Crystallography & Symmetry
patterns derived from their groups
Concept

Asymmetric unit — where it appears

The smallest part of a cell from which the group rebuilds the rest, and the part a crystallographer actually refines. Its volume is the cell's divided by the group's order, except that it is always a little more and the excess is the special positions counted whole.

Named by 7 essays across 4 fields — each of them below, with the objects they name alongside it.

Why p4 cannot be drawn with dots. The same group applied to a single dot and to a motif with no symmetry of its own. The dot's orbit turns out to have more symmetries than the group it was made with, so a figure drawn that way illustrates a different group from the one in its caption.

The motif must be a comma

A dot is too symmetric to illustrate most wallpaper groups. Its orbit acquires mirrors nobody asked for, and the resulting figure is quietly of a different group from the one in its caption.

classification · Accidental symmetry Growing the p4 orbit. One motif, then more of the group's operations applied to it, until applying another produces nothing new. The pattern is the orbit; the drawing is only its shadow.

The orbit is the pattern

A wallpaper is not designed and then found to have symmetry. It is the set of places a group sends a single mark, and once that is taken literally the pattern can be grown, checked, and caught out.

operations · What symmetry is 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 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.

restriction · Local symmetry A fundamental domain for p4m. One representative from every orbit of p4m, shaded, with the images that tile the rest of the cell. The domain was found by computing orbits rather than by drawing a region, and every sample's orbit was checked to meet it exactly once — so the region has neither a gap nor an overlap.

The fundamental domain

The smallest piece of a pattern from which the group rebuilds the rest. Drawing one is easy and drawing one correctly is not, because a region with a gap or an overlap looks exactly like a region without.

operations · Fundamental domain The general positions of P2₁/c. Space group P2₁/c, number 14, projected down c on a primitive monoclinic cell. 12 general positions, the orbit of a three-point asymmetric motif, each labelled with its height along c and marked with a comma where the operation that produced it reversed handedness.

One part in however many, and why it is never quite that

A crystal's contents are the asymmetric unit repeated by the group. The unit's volume is the cell's divided by the order of the group — except that it is always a little more, and the excess is exactly the special positions counted whole.

operations · Fundamental domain p4 inside p4m, by area. A fundamental domain for p4m beside one for p4, drawn by the same construction on the same grid. p4 sits inside p4m with index 2: it has 8 ÷ 4 = 2 times as few operations to rebuild the pattern with, so it needs 2 times as much of the cell to rebuild it from — measured here at 1.51 times as many samples. The two domains are one region and 2 copies of it, and the ratio between them is the index rather than a coincidence of shape.

Domains of a subgroup

A group with half the operations needs twice as much of the cell to rebuild the pattern from. That single sentence is the index arithmetic of the whole classification, and it turns the containments among the seventeen into a statement about area.

operations · Fundamental domain Observations per unknown, against resolution. Unique reflections divided by refinable parameters, for a triclinic cell, no angle a right angle, with three coordinates and six displacement parameters for every atom and one non-hydrogen atom per 18 ų, in a molecular crystal. The scale is logarithmic because the fall is a cube: 16.3 at 0.8 Å and 0.30 at 3 Å. The line at one is where a determination stops being over-determined, and it is crossed at about 2.0 Å.

The unknowns against the observations

A structure determination is a fit of some number of parameters to some number of measurements, and both counts can be worked out before any data exist. The ratio turns out not to depend on how large the crystal's cell is, or on how symmetric it is — only on the resolution, and on that as a cube.

diffraction · Resolution

Named alongside it

The objects these essays reach for when they reach for this one.

StabiliserFundamental domainOrbitSpecial positionRound tripAccidental symmetryClassificationCosetCountingEnumerationFormula unitsIndex

All concepts