leonarski_fandClaude Opus 5
ce3199748d
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Rotation processing no longer refuses to integrate a frame that fails to index on its own, which is
right - no other program does that - but it means a genuinely bad stretch of a sweep is now
integrated instead of quietly dropped. Some sweeps have a real problem behind that stretch: the
crystal partly or wholly out of the illuminated volume, off the rotation axis, or dying of dose.
That is actionable at the beamline ("recollect", "re-centre"), and until now nothing said it.
MeasureSweepQuality reports it as contiguous RANGES, never per-frame flags, and reports only - no
observation is excluded on the strength of it. A single weak frame is noise; forty consecutive ones
are a fact about the experiment, and the frames still carry signal worth merging.
The discriminator is that the incident flux is already out of the per-image scale before that scale
is fitted (DivideOutIncidentFlux runs from Ingest), so a drop in G that the beam does not explain is
on the sample side by elimination. Measured on one crystal with a dead arc: the flux proxy spans
1.4x across the run where the fitted scale spans 246x.
A range needs BOTH per-frame channels down: the scale, and the CC to merge. The CC channel is what
keeps a merely attenuated stretch out - absorption and flux scale a frame's intensities without
changing how well they correlate with the merged reference. Without it the clean high-multiplicity
control, whose per-image scale swings 4x on a 180 degree period, would be reported as a bad crystal.
It is not: it produces no ranges at all, and neither does the other control.
Five codes, each the field's own words and each a phrase a report can print:
no diffraction - essentially nothing was recorded from the indexed lattice over the range
out of beam - frames were lost: the range gets a scale far less often than the run does
weak diffraction - the frames all still index, with much less intensity; cause not determined
loss of centring - one cycle of modulation per revolution (autoPROC's words for the phenomenon)
radiation damage - the range runs to the end of a sweep whose quality was already decaying
Only the last two claim a cause, and each rests on its own evidence. Damage is progressive, so it
must have been setting in before the range and must not recover. Loss of centring rests on the one
signature that breaks a documented degeneracy: Evans (Acta Cryst. D62, 72-82) notes that illuminated
volume and absorption are indistinguishable, but a crystal's own shape absorbs on a 180 degree
period, so a dominant 360 degree fundamental over a full turn cannot be the crystal's shape. That
test runs on the total scale, flux included, unlike everything else here - the flux proxy is a
background, a crystal leaving the beam takes its own scattering with it, and the beam cannot be
periodic in an angle it does not know. Where the evidence does not reach, weak diffraction says so
rather than guessing.
Frame numbers are processed-image ordinals, inclusive at both ends, the numbering of _image.dat.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>