
- translational symmetry elements
Space groups describe symmetry of infinite objects (3-D lattices, crystals)
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Bravais lattices
but the symmetry of the crystal is defined by its content, not by the lattice metric
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Choice of cell
Selection of unit cell
- smallest
- simplest
- highest symmetry
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Rhombohedral cell 1
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Rhombohedral cell 2
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Rhombohedral reciprocal lattice 1
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Rhombohedral reciprocal lattice 2
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Rhombohedral reciprocal lattice 3
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Space group symbols
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321 vs. 312
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Left symmetry diagram
diagram of symmetry operations
positions of symmetry operations
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Symmetry operators symbols
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Left origin
origin position vs. symmetry elements
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Origin P212121
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Origin P212121b
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Origin C2
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Origin C2b
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Left asymmetric
unit
definition of asymmetric unit (not unique)
Va.u. = Vcell/N rotation axes cannot pass through the asymm. unit
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Asymmetric unit P21
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Left positions diagram
diagram of equivalent positions
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Right positions
equivalent positions
these are fractional positions
(fractions of unit cell dimensions)
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2-fold axes
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3-fold axis 1
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3-fold axis 2
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Various positions 1
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Various positions 2
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Various positions 3
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Various positions 4
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P43212 symmetry
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P43212 symmetry 1
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P43212 symmetry 2
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P43212 symmetry 2b
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Multiple symmetry axes
Higher symmetry axes include lower symmetry ones
4 includes 2 6 “ 3 and 2 41 and 43 “ 21 42 “ 2 61 “ 31 and 21 65 “ 32 and 21 62 “ 32 and 2 64 “ 31 and 2 63 “ 3 and 21
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P43212 symmetry 3
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P43212 symmetry 4
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P43212 symmetry 4b
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P43212 symmetry 5
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P43212 symmetry 6
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P43212 symmetry 7
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P43212 symmetry 8
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P43212 symmetry 8b
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Right special positions
special positions
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Special positions 0
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Special positions 1
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Special positions 2
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Special positions 3
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Special positions 3b
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Special positions
Special positions
on non-translational symmetry elements (axes, mirrors or inversion centers)
degenerate positions (reduced number of sites)
sites have their own symmetry (same as the symmetry element)
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Right subgroups
subgroups
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Subgroups
Subgroups
reduced number of symmetry elements
cell dimensions may be special
cell may change
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Subgroups 0
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Subgroups 1a
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Subgroups 1b
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Subgroups 3a
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Subgroups 3b
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Subgroups 2a
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Subgroups 2b
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Subgroups PSCP
Dauter, Z., Li M. & Wlodawer, A. (2001). Acta Cryst. D57, 239-249.
After soaking in NaBr cell changed, half of reflections disappeared
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PSCP orthorhombic diffraction 1
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PSCP orthorhombic diffraction 2
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PSCP hexagonal diffraction
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Right generators
group generators
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Generators 1
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Generators 2
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Generators 3
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Generators 4
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Generators 5
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Right absences
systematic presences (not absences)
systematic absences result from translational symmetry elements
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Absences 1
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Absences 2
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Left Patterson
Patterson symmetry
Patterson symmetry group is always primitive centrosymmetric without translational symmetry operations
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Personal remark
My personal remark:
I hate when people quote space groups
by numbers instead of name.
For me the orthorhombic space group
without any special positions is
P212121, not 19
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