Crystallography & Symmetry
patterns derived from their groups
Concept

Structure factor — where it appears

The sum over a cell's atoms of their scattering with a phase from each position, whose modulus is what a diffraction experiment records. Every systematic absence on this site is computed from that sum rather than looked up, which turns an extinction condition into a theorem.

Named by 55 essays across 9 fields — each of them below, with the objects they name alongside it.

A lattice and its reciprocal. The reciprocal lattice is where a crystal scatters. A long axis in the crystal gives closely spaced spots and a short one gives widely spaced spots, so the diffraction pattern is the structure turned inside out.

The reciprocal lattice

Nobody has seen a space group. Crystals are read from where they scatter, and where they scatter is a second lattice in which long has become short and short has become long.

diffraction · Diffraction What pg scatters. The diffraction pattern computed from the atom positions alone. Where a glide plane is present, alternate reflections along a row cancel exactly — and those missing spots are how the glide is identified in an experiment, since the glide itself is never seen.

Systematic absences

The most informative part of a diffraction pattern is the part that is not there. A glide plane cancels alternate reflections along a row, exactly, and those missing spots are how a symmetry nobody can see is identified.

diffraction · Diffraction The phase problem. The same structure rebuilt from its diffraction three ways: with the true amplitudes and phases, with the phases scrambled, and with the amplitudes discarded but the phases kept. The atoms survive the loss of the amplitudes and do not survive the loss of the phases, which is what an experiment throws away.

The phase problem

A detector records how much light arrives and not when it arrives, so half of every diffraction measurement is thrown away before it is written down. The half that is lost turns out to be the half that carries the structure.

diffraction · Diffraction What p3 scatters, and what the scattering shows. The structure on the left has point group 3, of order 3. The intensities it scatters, on the right, have point group 6, of order 6 — more symmetric than the thing that produced them. Reversing the sign of both indices conjugates every term in the sum and leaves the modulus alone, so a diffraction pattern always acquires a centre of symmetry, and in the plane a centre is a half turn. Both numbers are measured: the left from the operations, the right by testing each candidate against the computed intensities.

The symmetry diffraction adds

A diffraction pattern is always more symmetric than the crystal that made it. The extra symmetry is not a mistake in the experiment and no care removes it — it is a property of what a detector records, and it collapses the seventeen groups onto six.

diffraction · Accidental symmetry The eleven Laue classes. Adjoining the inversion to each of the thirty-two crystal classes collapses them onto 11 groups. Friedel's law says a diffraction experiment sees the crystal and its inverse alike, so this — and not the crystal class — is what a diffraction pattern's symmetry reports. The highlighted symbol in each row is the class that is already its own Laue class, which is to say the centrosymmetric one.

The eleven a diffraction pattern reports

A diffraction experiment cannot tell a crystal from its inverse. So the thirty-two classes collapse to eleven before a single reflection is indexed, and a structure determination begins by answering a different question from the one it was asked.

point-groups · Diffraction The h0l layer of P2₁/c. The h0l reflections of P2₁/c out to 4 in each index, with each spot decided by summing the structure factor over the group's operations: 44 survive and 36 vanish identically, whatever the atoms are. The pattern of holes is the condition h0l: l even, read back off the spots rather than imposed on them.

The reflections that are not there

A screw axis and a glide plane leave no mark on the intensity of any reflection. What they do is delete some, exactly, for every possible arrangement of atoms — and the pattern of deletions is computed here from the sum a crystallographer writes down, rather than read from a table.

diffraction · Diffraction p3, single and twinned. Left, the diffraction pattern of a single crystal of p3. Right, the same crystal twinned, with 50 per cent of it in one orientation. Not one spot has moved — the twin law is a symmetry of the lattice, so the two reciprocal lattices lie exactly on top of one another — and 72 of the 81 reflections drawn have changed intensity. At a fifty-fifty twin the pattern acquires the full symmetry of the lattice's point group and is indistinguishable from a crystal that genuinely has it.

A merohedral twin moves no spot at all

The twin law is a symmetry of the lattice, so the two individuals have reciprocal lattices lying exactly on top of one another. Nothing splits, nothing appears in a new place, and the only thing that changes is that pairs of intensities which were different have been averaged — which produces a diffraction pattern with a symmetry the crystal does not have and no sign that anything is wrong.

applied · Twinning A chain modulated at q = 0.211. The lower row is the lattice: 34 sites, evenly spaced. The upper row is the structure: the same sites displaced by a wave of amplitude 0.12 of a spacing and wavevector 0.211, drawn through them. Because 0.211 is not a ratio of small whole numbers, no cell of any size holds the structure — the displacement pattern never repeats — and yet the atoms are nowhere near random: each one is exactly where a single sine wave says it should be. That is what an incommensurately modulated crystal is, and its diffraction pattern is sharp.

The satellites that need a second integer

A crystal whose atoms are displaced by a wave of the wrong wavelength has no unit cell at all, and diffracts to sharp spots anyway. Indexing them takes two integers per reflection instead of one — and the intensities of the extra spots are Bessel functions, which is a check the arithmetic can be made to pass.

aperiodic · Modulation What each group extinguishes. The extinction conditions of 9 space groups, each derived by summing the structure factor over that group's own operations and reading the surviving rule off the result: P1 — nothing; P1̅ — nothing; P2 — nothing; Pm — nothing; P2/m — nothing; P222 — nothing; Pmm2 — nothing; P4 — nothing; P23 — nothing. 9 of the 9 extinguish nothing at all, and diffraction alone cannot distinguish those from each other.

