Crystallography & Symmetry
patterns derived from their groups
Concept

Electron density — where it appears

The distribution of scattering matter in a unit cell, whose Fourier coefficients are the structure factors. It is what a structure determination produces, and the difficulty is that a measurement gives the magnitudes of those coefficients and not their phases.

Named by 3 essays across one field — each of them below, with the objects they name alongside it.

Three atoms, four resolutions. A one-dimensional Fourier synthesis of the same three atoms, cut at four different resolutions. Nothing is approximate except the edge: every amplitude and every phase used is exact, and the only information withheld is the reflections outside the sphere. The peaks broaden as the cut-off comes in, and beside every peak sits a negative ripple that the coarsest map cannot distinguish from a real absence of density. Both effects are the transform of the sphere rather than anything about the structure.

As sharp as the sphere is wide

A map made from a truncated sum is not a blurred picture of the structure. It is the structure convolved with the transform of the sphere — so peaks acquire a width proportional to the resolution, and a negative ripple of twenty-two per cent that no improvement in the data ever reduces.

diffraction · Resolution 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 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

Named alongside it

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

Direct methodsPhase problemRefinementStructure factorCharge flippingConvolutionDifference mapFigure of meritFourier synthesisGibbs phenomenonLimiting sphereMeasurement

All concepts