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Rugnux --model: report the anomalous map's mean height at the model's anomalous scatterers

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ANOMALOUS_SCATTERER_MEAN_SIGMA= is the anomalous difference map, read at every
model atom from phosphorus up (S of Met/Cys, metals, Cl, I) with the same cubic
interpolation as ANOMALOUS_SITE_*, averaged in map sigma; ANOMALOUS_SCATTERERS=
is their count. One number for the anomalous signal of a merge that does not
depend on which ten atoms come out on top - what the battery tracks for the
long-wavelength standard-protein sets. A new key only: no report version bump.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB
This commit is contained in:
leonarski_f
2026-10-05 07:56:32 +02:00
co-authored by Claude Opus 5.5
parent 2624a69726
commit 7eb8e93a0a
6 changed files with 24 additions and 2 deletions
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rugnux/ModelValidation.cpp
+11
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@@ -80,6 +80,10 @@ constexpr double ANOMALOUS_INVERSION_SIGMA = 5.0;
// signal is there and what carries it; a full site list is what the map file is for.
constexpr size_t MAX_ANOMALOUS_SITES = 10;
// The lightest element counted as an anomalous scatterer: phosphorus. Below it (C, N, O, Na, Mg) f''
// is a fraction of sulfur's at any wavelength these data are taken at.
constexpr int ANOMALOUS_SCATTERER_MIN_Z = 15;
// How many random placements of the same model the real fit is compared against. The verdict is
// (real - mean)/sd of this sample, so what matters is not the mean but how well the SPREAD is
// pinned: the relative error on an sd from n draws is 1/sqrt(2(n-1)), and a sample that happens to
@@ -1290,6 +1294,7 @@ ModelValidationResult Validate(const std::vector<MergedReflection> &merged,
const gemmi::Grid<float> grid = map_from_coefficients(mapanom);
const double rms = write_ccp4(grid, output_prefix + "_anom.ccp4");
std::vector<ModelValidationResult::AnomalousSite> sites;
double scatterer_sum = 0;
for (gemmi::Model &m : st.models)
for (gemmi::Chain &ch : m.chains)
for (gemmi::Residue &r : ch.residues)
@@ -1300,7 +1305,13 @@ ModelValidationResult Validate(const std::vector<MergedReflection> &merged,
r.seqid.str()),
rms > 0 ? grid.interpolate_value(a.pos, MAP_INTERPOLATION_ORDER) / rms
: 0.0});
if (a.element.atomic_number() >= ANOMALOUS_SCATTERER_MIN_Z) {
scatterer_sum += sites.back().sigma;
result.anomalous_scatterers++;
}
}
if (result.anomalous_scatterers > 0)
result.anomalous_scatterer_mean_sigma = scatterer_sum / result.anomalous_scatterers;
std::sort(sites.begin(), sites.end(),
[](const auto &x, const auto &y) { return x.sigma > y.sigma; });