Where the experiment runs out

Absences narrow the space group down and often not to one. Two groups can extinguish exactly the same reflections and scatter with exactly the same symmetry, and telling them apart needs something the diffraction pattern does not contain.

diffraction · Diffraction Friedel's law, as an equality rather than a resemblance. Each pair of bars is a reflection and its opposite for a structure of three atoms in no particular arrangement. They are the same height, and not approximately: with real scattering factors, negating the indices conjugates the structure factor, and conjugation does not change a modulus. The test behind this figure requires the largest difference over 40 pairs to be below 10⁻⁹ and it comes back exactly zero. This is why a diffraction pattern is centrosymmetric whatever the crystal is, and why the thirty-two classes collapse to eleven before a structure is even proposed.

The law that hides handedness

With real scattering factors, negating the indices conjugates the structure factor and leaves the intensity exactly alone — so every diffraction pattern is centrosymmetric whatever the crystal is. The escape is an imaginary component that the negation does not touch, and it is how the handedness of a molecule is measured.

diffraction · Friedel's law Two species on one lattice, ordered at index 2. Every position is a lattice point of the parent and none of them has moved. What has changed is which atom sits where: the larger marks are a sublattice of index 2, the smaller ones its other 1 coset, and the outlined cell is the new repeat. The lattice of positions is untouched and the repeat of the contents is 2 times as large, which is the whole of what an ordering transition does and the reason its signature is in reciprocal space rather than in the positions.

The reflections a superlattice adds

Centring a lattice makes reflections vanish. Ordering two kinds of atom onto a sublattice makes new ones appear, exactly n − 1 of them per parent cell, and their intensity is a difference rather than a sum — which is why an ordered alloy of two neighbouring elements can be invisible to X-rays and obvious to neutrons.

lattices · Sublattices Two candidates, and the sign that chooses. The phase of reflection (2, 3), recovered from three measurements and no model. The circle is every complex number of the measured amplitude; the isomorphous difference fixes the cosine of the angle between the unknown phase and the heavy atom's, leaving the two candidates marked; the anomalous difference fixes the sine, which picks one. The recovered phase agrees with the true one to fifteen decimal places, and the true phase was never used in the calculation.

One experiment gives the cosine, the other gives the sine

Friedel's law holding exactly is what makes the phase unreachable. Its breaking is what hands it back: an isomorphous difference fixes the cosine of the phase and leaves two candidates, and the anomalous difference fixes the sine, which chooses.

diffraction · Friedel's law Two structures on 8 sites with the same vectors. Two arrangements of 4 atoms on a ring of 8 positions. They are not the same arrangement — no rotation of the ring and no reflection carries one onto the other — and every interatomic vector occurs the same number of times in both. The bars below are the shared vector counts, which is the Patterson function of each: the tall one at the origin is the atom count and carries no information, and everything else is what a diffraction experiment measures. Their diffraction patterns are identical in every intensity, so no measurement of intensities, at any resolution, distinguishes them.

Two structures, one Patterson

Eight arrangements of four atoms on a ring of eight sites, and only seven distinct sets of interatomic vectors between them. Two of the arrangements are genuinely different and no measurement of intensities can tell them apart — at any resolution, for ever.

diffraction · Homometry Where a homometric pair comes from. A set that factors as a sumset gives its own partner. If every point of A is a sum b + c with b in B and c in C, and every sum arises once, then reversing C produces a different set with the same vectors — because reversing a factor and reversing its conjugate cancel in the product that the vector set is. Both factors must be asymmetric, which is the constraint that decides where the construction can be used: a two-point set is its own reflection up to a translation, so the smallest useful factorisation is three points by three points, and the smallest structure it builds has nine atoms.

Where the pairs come from

A structure whose atoms are the sums of two smaller sets has a partner: reverse one factor and the interatomic vectors do not notice. The construction is Patterson's own, it explains why homometry exists, and the smallest structure it can build has nine atoms for a reason worth following.

diffraction · Homometry 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 -2 0 -3 is forbidden and is reached 64 ways. A layer of the reciprocal lattice of Cc: pale spots are reflections the group extinguishes, solid ones are allowed. The path shows a detour — the beam diffracts once at -3 -3 -3 and again at 1 3 0, and the two together send it in exactly the direction a single reflection at -2 0 -3 would. That reflection is forbidden, so intensity arrives where the symmetry said none could. There are 64 such routes to this one spot inside this window alone.

The absence that fills itself in

A systematic absence is the strongest evidence this subject has: a whole zone of reflections cancelling exactly, for reasons of symmetry rather than of arithmetic accident. The exactness belongs to a model — that the beam scatters once. A beam that has already been diffracted can be diffracted again, and the two events together land where the group said nothing could.

diffraction · Diffraction pmg: 80 of 80 restricted. The reflections of pmg inside a window of ±4, with the ones whose phase symmetry restricts to two values picked out. Every solid spot has a structure factor that must be real up to a fixed rotation — a sign, in effect — whatever the atoms turn out to be, and the pale ones have a phase symmetry says nothing about. The 4 palest spots carry two incompatible restrictions at once, which leaves them nothing to be but zero. Which spots these are was computed from the operations, before any structure existed.

