MINPK asks how MUCH of the expected profile is readable. It does not ask WHERE, and
the two are not the same question. The renormalisation argument the rescue rests on -
a fit over a subset of a normalised profile is unbiased - needs the pixels to go
missing for reasons unrelated to the reflection. A gap, a mask or the edge of the
sensor is such a reason: the loss is set by the detector, and the fit renormalises
over what is left. A pixel invalidated BY THE FLUX IT SAW is not: it goes missing
because the reflection was bright, and it is the peak.
Measured on the combined fulls, against the mean of the complete observations of the
same reflection, in the innermost resolution shell of the high-multiplicity control
and of a weaker crystal: a rescued reflection whose unreadable pixel sits within a
pixel of the predicted centre reads |I - <I>|/I of 0.50 and 0.53, against 0.073 and
0.212 for a complete observation - 6.8x and 2.5x - and carries several times the mean
intensity of its shell. On the control that is 0.21% of the shell's observations
supplying 1.77% of the R_meas numerator; on the weaker crystal 0.52% supplying 6.82%.
Rescues that lost only rim pixels are unremarkable by the same measure, 1.19x and
0.88x. Dropping the peak-losers alone takes the shell's R_meas from 7.440% back to
7.315% (unrescued: 7.307%) and from 22.03% to 21.06% (unrescued: 21.28%) - which is
the whole of the low-resolution R_meas the rescue cost, and on the second crystal
rather more.
Raw frames say what they are. The pattern is a dead-centre invalid pixel with 5878,
9875 and 27583 counts around it: the detector's per-frame invalid marker on the
brightest reflections. MINPK cannot catch them because it cuts on profile MASS, and
the peak of a broad spot is a few percent of the mass.
So a second condition, in the loop that already measures the readable fraction: no
unreadable pixel may carry more than 0.9 of the profile's own peak value. A fraction
of the peak rather than a radius in pixels because the peak is as wide as the spot -
for a Gaussian the cut is at sqrt(-2 ln f) sigma, 0.46 sigma here, which is the peak
pixel alone where sigma is 0.8 px and the crest of the ridge where the profile is a
bandwidth streak. Swept against the alternatives on two crystals: a fixed radius
needs 1.0-1.5 px to do the same work and costs 3-9x more observations for it, and
0.5 px does not reach the peak of a sub-pixel-offset prediction at all; tightening
the fraction to 0.5 or 0.2 buys nothing beyond 0.9 and costs 7x more.
Six crystals, three detectors, against the rescue as it stands: the rule keeps
99.86-99.96% of the recovered observations and returns R_meas to its unrescued value
or below (4.6 -> 4.5%, 6.7 -> 6.6%, 25.1 -> 25.0%), R_meas in the innermost shell
likewise (2.7 -> 2.6%, 5.9 -> 5.3% against 5.4% unrescued, 16.5 -> 16.4%), <I/sigma>
up or level everywhere, and every unique reflection the rescue won is kept. Raising
--overlap-minpk to 0.90 instead reaches the same place on two of them and short of it
on the third, while discarding 0.8% of the recovered observations rather than 0.05%.
An elongated pink-beam profile on a 9M detector and an EIGER2 16M dataset are both
untouched at 99.9%, so the crest protection does not over-reject a streak.
One crystal is not improved: a dataset whose error model rugnux declines to fit for
want of strong reflections, whose <I/sigma> is <= 0 in eight of its ten shells and
whose R_meas is undefined in as many. There the rule costs about 3% of <I/sigma> in
the one shell that has signal, reproducibly, on top of the 9% the rescue itself costs
there - while its overall R_meas moves 1.5 points on nothing but the thread count.
The parity test gains four sections. Unreadable pixels were only ever punched into
empty sky, so neither the rescue nor this rule had any CPU/GPU coverage at all;
they now go into the signal disks - the peak of every fifth reflection, ~1.1 sigma
out of every seventh, the disk edge of every eleventh - for both profile modes, a
box sum and an elongated stencil, with a check that the clipping actually costs
reflections so the coverage cannot go quietly vacuous.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Full 38-crystal rotation battery against the rescue without this rule, both on the
same base:
ISa better 19 / worse 4, +0.73
CC1/2 better 3 / worse 1, +1.3
R_meas_lo better 4 / worse 3, -0.3
space groups unchanged
for 17 770 observations, 0.09 % of the run total and under 2 % of what the rescue
had won. The two crystals whose peak-loss population was measured beforehand
land on their predicted values: a tetragonal reference goes R_meas_lo 2.7 ->
2.6 % and ISa 27.11 -> 27.42, a cubic insulin 5.9 -> 5.3 % and 20.34 -> 20.65.
One crystal pays: a cubic case with 2381 unique reflections goes R_meas 8.8 ->
9.6 % and ISa 4.08 -> 3.49. It is the crystal in the battery with the fewest
uniques, so its rescued population is small and its shell statistics are coarse,
but the loss is real and not noise in the R_meas. The R_meas sum over the battery
reads +1.3, of which +3.2 is one crystal whose R_meas moves 1.5 points on thread
count alone; without it the sum is negative.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
leonarski_fandClaude Opus 5
e4ce573075