leonarski_fandClaude Opus 4.8
d6924aa901
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>
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.