Crystallography & Symmetry
patterns derived from their groups
Series

Statistics — the series

6 essays on one idea, from the one that introduces it to the one that assumes the rest.
  1. N(z): the fraction of reflections weaker than z. The cumulative distribution of normalised intensities, measured on two structures built from the same atoms — one with an inversion centre, one without — and drawn against the two closed forms, 1 − e^(−z) without a centre and erf(√(z/2)) with one. The curves are furthest apart at small z, which is the useful end: a centrosymmetric structure has far more nearly-absent reflections, because its structure factor is a single real number that can pass through zero rather than a complex one that rarely does.

    Whether there is a centre is a statistic

    Everything else on this site is decidable: a pattern has a symmetry or it does not, and the detector settles it in integers. Whether a structure has an inversion centre is not like that. No single reflection carries the answer — the distribution of all of them does.

    part 1 · diffraction
  2. 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.

    part 2 · diffraction
  3. 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.

    part 3 · diffraction
  4. The twin fraction, recovered from a moment and nothing else (12 atoms). A structure of 12 atoms twinned at each of 6 fractions, with the second moment of its intensity distribution measured and the fraction solved back out of it. The recovery is within a few hundredths as far as thirty per cent — 4 rows here — and 4 of the 6 fractions get a number at all. Beyond thirty per cent the relation flattens: the derivative of 2α(1−α) vanishes at a half, the two roots meet, and a small error in the moment becomes a large one in the fraction. Where the sampled moment falls below 1.5 the quadratic has no real root and the estimate refuses rather than clamping, which is why a nearly perfect twin is the hard case in practice rather than the easy one.

    A twin hides in the statistics

    A twinned crystal scatters as two orientations at once and the detector cannot separate them. What arrives is a sum of two intensities — and adding two independent quantities narrows a distribution, which is a signature no model of the structure is needed to read.

    part 4 · diffraction
  5. Two populations, and neither of them empty. The reflections of a structure in which three quarters of the atoms are paired by a half-cell shift, sorted by the parity of h + k and each class scaled by its own mean. The two histograms have the same shape, which is the point: each class on its own is an ordinary acentric distribution. What differs is the scale — the odd class is a sixth of the even one on average — and no odd reflection is absent, so no extinction rule fires and nothing about the space group is affected.

    A translation that is nearly there

    Half a structure copied onto the other half by a half-cell shift, with nothing exact about it. No reflection vanishes, so no extinction rule fires — and the test for a centre of symmetry answers yes about a structure that has none.

    part 5 · diffraction
  6. How many reflections the centre test needs. The error rate of two tests for a centre of symmetry against the number of reflections used, measured on 60 centrosymmetric and 60 non-centrosymmetric structures at each point. The moment test — the one in every textbook, comparing ⟨|E|² − 1⟩ to its two theoretical values — reaches one error in twenty at 160 reflections and one in a hundred at 320. A likelihood ratio, which uses each reflection's own value instead of one average, reaches the same at 40 and 80. The gap is the price of summarising a distribution by its mean, and it is about a factor of four.

    How many reflections it takes to know there is a centre

    The test for a centre of symmetry compares one average of the intensities against two theoretical values a quarter apart. Whether that is a measurement depends on how many reflections went into the average, and the only honest way to find out is to run the test on structures whose answer is already known and count the mistakes.

    part 6 · diffraction

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