The zones that behave as if there were a centre

The phase problem is usually stated as though symmetry had nothing to say about phases. It is true of most reflections and false of some, and which is decidable from the group alone: where an operation carries a reflection onto its own negative, the phase is confined to two values half a turn apart, computed from that operation's translation.

diffraction · Statistics ⟨cos Φ⟩ against κ, 379 triplets. The mean cosine of the triplet, binned by the concentration κ = 2|E₁E₂E₃|/√N, for the 379 triplets of a structure of 24 atoms whose reflections all exceed |E| = 1.2. The curve is Cochran's I₁(κ)/I₀(κ), computed from the distribution and not fitted to anything; the points are measured, with the number of triplets in each bin printed above. They agree to 0.1 root-mean-square. The measured points sit slightly above the curve throughout, which is the finite structure showing: Cochran's derivation assumes atoms placed at random and there are only 24 of them.

Three phases that do not move when the origin does

A phase is a property of the description, not of the crystal: shift the origin and every one of them changes. A sum of three phases whose indices add to zero does not change, because the shifts cancel. That sum is the smallest thing about a structure that a diffraction experiment could in principle know, and it is not distributed at random.

diffraction · Direct methods p4m from 3 orbits of waves — detected p4m. A density built as a sum of 3 symmetry-adapted waves of p4m, each of them the average of a plane wave over the group, shaded from light to dark across one cell. The level set of this density — the darkest points of it — was handed to the same detector the pattern figures use, and it reports p4m, which is exactly the group the waves were built from. The waves are invariant by construction, so the density can never have less symmetry than the group; the interesting direction is the other one.

How many waves a group permits

A pattern can be written as a sum of waves instead of as an orbit of a motif, and then the group ties the coefficients together and forbids some outright. Building a density from the permitted ones and handing it back to the detector closes the same loop through a different door — and at low resolution the density has symmetry the crystal has not.

classification · Seventeen B = 3.45 against 3.4, K = 0.37 against 0.37. The mean intensity of each resolution shell of a cell of 1194 reflections, divided by Σf² computed from the cell's content alone, and logged. The points fall on a line whose slope gives B = 3.45 against the 3.4 put in, and whose intercept gives a scale of 0.37 against 0.37 — both recovered before a single atom has been placed. The atoms here are independent, so the line is straight at every resolution; the shells below the cutoff are marked in the second colour.

The average that knows the atoms and not where they are

Square a structure factor and average it over a shell of reflections at one resolution. The cross terms — every one of which carries a fact about the arrangement — cancel, and what is left is a sum over the *content* of the cell with no position in it anywhere. A scale and a temperature factor come out of that before a single atom has been placed.

diffraction · Statistics One crystal, two rows: one streaks and one does not. Two rows of reflections from the same faulted crystal, at a fault rate of 0.05, each drawn against the same row from a perfect one. The upper row has h − k not divisible by three, so each layer contributes a different cube root of unity and the sequence of layers enters the sum: the sharp peaks collapse into a streak. The lower row has h − k divisible by three, the phase factor is one, every layer scatters in step, and the peaks are exactly as sharp as in the perfect crystal. The sorting is an integer condition — a reflection either can see the stacking or cannot, decided by h − k modulo three — which is the most direct evidence there is that the disorder is in the stacking and not in the layers. The profiles are averaged over 16 independently faulted crystals, because one crystal gives speckle rather than a diffuse profile.

The streaks a faulted stack makes

Close packing settles two directions and leaves the third to chance. A crystal that chooses wrongly now and then has a lattice in the plane of its layers and none across them — and its diffraction pattern says so, with some rows of spots as sharp as ever and others smeared into streaks, sorted by an integer condition.

diffraction · Diffraction The diffuse intensity of an alloy with α₁ = -0.46. The diffuse part of the scattering across the wavevectors an 12 × 12 block can be asked about, one square per wavevector with darkness the intensity. The marked squares are where the average structure scatters — the sharp part, which is what a Bragg reflection is. The diffuse maximum here is at (0.50, 0.50), which is the zone boundary: the alloy is trying to alternate, and a crystal that succeeded would put a sharp reflection exactly there. Summed over every wavevector, the intensity is exactly one per site whatever the correlations are — order moves scattering about, it does not create it.

The average scatters sharply and the rest does not

A crystal whose lattice is perfect and whose occupation is not scatters in two parts: the average structure gives Bragg reflections, and the variance is spread over everything between them. The split is exact, the total is one unit per site whatever the disorder does, and an ensemble of n arrangements mislays exactly a fraction 1/n of it.

diffraction · Disorder A map from amplitudes alone, 0.59 grid steps out. The density after 150 cycles of flipping, with the atoms that produced the data drawn as rings — moved into the origin and the handedness the solution chose, because a phase set does not fix either and comparing without allowing for them measures the arbitrariness of the description. Every peak of the map is an atom and every atom has a peak. Nothing about the arrangement went into the calculation: the input was a list of amplitudes and a random set of phases.

The solver that knows no symmetry

Compute a map from amplitudes and random phases, reverse the sign of everything below a small threshold, transform back and keep the phases. Repeat. The structure appears — and so does its space group, which was never supplied.

diffraction · Direct methods The cross, from the selection rule alone. The layer lines of a helix with the first maximum of each marked on both sides. Nothing here is a picture of a photograph: each mark is at the radius where the Bessel function of the lowest order the selection rule permits on that layer line first peaks, and that radius is proportional to the order. The order rises by one per layer line until the middle of the repeat, so the maxima lie on two straight lines through the origin — the X — and the larger marks are the layer lines that reach the axis.

