Crystallography & Symmetry
patterns derived from their groups
Concept

Special position — where it appears

A point some operation of the group leaves fixed, so that its orbit is smaller and its multiplicity lower than a general point's. They are where atoms sit, where a structure's formula comes from, and where a careless motif destroys the group it was meant to illustrate.

Named by 14 essays across 5 fields — each of them below, with the objects they name alongside it.

{111} in class m3̅m. The form {111} of crystal class m3̅m: 8 faces, being the orbit of one face under the 48 operations of the class, with a stabiliser of order 6. 4 poles lie in the upper hemisphere or in the plane of the page and are drawn filled; the other 4 lie below and are drawn open at the same positions, which is the stereographic convention and the reason only the upper ones carry their indices. The form is closed: the faces enclose a volume, so a crystal can be bounded by this form alone.

A form is an orbit, and whether it closes is an integer question

Name one face of a crystal and its class names the rest. That set is a form, it is an orbit in exactly the sense this site has used since its first essay, and whether it encloses a volume — whether a crystal could be bounded by it alone — is decided without any lengths or angles entering the calculation anywhere.

applied · Forms 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 Special positions in p4m. Every point of a 12×12 grid inside the cell of p4m, drawn at a size set by how many operations fix it. 80 of the 144 are general — nothing but the identity leaves them alone, so their orbit is the full 8 points. The other 64 are special, and fall into 3 kinds: 60 points fixed by 2 operations, with orbits of 4; 2 points fixed by 4 operations, with orbits of 2; 2 points fixed by 8 operations, with orbits of 1.

The points a group treats differently

Almost every point of a cell has an orbit as long as the group. The exceptions are the points some operation leaves alone, and they are where atoms sit, where a structure's formula comes from, and where a careless motif destroys the group it was meant to illustrate.

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 P2₁2₁2₁: the sections its symmetry forces. The Patterson cell of P2₁2₁2₁ with the sections marked. Each operation (M, t) sends an atom at x to Mx + t, so the vector between them is (I − M)x − t; where I − M is singular that vector cannot leave a plane, and the plane's equation comes from the left null space in integers. This group has 3 such operations, giving the sections w = 0.5, u = 0.5, v = 0.5. A heavy atom's vector to its own image is somewhere on one of them, which is what made structure solution possible before computers: a plane can be searched by eye and a volume cannot.

Where symmetry stacks the vectors

A Patterson map of a real structure is a blur with thousands of overlapping peaks. A screw axis rescues it: the vectors between symmetry-related atoms cannot leave a plane, so the search for a heavy atom is a search of a section rather than of a volume — and which plane it is falls out of the operation's matrix in integers.

diffraction · The Patterson function p4m: 10 of 36 wavevectors have to be visited. The Brillouin zone of the square lattice with a grid of 36 wavevectors on it, of which 10 are drawn solid: one per star, which is everything a calculation over a p4m-symmetric operator has to visit. The share is 27.8 per cent against the 12.5 per cent that the order of the point group would give, and it is larger for a reason worth naming — the wavevectors on the boundary of the wedge have short stars, so they are over-counted by any argument that only divides by the group order. The identity that is checked is that the star sizes add to the whole grid.

The domain in reciprocal space

A fundamental domain is the piece of a pattern the group repeats, and this collection has drawn several. The same idea in reciprocal space is what makes a calculation over a crystal affordable — and its share of the zone is larger than one part in the group's order, for a reason worth measuring.

operations · Fundamental domain Dropping one invariant of 3m makes two orbits agree. Every lattice point within four cells of the origin, coloured by the values a proper subset of 3m's invariants takes on it — the 2 generators with the first one removed, over a window of 4 cells. With the full set, the 25 orbits of the group take 25 distinct sets of values, one each, so the invariants are a complete set of coordinates on the quotient. With one removed, the two circled points — in different orbits, so no operation of the group carries one to the other — take the same values and become indistinguishable. That is the whole content of the statement that a complete set of invariants separates orbits: the completeness is what is doing the work.

An orbit is what the invariants cannot tell apart

Two points of the plane lie in the same orbit of a group exactly when every invariant polynomial takes the same value on both. One direction of that is a definition; the other is a theorem, and it is checked here by comparing every pair of points in a window both ways.

operations · Counting orders 5 and 7 reach a site of symmetry 1 and no more. A molecule whose only symmetry is one n-fold axis, and the highest site symmetry it may occupy in any of the 45 space groups this site builds. The site's symmetry has to be a subgroup of the molecule's, so the site's order must divide n and the site group must be cyclic. Orders 1, 2, 3, 4 and 6 reach a site of their own order. Orders 5 and 7 reach one, because no site symmetry in any space group contains an operation of order five or seven — the orders available are 1, 2, 3, 4, 6, computed by asking every operation of every group whether it moves a point. A five-fold molecule keeps its axis; the crystal simply has no use for it.

