Crystallography & Symmetry
patterns derived from their groups
Concept

Heavy atom method — where it appears

Phasing a structure from the position of one much heavier atom, found in a Patterson map where its vectors stand above every other peak. The added symmetry of the map is what makes the search feasible, by concentrating those vectors onto sections rather than spreading them.

Named by 8 essays across one field — each of them below, with the objects they name alongside it.

A structure, and the vectors between its atoms. On the left, 4 atoms in a cell. On the right, every one of the 16 vectors between them, each drawn from a common origin: 13 distinct positions, with the 4-fold peak at the origin being each atom paired with itself. That right-hand picture is what a Patterson map shows, and it is the thing a diffraction experiment gives without phases. It has more peaks than the structure has atoms — n² against n — which is why interpreting one is hard, and why it is always symmetric about its centre.

The map that needs no phases

A diffraction experiment measures intensities and loses phases, so the electron density cannot be computed from it. One map can be: the transform of the intensities, whose peaks are not atoms but the vectors between them — every ordered pair, brought to a common origin.

diffraction · The Patterson function 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 Every vector between every pair of atoms. The Patterson map of a four-atom structure: the transform of the intensities with every phase set to zero, so it is computable from a measurement and nothing else. Its peaks are not atoms but the vectors between them, and the ringed one is the strongest that is not the origin — taken here as an interatomic vector exactly as a crystallographer takes the vector between two heavy atoms. That it really is one of the structure's own vectors is checked rather than assumed: it lands within 0.0031 of a cell of a difference of two positions, and it sits 0.67 of a cell from the origin, well outside the skirt of the tall peak there. A candidate taken too close to the origin is the same peak seen again and the whole method fails quietly.

Solving from the vector set

A Patterson map contains a copy of the structure laid over every atom in turn. Shift it by one interatomic vector, take the pointwise minimum with itself, and the copies that fail to coincide are cut away — leaving the structure, together with its inverse, from a measurement that carries no phases at all.

diffraction · The Patterson function 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 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 Success of the flipping solver against how far off the subtracted lead is. The share of forty starts on the cell of nineteen carbons and one lead that the flipping solver solves, with the lead's density subtracted at a position displaced from the true one by up to sixteen grid steps, half the cell. The rate does not fall with the offset: the points scatter without a trend about the pooled rate of 40%, the band marking two binomial standard deviations, and the original solver, with nothing subtracted, solves none. Refining the position from the map does no better than holding it.

The lead is wherever it is taken out

Charge flipping solves a cell of nineteen carbons and one lead once the lead's own density is taken out before each flip and put back after. The obvious worry was precision: a lead subtracted a fraction of a grid step from where it really is leaves a residual larger than any carbon. The residual is there, larger than a carbon at a tenth of a step. It does not matter. Subtracted two steps away, or half the cell away, the lead still lets the solver succeed at the same rate, because the solver builds the whole structure round wherever it is put.

diffraction · Direct methods 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 Success of the flipping solver against the error in the vector between two subtracted leads. The share of 80 starts on a cell of eighteen carbons and two leads that the flipping solver solves, with both leads' density subtracted, the first at its true place and the second displaced from its true place by an error in a random direction. The rate holds to a quarter of a grid step (21, 19, 18, 11, 0, 0, 0 successes at errors of 0, 0.1, 0.25, 0.5, 1, 2, 4 steps), falls by half at half a step, and is zero from one step on. With one lead the place did not matter at all; with two, the vector between them does.

Two leads need their vector to half a step

With one heavy atom in a cell with no symmetry, charge flipping did not care where the atom was subtracted: it rebuilt the structure round whatever place it was given. With two heavy atoms that freedom runs out, as predicted, because no translation can put both under wrong references at once. Subtract one of them a whole grid step from where it belongs and the solver never succeeds. But the tolerance is five times looser than the estimate it was predicted from: up to a quarter of a step the rate does not move, at half a step it halves, and the residual the solver absorbs is three carbons' worth, not one.

diffraction · Direct methods

Named alongside it

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

Phase problemDirect methodsHeavy atomInteratomic vectorThe Patterson functionElectron densityStructure factorAutocorrelationConvolutionHarker sectionOrigin choiceExhaustive search

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