What a thread scatters

A helix with ten subunits in a turn is not a screw axis a crystal may have, and nothing about its diffraction pattern is lawless. The pattern lies on layer lines, and on each one only certain angular orders may contribute — a selection rule as hard as any extinction condition. The lowest permitted order rises by one per layer line, a Bessel function of order n does nothing until its argument is about n, and the maxima therefore lie on two straight lines through the origin.

classification · Subperiodic Two kinds of atom, and more ambiguity rather than less. Exhaustive searches on rings of four sizes. The third column counts homometric groups when every atom is identical; the fourth counts them when each atom may be one of two kinds. The fourth is larger at every size, and at nine and ten sites the third is nothing at all — there is no pair of arrangements of four identical atoms that a diffraction experiment cannot separate, and there are six and four once the atoms may differ. Distinguishing the atoms adds information to the structure and adds ambiguity to the measurement.

When the atoms are not all the same

Every homometric pair found so far is a pair of point sets, where an atom is a point and counts once. Give the atoms different scattering powers and the ambiguity does not go away — it grows. On a ring of nine there is no pair of four identical atoms that diffraction cannot separate, and there are six once two kinds of atom are allowed.

diffraction · Homometry Square ice scatters a pinch at the origin. The intensity scattered by the horizontal arrows of square ice, averaged over 100 configurations on a 32 by 32 torus, over the whole Brillouin zone with the origin at the centre; darker is more intense. Along the horizontal axis through the origin the intensity falls to zero — 2.9e-32 at the smallest wavevector — while along the vertical axis it stays near 1.75, so the two meet at the origin in a pinch.

The ice rule is a conservation law

Two arrows in and two out at every vertex is a statement that nothing flows in or out anywhere. That makes one half of the arrow field vanish identically, in every arrangement and not merely on average, and what is left scatters with a pinch at the origin: an intensity that approaches different values from different directions. Break the rule now and then and the pinch acquires a width Debye and Hückel predicted for a salt solution.

aperiodic · Entropy 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 The same structure, mapped from intensities and from differences. Left, the ordinary Patterson map of the structure: 14762 interatomic vectors, a continuous field of overlapping peaks, and the two vectors between the anomalous scatterers — circled — nowhere among its strongest. Right, the map from squared Bijvoet differences over the same reflections: two peaks after the origin, and they are those two vectors. The difference map is 7381 times smaller a problem to read.

A map of the atoms that break the law

Feed a Patterson synthesis the differences between the two halves of each Friedel pair instead of the intensities, and the map that comes back holds the vectors between the anomalous scatterers and nothing else. Two atoms among a hundred and twenty-two: 14,762 vectors become two.

diffraction · The Patterson function One change of setting, four rules. The four things a structure report contains and the rule each obeys under a change of setting with basis change P and origin shift p. The cell and the indices are multiplied by P; a coordinate is multiplied by its inverse, after the origin has been subtracted; and an operation is conjugated and then shifted by (W − I)p, a term the other three have no equivalent of. Applied to Pnma with the change below, the operations still close into 8, the orbit maps point for point, and every |F| is unchanged.

One matrix, four rules

Changing the setting of a structure is one matrix and one origin shift — and the cell, the coordinates, the indices and the operations each obey a different rule under it. Three of the four ways of getting it wrong still leave a closed group of the right order, so closure catches none of them.

space-groups · Settings 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 What refinement takes back from a wrong disorder model. Every directed pair of disorder models sharing an occupancy, 462 in all: data made from one model's averaged structure, the other model refined against them with positions on its own loci, two-component displacement parameters and fixed occupancies. Across is the residual between the two ideal structures; up is the residual after refinement. Points on the dashed line lost nothing to refinement; the median point lost 58 per cent of its residual. Every point on the floor, where the wrong model fits exactly, is one whose loci contain the true model's.

What refinement takes back from a wrong model

Two disorder models sharing an occupancy leave averaged structures typically a sixth apart. Refine the wrong one against the right one's data and it takes back more than half of that — all of it wherever its loci contain the true ones. Yet the data still choose, even for a molecule of sixty-four atoms, because a likelihood summed over every reflection sees what no single reflection can, and the wrong model's partial atoms give it away through the size of their displacement parameters, not their shape.

restriction · Local symmetry Better counting makes an uncorrected smooth error choose the wrong model. Eighteen pairs of disorder models, each decided by the likelihood ratio at the 0.1 per cent level, at sixty-four and a hundred and twenty-eight atoms, as the random error falls from 3% to 1% to 0.3% of the mean amplitude. In each group, the first bar has random error only, the second adds a smooth scale error of 3% across reciprocal space, and the third adds the same error with a degree-two scale surface refined alongside the structure. With random error only, better counting decides more pairs correctly. With the uncorrected smooth error it stops helping and the number decided for the wrong model grows, to three at a hundred and twenty-eight atoms. With the surface refined, the result is the random-only one in every group.

Better counting, and the wrong model

A smooth error across reciprocal space, as large as the random one, hardly changes which disorder model the data choose: it enters both models' residuals and cancels from their difference. What it changes is where better data lead. With random error alone, counting harder decides more pairs correctly. With the smooth error left in, counting harder stops helping and starts deciding pairs for the model that did not make the data — at the 0.1% level, and more of them the better the counting.

restriction · Local symmetry The sign turns when the cross terms go weak. Every quartet among the strong reflections of a small structure, sorted by the mean of its three cross terms, with the mean cosine of the phase sum in each bin. Where the cross terms are strong the quartet behaves like a triplet and the cosine is near one. Where they are weakest it is -0.698 — negative — and 93 per cent of those quartets have a cosine below nought. The four reflections of the quartet are equally strong in every bin; what changes is three reflections that are not in the sum at all.

