Crystallography & Symmetry
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A 5-fold cluster in a crystal that has no 5-fold axis

A 5-fold cluster in a crystal that has no 5-fold axis
A 5-fold cluster in a crystal that has no 5-fold axis. A cluster of 10 points with an exact 5-fold axis at the centre of each cell, repeated by the lattice. Two measurements, on the same points. The cluster is carried onto itself by a turn of 72° to within 2e-16 of a cell — exact, as far as the arithmetic goes. The pattern is not: applying the same turn about a lattice point sends some atoms 1.19 of a cell from the nearest atom, which is most of the way across it. Both are true at once. The axis is a symmetry of the contents of one cell and not of the crystal, which is what non-crystallographic symmetry means and why a virus with a sixty-fold capsid can crystallise in an ordinary space group.

A cluster of 10 points with an exact 5-fold axis at the centre of each cell, repeated by the lattice. Two measurements, on the same points. The cluster is carried onto itself by a turn of 72° to within 2e-16 of a cell — exact, as far as the arithmetic goes. The pattern is not: applying the same turn about a lattice point sends some atoms 1.19 of a cell from the nearest atom, which is most of the way across it. Both are true at once. The axis is a symmetry of the contents of one cell and not of the crystal, which is what non-crystallographic symmetry means and why a virus with a sixty-fold capsid can crystallise in an ordinary space group.

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A 5-fold cluster in a crystal that has no 5-fold axis. A cluster of 10 points with an exact 5-fold axis at the centre of each cell, repeated by the lattice. Two measurements, on the same points. The cluster is carried onto itself by a turn of 72° to within 2e-16 of a cell — exact, as far as the arithmetic goes. The pattern is not: applying the same turn about a lattice point sends some atoms 1.19 of a cell from the nearest atom, which is most of the way across it. Both are true at once. The axis is a symmetry of the contents of one cell and not of the crystal, which is what non-crystallographic symmetry means and why a virus with a sixty-fold capsid can crystallise in an ordinary space group. What a lattice forbids

A fivefold axis in an ordinary crystal

A virus with sixty-fold symmetry crystallises in a space group that has none of it. The restriction forbids a fivefold axis to the lattice and says nothing about what sits inside one cell — so the axis is exact, the crystal genuinely lacks it, and both statements are measurable on the same set of atoms.

 p2 in one cell, p4 on average. On the left, a molecule in one orientation at a site whose symmetry is larger than its own: the arrangement has 2 operations and the detector says p2. On the right, the average over the 2 orientations the site offers, which is what a diffraction experiment measures because different cells choose differently and nothing prefers one choice. The average has 4 operations — it is p4 — and every atom in it is present in half of the cells. Both groups are detected from the point sets rather than assumed, and the difference between them is the reason a refined structure can have symmetry no molecule in the crystal has. What a lattice forbids

The symmetry of an average

A diffraction experiment measures an average over some 10²⁰ unit cells, and the average of several orientations is more symmetric than any of them. So a refined structure can carry symmetry that no molecule in the crystal has — including, in the worst case, a centre of inversion in a crystal built entirely of one hand.

 The most of an icosahedron a crystal can keep. Every subgroup of the sixty rotations of an icosahedron, found by closure, with the crystallographic ones marked — those whose rotation orders are all among the 1, 2, 3, 4 and 6 that a three-dimensional lattice admits. The largest is 23, of order 12, at index 5; everything containing a fivefold axis is refused. So a crystal containing an icosahedral molecule may fix a twelfth of the molecule's own symmetry and no more, and the remaining 5 orientations have to be related by something other than the site's symmetry. What a lattice forbids

The most of an icosahedron a crystal can keep

C₆₀ sits in crystals and virus capsids sit in crystals, and neither of them stops being icosahedral. What a lattice can fix is a subgroup — and the largest crystallographic subgroup of the sixty rotations has order twelve, at index five. The five are Kepler's five cubes.

 5 units of 70.53°: 7.36° left. 5 tetrahedral units of face-centred cubic metal, each the mirror image of its neighbour in a {111} plane, arranged about a common ⟨110⟩ edge. The angle between two such planes is arccos(1/3) = 70.53°, computed from the plane normals rather than quoted, and 5 of them come to 352.64°. The shaded sector is what is left over: 7.36°, or 2.04 per cent of a full turn, which must be taken up by strain, by a gap, or by a defect along the axis. What a lattice forbids

Five copies, and the gap they leave

Gold, silver and silicon grow particles with a five-fold axis down the middle, out of a lattice that forbids one. Nothing is violated: five tetrahedral pieces of ordinary face-centred metal, each the mirror image of its neighbour, come to three hundred and fifty-two and a half degrees rather than three hundred and sixty — and the seven degrees left over have to go somewhere.

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