What a molecule gives up to sit in a crystal

A molecule brings its own symmetry. A crystal offers sites with symmetries of their own, and the two have to be compatible — the site's symmetry must be a subgroup of the molecule's. So a molecule may always keep more than its site offers, and a molecule with a five-fold axis may sit only where the crystal offers nothing at all.

restriction · Local symmetry 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 What each Laue class buys, in measurements per reflection. The eleven Laue classes, with how many distinct reflections a block of indices holds under each and how many times a data set measures the average one. The redundancy is always below the order of the class and the gap is the special reflections. This is the number an experiment is planned around: repeated measurements of what symmetry says must agree are the only estimate of precision that does not come from a model, so a triclinic crystal has to be turned through far more of the sphere than a cubic one to be measured as well.

Every reflection, several times over

A diffraction experiment does not measure each reflection once. Symmetry relates a reflection to the others of its orbit, and those are the same reflection seen from another direction — so a hundred thousand measurements may contain twelve thousand reflections, each observed eight times.

diffraction · Resolution 19 site symmetries, and the counts each can impose. Every distinct site symmetry across the space groups this site builds, named by the multiset of its operation types, with the orientation counts a disordered molecule there may take. The counts are the indices of the site group's subgroups, computed by closing subsets under multiplication rather than looked up. Nearly every row offers every divisor of its order. One does not: a site of order twelve whose group is the tetrahedral rotation group refuses an orientation count of two, because that group has no subgroup of order six.

How many orientations a disorder needs

A molecule at a site with more symmetry than it has resolves the contradiction by occupying several orientations at once. How many is not fitted: it is the index of the molecule's symmetry in the site's, so the occupancy is the reciprocal of a whole number — and one site in the census refuses a divisor of its own order.

restriction · Local symmetry Disorder models against occupancies, site by site. Every distinct site symmetry in the space groups built here — 19 of them — with its order, its number of subgroups, the number of distinct disorder models, which are the subgroups up to conjugacy by the operations of the site symmetry, and the number of different occupancies those models can have. The last column is the largest number of models that share one occupancy. In all, 162 models share far fewer occupancies; the most crowded is 4/mmm, where 11 different models all give an occupancy of 1/4. At every site, the classes of operation a model keeps separate it from every other model with the same occupancy.

The occupancy does not name the disorder

A molecule disordered on a special position takes a number of orientations fixed by a group index, and its occupancy is the reciprocal. Many different disorders share one occupancy — eleven at a single kind of tetragonal site — and what separates them is which of the site's operations the molecule keeps, which the averaged structure records and the occupancy does not.

restriction · Local symmetry The average is the site's orbit, with occupancies. A molecule at a site of symmetry mmm keeping a subgroup of order two takes four orientations, and the average over them is the site group's orbit of each of the molecule's atoms, every image at one over the length of its own orbit. Atoms in general positions give eight images at an eighth each, and give the same eight whichever subgroup the molecule keeps. Atoms on a locus the model keeps give a shorter orbit at a higher occupancy, drawn larger and darker, and those are the only atoms that differ between models. The total scattering is the same for every model, so all of them agree exactly at zero scattering angle.

The molecule size that hides a disorder

Two disorder models with the same occupancy leave averaged structures that differ only in a handful of partial atoms. The difference is 20% in structure factors for a ten-atom molecule and 3% for a sixty-atom one — so the data choose between the models for a small molecule and stop choosing for a large one, and seven pairs are identical at any size.

restriction · Local symmetry Two symmetric structures a diffraction pattern cannot separate. Two arrangements of 6 atoms on a 6 × 6 torus, each invariant under the plane group p6m, drawn beside the Patterson they share. No translation and no inversion carries one onto the other, so they are different structures; every one of the thirty-six interatomic vector counts is the same, so every diffracted intensity is the same and no measurement at any resolution separates them. Of the 4 structures with this symmetry and this many atoms, there are only 3 Pattersons — so imposing the most symmetric of the seventeen plane groups has not removed the ambiguity.

Symmetry does not rescue a Patterson

Every homometric pair found so far sits on a bare ring with no operations imposed, and a real crystal sits in a space group. Impose one and the ambiguity does not go away: 12 of the 13 groups searched still have pairs, and at six atoms the hexagonal groups are indistinguishable two to three times as often as the general position.

diffraction · Homometry

Named alongside it

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

OrbitStabiliserMultiplicitySite symmetryAsymmetric unitAverage structureEnumerationOccupancyStructure factorSubgroupWyckoff positionsDisorder

All concepts