The relation that can say no

Every phase relation before this one pushes a sum towards zero, so none of them can contradict another — a phase set satisfying all of them badly is still satisfying them in the same direction. A quartet can be estimated at π instead, and it is when its three cross terms are weak, so the information arrives from the reflections nobody would have thought worth measuring.

diffraction · Direct methods Which sites a smooth error can mislead. For the eighteen pairs of disorder models at three site symmetries, under a smooth scale error of degree two (five molecule sizes) and of degree four (three sizes): how many verdicts of perfect counting go the wrong way, how many pairs no data can decide, the largest correlation between the error and the two models' difference, and how many harmonics of the error's degree the site's group leaves unchanged. At the cubic site the degree-two error correlates with nothing, to rounding, and decides no pair wrongly; the degree-four error, which the cubic site keeps one harmonic of, reaches it.

A cubic site is blind to a degree-two error

A smooth scale error left uncorrected made perfect counting choose the wrong disorder model for eight of ninety pairs and sizes, and the obvious way to predict which is to correlate the error with the two models' difference before refining anything. That correlation predicts none of them. What it does predict, exactly, is which pairs can never go wrong: at a cubic site a scale error of degree two correlates with nothing and is absorbed by nothing, because a cubic group keeps no harmonic of degree two. A degree-four error, which it keeps one of, reaches the cubic site at once.

restriction · Local symmetry An equality, with a known factor in it. Sayre's identity says the structure factor is proportional to the convolution of the structure factors with themselves — an equality, not a probability — with a factor that depends on the atoms and the resolution and on nothing else. Computed for a structure of Gaussian atoms, the ratio of the two sides falls with resolution exactly as predicted: the logarithm of the ratio is a straight line in the squared index, its slope is minus half the width in the atomic factor, and the ratio is very nearly real and positive, so the identity relates the phases and not only the amplitudes.

The relation that is an equality

Every relation of this kind so far is a probability — right nine times in ten, useless applied once and decisive applied ten thousand times. One is not. For a structure of equal, resolved atoms the squared density has peaks in the same places, so every structure factor is exactly a convolution of all the others, with a factor that depends only on the atom. It is exact, and on its own it is useless.

diffraction · Direct methods The first-order prediction against the actual verdict, for every pair and size. The 85 decidable pairs of disorder models at five molecule sizes, each placed by the first-order prediction of the wrong model's misfit minus the right model's, made from the two error-free refinements and their Jacobians, and by the actual difference after refining against data with a 3% smooth error. Shaded quadrants are agreement. 77 agree. Of the 8 wrong verdicts, ringed, 4 are predicted; 4 right verdicts are predicted wrong.

The wrong model moves too far for first order

Which disorder models a smooth error will turn the wrong way was left as a calculation to make before any data exist: project the error onto the directions each refinement's parameters can move. Made, it gets the sign of the verdict right in seventy-seven of eighty-five cases, catches four of the eight wrong verdicts and raises four false alarms. Every case it gets wrong is either a near-tie or a refinement that absorbed more than twice, or less than half, of what its first-order directions allow.

restriction · Local symmetry Two waves that are each symmetric enough make a lopsided pair. The first-order satellite amplitudes at h − q and h + q around the main reflections h = 1 to 4, for three chains: an occupation wave on the lattice, whose pairs are equal; the strain wave alone, the displacement the size effect produces with every site equally full, whose satellites are weak and grow with h; and both together. Together the pairs are unequal, the low side stronger, by an amount that grows from one reflection to the next — an imbalance neither wave has on its own, from a displacement of less than a hundredth of a spacing.

The strain wave that tips the satellites

An occupation wave puts equal satellites on both sides of every main reflection, and a strain wave a hundredth of a lattice spacing high is enough to tip them. Real composition waves drag such a strain with them, because atoms of different sizes want different spacings, and the tilt that results is not a nuisance. To first order it does not depend on how strong the occupation wave is at all. It reads the size mismatch directly, and its sign says which species is the larger.

aperiodic · Modulation How many superstructures a diffraction pattern tells apart. For two-species superstructures of the square lattice with one to twelve sites in the primitive cell: the number of structures, and the number of classes that the positions of their superlattice spots separate them into, the positions together with the composition, and every intensity. At twelve sites 2,012 structures give 167 sets of spot positions, 504 with the composition and 1,815 sets of intensities. At five, seven and eleven sites the positions distinguish only the cells; the intensities distinguish everything. The bar shows the share resolved by positions, dark, and by intensities, light.

The spots say the cell and little else

Of the 2,012 two-species superstructures of the square lattice with twelve sites in the cell, more than half light every superlattice spot their cell allows, so the positions of the spots say which cell and nothing more. Positions separate the 2,012 into 167 classes, the composition takes that to 504, and every intensity to 1,815. At a prime number of sites no spot is ever missing, because a sum of distinct p-th roots of unity cannot vanish.

operations · Counting The h = 1 anomaly moves with the length of the chain. For a size-coupled chain with ε = 0.03, the ratio of the second-order pair's tilt, divided by k², to the first-order tilt at h = 1, from plain sums over the sites and from sums with a smooth window, for 22 chain lengths from 10,000 to 480,000 sites. The plain ratio swings between -0.08 and 5.60; at 30,000 and 120,000 sites, the two lengths first tried, it sits near 0.31 both times. The windowed ratio is one half at every length.

