T

leonarski_fandClaude Opus 5 799381d027 rugnux: --model names the strongest anomalous scatterers, not just R-free

Where the merge kept the Bijvoet split - which the default Friedel-averaged
merge does, so this needs no -A - --model now computes an anomalous difference
Fourier, coefficients F(+)-F(-) on the model phase turned back by 90 degrees
over the acentric reflections, writes it as <prefix>_anom.ccp4, and reads it at
the model's own atom centres. The ten highest are logged and land in the results
report as ANOMALOUS_SITE_01..10, each named by the atom, residue and chain it
sits on, with its height in map sigma. Reading at the sites rather than
searching the map for blobs is what ANODE does, and it says what carries the
signal instead of leaving coordinates to look up; a scatterer the model does not
contain is by construction absent from the list, which is what the map file is
for.

The list is always ten long, so its information is in the heights. On an
S-SAD dataset at 5 keV the six cysteine sulfurs take ranks 1-6 (10.1 down to
4.2 sigma) and rank 7 falls to 2.2; the same crystal at 13 keV, where sulfur has
no anomalous signal to speak of, tops out at 2.7 sigma with a water and a main
chain carbon inside the top five. So the same list reads as a signal / no-signal
gate, not only as a ranking.

The reading is cubic. Grid::interpolate_value defaults to trilinear, and on the
d_min/3 map grid that under-reads a peak this sharp by up to a quarter, unevenly
enough to reorder the sites; cubic on the same grid is within about 2% of a
sample-rate-10 one. The map r.m.s. is unchanged by the sample rate, so the
normalisation was never at fault. The 2Fo-Fc reading behind
MEAN_ATOM_DENSITY_SIGMA is deliberately left on the default so a number already
in existing reports does not move.

An anomalous merge keeps each Bijvoet mate as a row of its own and both rows
carry the same F(+)/F(-) pair, attached to the + index of the Friedel ASU of the
frame the merge was made in, so the differences are read from the merged
reflections as they came in - carried into the model's frame here, on the +
rows only. Taking the - rows as well would give one reflection both signs of its
difference and let the last row written decide.

write_ccp4 splits into an FFT and a write so the anomalous map can be both
written and sampled from one transform; the 2Fo-Fc atom-centre score, which used
to repeat that FFT, now reuses the grid.

Cross-checked against ANODE run on this output: identical identification - its
three peaks are the three disulfides, each maximum 0.64-0.70 A off a sulfur we
name - with our heights about 1.35x lower. Sharpening, grid and sigma
normalisation are excluded; the residual is SHELXC's FA preparation, which fed
ANODE 2166 reflections against our 2534.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_014zTy4Bpi4pPHw4bybf7q2R

2026-08-27 22:09:51 +02:00