leonarski_fandClaude Opus 5
0c3e1462ef
CalcPossibleReflections was handed d_min/d_max derived from the reflections that came out of the merge, so a loss at either extreme took the numerator and the denominator with it. At the high end that is right: d_min is the finest d reached anywhere and the denominator is the full sphere down to it, so anisotropic loss shows. At the low end it was a tautology - d_max was the coarsest reflection that happened to survive, so anything the beam-stop shadow mask (on by default), a detector mask or the low-resolution limit itself removed left the denominator along with the data and could not be reported as missing. Both statistics paths now bin, and count, between the DECLARED low-resolution limit and the finest d reached: MergeOnTheFly::MergeStats (stills) and RotationScaleMerge::MergeAndStats (rotation). The grid and the denominator keep sharing their bounds, so no possible reflection falls outside a shell. An undeclared low limit is the whole sphere - 1/d^2 down to 0 - spelled as an infinite d_max, which ResolutionShells already handles and which gemmi's for_all_reflections special-cases; the change therefore reads correctly whether or not the 50 A default stays. The innermost shell keeps a finite d_max label, falling back to the coarsest reflection measured when the bound is infinite. This makes the shell boundaries the ones the integration document already claims: XDS lays its nine 1/d^2 bins between INCLUDE_RESOLUTION_RANGE's two values, not between the extremes of the surviving data, and counts POSSIBLE against the declared low limit - which is why its innermost shell reports the beam stop's loss. Verified against a CORRECT.LP: all nine boundaries reproduce to the printed precision from the declared 50 A, and not from the coarsest observed reflection. Measured on stored merges of seven rotation datasets, small-molecule and protein, re-scaled with --mode scale: the overall denominator moves by 0 to 2 reflections out of 70,000-100,000, because on every one of them the coarsest reflection the declared limit allows was itself measured - the corpus has no dataset whose stop eats a whole low-resolution class. What does move is the shell grid: the innermost boundary shifts by 0.1-0.4% in d (e.g. 7.21 -> 7.22 A), which changes the innermost shell's counts by up to a few per cent and its R_meas by around 0.1 percentage points. Stored battery baselines for rmeas_lo must therefore be regenerated, not compared across this commit. Two decisions read merged completeness (the two-pass wrong-cell guard, which only fires above 100.5% and only under -S); a larger denominator can only lower the figure, so the guard can fire less often, never more. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
Jungfraujoch
Application to receive data from the PSI JUNGFRAU and EIGER detectors.
All documentation is now placed in docs/ subdirectory and for the current version hosted on Jungfraujoch Read The Docs page.