The satellite beside the zero-order reflection

An earlier essay found that the second-order satellites of a modulated chain tilt half as far as the first-order ones at every reflection but the first, where they tilted a third as far, the same on chains of 30,000 and 120,000 sites. It left the departure unexplained and proposed a higher order of the expansion. The expansion was never wrong. The weak satellite at h = 1 sits a quarter of a reciprocal unit from the strongest reflection a chain has, and a plain sum over a finite chain carries that reflection's tail, which does not shrink steadily as the chain grows. It swings, and the two lengths tried happened to swing to the same place.

aperiodic · Modulation When a three-species superstructure's spots can go dark. Every structure of three species on the square lattice with three to eight sites in its primitive cell, using all three species, and every superlattice spot of each, sorted by whether the spot is dark for every choice of scattering contrasts, dark at exactly one ratio of the two contrasts, or never dark; with the number of distinct ratios and their degree over the rationals. At the primes 3, 5 and 7 no spot is dark for all contrasts and no dark ratio is rational: none at three sites, quadratic ones at five and cubic at seven. At four and six sites every dark ratio is rational, at eight some are and some are not, and at six and eight some spots are dark for every contrast.

Three species hide a spot at the golden ratio

With two species and a prime number of sites in the cell, no superlattice spot can ever be missing, because a sum of distinct roots of unity of prime order vanishes only when it is all of them. With three species the structure factor weighs two sums against each other with two scattering contrasts, and the argument changes shape without breaking. At a prime size no spot is dark for every contrast and none at a rational ratio of them, but a spot can be dark at one irrational ratio: at five sites, a power of the golden ratio. It happens only in structures with a centre of symmetry.

operations · Counting Where an antiferromagnet's reflections land. Two cubic antiferromagnets, with their nuclear reflections as dots and their magnetic reflections as triangles, in units of the conventional reciprocal lattice. On the left, a simple cubic lattice with every neighbour opposite: the magnetic reflections sit at half-integer indices, in a layer the nuclear pattern never visits. On the right, a body-centred lattice with the corners up and the centres down: the magnetic reflections sit at integer indices with an odd sum — exactly the reflections the body centring had extinguished, lit up again by the moments. In both, no magnetic reflection falls on a nuclear one.

Magnetic reflections land where nuclear ones cannot

An antiferromagnet scatters neutrons into places its chemical structure leaves dark, and never into a place it lights. The reason is one line of algebra: the magnetic pattern is the nuclear pattern shifted by half a reciprocal-lattice vector. Each of a lattice's seven halvings is one such shift, and how many of them its symmetry keeps decides how many kinds of domain the magnet must form.

point-groups · Magnetic The second-order satellites alone cannot measure the curvature of a size effect. The Cramér–Rao error in the quadratic size coefficient ε₂, as a fraction of its true value, from six sets of satellites of a modulated chain of 30,000 sites with 2% intensity error, and the correlation between the errors in ε₂ and the linear coefficient ε₁. From second-order satellites alone the error is thousands of times ε₂ at one reflection and still a hundred times it at three, with the two coefficients correlated at 1.000. With the first-order satellites added, one reflection gives ε₂ to about a third of itself and three to about a tenth.

The second order cannot see a curved size effect alone

When the spacing between atoms depends on composition along a curve rather than a line, the displacement of a modulated chain gains a second harmonic, and the second-order satellites should measure it. They cannot do it on their own. At every reflection a second-order satellite sees the straight part and the curved part of the size effect in almost the same proportion, so adding reflections adds copies of one equation. The first-order satellites, which see only the straight part, are what separates them.

aperiodic · Modulation Heavier atoms spoil the line, and then mend it. Above, the scatter of Sayre's ratio about its fitted line, averaged over four random cells, as a quarter of the atoms is made heavier, for cells of eight and of twelve atoms. Below, one minus the square of ρ, the correlation between the density's transform and its square's, computed from the composition alone. The spread of atomic numbers grows without limit along this axis, but ρ does not keep falling: it is lowest near a weight of three and climbs back towards one as the heavy atoms come to dominate, because a cell ruled by a few equal heavy atoms is nearly a cell of equal atoms. The scatter rises and falls with it. At equal weight what scatter remains comes from atoms that overlap, more of them in the larger cell.

Unequal atoms break the equality, and very unequal ones mend it

Sayre's identity is exact for a cell of equal atoms. Give a quarter of them more weight and the line it predicts scatters, reflection by reflection, by exactly the difference between weighting atoms by Z and by Z squared. Make them heavier still and the scatter shrinks again, because a cell ruled by a few heavy atoms is nearly a cell of equal ones. The scatter measures the cell, but only if the phases are already known.

diffraction · Direct methods What each kind of satellite of a two-wave chain says about the curvature of the size effect. The Cramér–Rao error in the quadratic size coefficient ε₂, as a fraction of its true value, from seven sets of satellites of a chain modulated by two incommensurate waves, with 2% intensity error: with the two modulation amplitudes refined as well (upper bar of each pair) and with them known (lower bar). The sum or the difference satellites alone say almost nothing either way. Together, with the amplitudes known, they fix the curvature to under one per cent from a single reflection; with the amplitudes free they do not, and adding the first-order satellites, which fix the amplitudes, restores it.

Two waves measure the curvature one wave hides

A chain modulated by one wave cannot tell a curved size effect from a straight one at second order: every second-order satellite sees the two in the same proportion. Modulate it by two incommensurate waves and the curvature puts the product of the waves into the displacement, at their sum and at their difference. The satellites there see the curvature with opposite signs. Two equations of opposite sign separate two unknowns, and once the two waves' amplitudes are known, the mixed satellites of a single reflection fix the curvature to under one per cent.

aperiodic · Modulation Which cells the flipping solver finds. For four cells of twenty atoms — all carbon, a quarter sulphur, one sulphur, one lead — the share of random starting phase sets that charge flipping takes to the right structure within 250 cycles, against the threshold below which density has its sign reversed. Each point pools several random arrangements of atoms with several starts each, and the atoms fall off with angle as real atoms do. The cells with sulphur are solved more often than carbon alone, the quarter-sulphur cell most of all, each at a threshold near one standard deviation; the lead cell is never solved at any threshold.

