ModelValidation now fits the scaled model to each reindexing of the observed
reflections (identity plus the twin laws from ReindexAmbiguityOperators) and
keeps the one with the lowest R-free. The scale + per-shell + R computation is
factored into a per-candidate lambda so every candidate is scored identically.
No-op for a holohedral crystal (no twin laws), e.g. lysozyme, where the only
candidate is the identity. The enantiomorph/screw ambiguity is still resolved
from the model hand, not probed - |Fcalc| is the same for both hands so R-free
cannot distinguish them.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Two ways the processing now adopts symmetry from an external reference:
- Reference MTZ (-z) fixes the space group and unit cell, unless -S / -C override them
(the explicit flag always wins - so -S with the "wrong" enantiomorph is allowed). The cell
is a soft reference: indexing may still drift within tolerance, as with -C.
- rugnux --model: when the data was merged in the enantiomorph of the model's space group
(e.g. data P4(1)2(1)2, model P4(3)2(1)2 - the merged intensities cannot tell them apart),
ValidateAgainstModel reindexes the observed reflections into the model's hand (via gemmi
change_of_hand_op). This keeps the data setting consistent with the model; it does not change
the R-factors, which use |F|.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
New offline capability: `rugnux --model model.pdb` validates the merged intensities
against a PDB model. It computes structure factors from the model on a grid (IT92 x-ray
form factors, FFT), adds an optimized flat bulk solvent (SolventMasker + gemmi Scaling:
k_sol, b_sol, overall k and anisotropic B) and a per-resolution-shell scale, then reports
R-work / R-free and writes 2Fo-Fc and Fo-Fc CCP4 maps plus a map-coefficient MTZ
(FP, FC, PHIC, FWT/PHWT, DELFWT/PHDELWT, FREE). No refinement of the structure itself;
the model is only re-fractionalized into the data cell (a rigid cell adjustment).
The observed amplitudes are the French-Wilson |F| already on the merged reflections
(MergedReflection.F, computed at end of merge), so the R-free/maps use exactly the same
amplitudes as the written reflection file.
ModelValidation.{h,cpp} holds the logic; wired via --model (ProcessConfig.model_path) into
both the full pipeline (Rugnux::Run write site) and the --scale re-merge path. Links the
unified `gemmi` static target for the model / structure-factor / map headers.
Verified on lyso_ref: R-free 0.346, mean 2Fo-Fc at atom centres +2.16 sigma, maps written.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
leonarski_fandClaude Opus 4.8