From two independent code reviews of the model-validation work. Nothing here
changes a verdict: the acceptance set still reads +17.69 / +1.70 / -0.37 sigma and
the rejected runs still write files byte-identical to a run with no model.
THE RUN'S OUTPUT. Model validation runs BEFORE the reflection files are written,
and two paths through it could throw: the null's replicates (rotated models fed to
a scaling path that fails outright on data it cannot pair up - the adversarial
input for it), and the mmCIF coordinate writer. Either would have taken the .mtz,
.cif, .hkl and _unmerged.mtz with it, after the merge had already been paid for. A
null that cannot be built is a question that could not be put, which is the
NOT_TESTED state this design already has; a coordinate file that cannot be written
is a lost convenience. Both now degrade instead of aborting.
THE ORIGIN GAUGE. Translating the whole cell content along a free-origin direction
- all three in P1, the unique axis in a polar group - leaves every |F| exactly
unchanged. The code said the LM damping and the R-free gate made that harmless
between them. Neither does: the gate is a function of |F| and is blind to exactly
this, and the gauge column of the Jacobian is not zero but noise divided by the
difference step. It is now projected out after every zone, against the group's own
common fixed subspace. P2_1 alone is a large share of deposited structures, and
the reported shift was partly fiction in every one of them.
TWO CLAIMS THAT WERE FALSE. The report told the user R-work carries the decision
"because nothing was refined against it", six lines from where six placement
parameters are refined against it; the real argument is that the null is placed
the same way, so the optimism is common-mode and cancels. And the constant's own
comment quoted a +4 vs +1 sigma gap where the measurement is +17.7 vs +1.7.
Also: the map file's phase columns are back to [0, 360), the convention they
carried before sigma_A weighting; with no data space group the map file follows
the reflections into P1 rather than taking the model's group; the sigma is floored
against a near-zero null spread rather than only an exactly-zero one; the model is
restored whether or not the solver reported a usable answer; and the zone list is
the ladder walked rather than the ladder planned.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
leonarski_fandClaude Opus 5
b2c0a5ea48