The heavy atom the flipping solver cannot see past

Sayre's identity degrades as a cell's atoms become unequal, most of all for a quarter of heavy atoms three times the weight of the rest, and the obvious prediction is that a solver built on the same sparseness should struggle there too. It does not. Charge flipping solves a cell of carbon with sulphur in it more often than carbon alone, and never solves a cell with one lead atom — because a threshold stated in standard deviations belongs to whichever atom owns the map's variance.

diffraction · Direct methods At the sum of all three wavevectors the cubic and the quadratic paths nearly cancel. The intensity of the satellite at h + q₁ + q₂ + q₃ for the first four reflections, computed with only one size coefficient switched on at a time and with all three. The cubic coefficient alone gives about 3 × 10⁻⁷ at h = 1, the quadratic alone about 2 × 10⁻⁷, the linear alone less than 10⁻¹⁰. With all three the satellite is ten times weaker than with the cubic alone, because the cubic term's displacement and the quadratic term's pair harmonic times a first-order wave arrive with opposite signs.

Three waves measure the cube through the slope

A size effect that bends twice puts the product of three modulation waves into the displacement, at the sums and differences of all three wavevectors, and nowhere else does a cubic term reach so directly. The satellites there were expected to measure it. They see it, but the strongest of them is ten times weaker than the cube alone would make it, because the quadratic term arrives at the same place with the opposite sign, and against any realistic background they say nothing. The cube is measured instead by the strongest satellites of all, the first-order ones, because it makes each wave's slope depend on how strong the other two waves are.

aperiodic · Modulation Diffuse scattering gathered under every Bragg peak. The one-phonon thermal diffuse scattering of a square lattice with springs to nearest and next-nearest neighbours, over the reciprocal plane from minus 2.5 to 2.5 in each index, with the Bragg reflections marked. The intensity rises as one over the squared distance to every reflection, because the acoustic phonons' frequencies vanish there, and it grows with the square of the scattering vector, so the lobes are strongest far from the origin. The lobes are not round: a small step from (1,0) along k gives 2.7 times the intensity of the same step along h, because it probes transverse phonons, which are softer, and that ratio is what an experiment reads the elastic constants from.

A warm plane crystal has no Bragg peaks

Thermal motion is disorder that moves, and in space it costs a crystal a little of each Bragg peak and gathers it into diffuse scattering underneath. In a plane it costs more than a little. Computed exactly from the phonons of a harmonic square lattice, an atom's mean-square wandering grows by the same amount every time the crystal doubles in size, so no Debye–Waller factor survives, and every Bragg peak fades as a power of the crystal's size — a power proportional to the temperature times the square of the reflection's distance from the origin.

diffraction · Disorder The worst edge pair is the two most anomalous wavelengths. For each pair of the four wavelengths, and for the peak, inflection and high remote together, the median error of the phase difference between the whole structure and its anomalous atoms, recovered from both Friedel mates at each wavelength with a 1% error on every intensity. Beside each, the spread of f′ across the chosen wavelengths. The pairs that include a remote wavelength and one on the edge phase to seven or eight degrees; the peak and the inflection together, the two with the largest anomalous effect, to eighteen; the two remotes to fifty-five.

The two most anomalous wavelengths are the wrong pair

A MAD experiment measures both Friedel mates at two wavelengths near an absorption edge and solves for a phase. The obvious choice is the two wavelengths where the anomalous effects are largest, the peak of f″ and the dip of f′. Of all the pairs that use the edge, it is the worst. The sine of the phase is carried by f″, but the cosine is carried by how much f′ changes between the two wavelengths, and two points on the same edge barely change it.

diffraction · Friedel's law Three difference maps of one substructure, and the map they approximate. Patterson syntheses over 1,681 reflections of a structure with 120 light atoms and two anomalous scatterers, from squared Bijvoet differences at one wavelength, squared dispersive differences between two wavelengths, and the two normalised and summed; the fourth panel is the Patterson of the anomalous atoms' own intensities. Circles mark the two vectors between the anomalous atoms. Each map's correlation with the exact one is printed beneath it: Bijvoet 0.775, dispersive 0.838, combined 0.999.

A second wavelength completes the map

The Bijvoet difference carries the anomalous substructure's intensity times the sine squared of a phase; the dispersive difference between two wavelengths carries it times the cosine squared. Normalised and added, the two make the substructure's own Patterson, correlation 0.999. It needs no fewer reflections than either half, because the threshold was never the average. What the dispersive half brings is a way of failing the Bijvoet half cannot have: two datasets, and a scale between them.

diffraction · The Patterson function Where the third wavelength should go. The median Cramér–Rao bound on the phase difference for two hundred reflections, measured at the inflection and the high remote and at a third wavelength whose energy runs across the edge, twice: with f′ known everywhere, and with f′ at the edge energies refined from the data. Known, the best third sits 1 eV above the edge at 6.26°, and a repeat of either wavelength is nearly as good. Refined, both repeats determine nothing, and the best third moves to +2 eV at 6.30°.

The third wavelength is there to measure the edge

A three-wavelength MAD experiment is usually justified as more anomalous signal: a third look at the edge, placed where the first two left the most out. Counted with the scattering factors known, a third wavelength buys nothing a longer look at the best pair would not buy better. Its real job appears only when f′ at the edge has to be found from the data, which it always does. Two wavelengths then carry one equation too few, and any third energy that is not a repeat supplies it, for two hundredths of a degree.

diffraction · Friedel's law A scale error between two wavelengths has a sign. The contrast of the substructure's vectors in a dispersive difference Patterson, the weaker of its two peaks over the strongest other peak, as the second dataset is scaled wrongly, with no metal atom and with two metal atoms that do not scatter anomalously. An error that weakens the second dataset loses the map at 3.7% with no metal; one that strengthens it at 50%. The dashed line is where the substructure's peak is predicted to reach zero, a quarter of the fractional change in f′ between the wavelengths. The metals shorten the strong side and hardly move the weak one.

A scale error between two wavelengths has a sign

A dispersive difference compares two datasets, so a wrong scale factor between them adds the whole structure to it. On a structure whose own Patterson is a haze, the substructure's vectors survived a scale error of fifty per cent, and heavy atoms that do not scatter anomalously were expected to take over much sooner. They do, but only in one direction. Scale the second dataset the other way and the substructure is erased at four per cent whatever else is in the crystal, because the error's linear term cancels the signal. Scaling the datasets onto each other is itself an error of that sign.

diffraction · The Patterson function No triple of wavelengths is best for both the phase and the edge. Every triple of energies on a grid across a model selenium edge, placed by two Cramér–Rao bounds with the edge's position and white line refined from the data: the median phase error across, and the error in the edge's position up, on a logarithmic scale. The front of triples that no other beats on both runs from +1, +2, +150 eV (6.15°, ±0.066 eV) to -120, -1, +3 eV (7.54°, ±0.022 eV). The classic peak, inflection and high remote sits on it, at 6.42° and ±0.026 eV.

The wavelengths that phase best do not find the edge

A MAD experiment refines the anomalous atom's scattering factors so that it can solve for the phases, and those same factors report where the absorption edge sits and how tall its white line stands, which is chemistry. Scored for the edge instead of the phase, the best triple of wavelengths moves: two straddling the step and one far below it, where the phase-best triple put two on the step and one far above. No triple is best at both, and the textbook peak, inflection and remote turns out to be the compromise between them.

diffraction · Friedel's law Four flipping rules on four cells. The best success rate of the flipping solver, pooled over five arrangements and eight starts, on four cells: twenty carbons, a quarter sulphur, one sulphur among twenty and one lead among twenty. Four rules for what is flipped: below a number of standard deviations of the map, below a height set by the lightest atom's weight, the same height above the map's mean, and the original rule with the known heavy atom's density removed first. On the lead cell only the last solves anything, 55% against nothing; on both sulphur cells it raises the rate to near certainty; on carbon alone it is the original rule.

The lead taken out solves what no threshold could

Charge flipping never solved a cell of nineteen carbons and one lead, and two repairs were proposed: a threshold set by the composition rather than by the map's spread, and the lead's own density removed before each flip. The threshold does nothing for the lead cell at any setting, measured from zero or from the map's mean. Removing the lead takes it from nought to fifty-five per cent, and lifts both cells with sulphur in them to near certainty. The trouble was never where the threshold sat.

diffraction · Direct methods Three-species arrangements whose sums are parallel at every spot, with and without a centre. Every arrangement of three species, all present, on a cyclic cell of four to nineteen sites. The third column counts those whose two phase sums are parallel at every superlattice spot, the fourth those among them with a centre of inversion, the fifth those without one, and the last how many kinds the exceptions make up to translation, inversion, relabelling the spots and renaming the species. Primes are shaded. At 5, 7 and 11 sites every parallel arrangement has a centre; at 13 sites 936 do not, and they are all one arrangement; at 17 there are 17 kinds and at 19 there are 48.

Thirteen sites obey Friedel's law without a centre

At five and seven sites the earlier census found that a three-species structure has a contrast that darkens a spot exactly when it has a centre, and asked whether that is a theorem. It is not. The two phase sums are parallel exactly when the A–B pairs are as common at every separation forwards as backwards, and exactly when no anomalous scatterer can produce a Bijvoet difference anywhere in the pattern. At 5, 7 and 11 sites only a centre achieves that. At 13 sites one arrangement does it without one.

operations · Counting Fitting the outer shells makes it worse, and correcting the fit recovers it. The substructure's weaker peak as a share of its height with no scaling, on data with no error, with the scale error each scaling builds in, for five falloffs and three scalings. Fitting everything loses 42% with no falloff and less as the falloff grows. Fitting only the outer shells loses more, and at the steepest falloffs builds in a large error of the opposite sign. The fit corrected by the ratio the composition expects recovers the whole peak at every falloff, within a few per cent.

Fit the scale, then put the lean back

Scaling two wavelengths to each other builds in an error of the cancelling sign, because their means differ for a physical reason. The proposal was to fit against the part the edge does not touch, at high resolution. It does the opposite: f₀ falls with angle and f′ does not, so the outer shells lean furthest and fitting them costs more. Taking the scale from the composition alone reproduces the lean as well. What works is fitting as usual and then putting back the difference the composition expects, and that recovers the whole peak.

diffraction · The Patterson function

Named alongside it

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

Phase problemFriedel lawAnomalous scatteringResolutionSystematic absenceMeasurementThe Patterson functionDirect methodsLaue classAverage structureDisorderEnumeration

All concepts