leonarski_f
c4d2d419ce
Three terms of the score of a model - the same F_model at every stage, the as-given start and the refined end alike - and a breakdown of it: - Riding hydrogens from the start: the dictionary's hydrogens are added before the model is first scored (REFMAC's 0-cycle restores them; they move R by 0.010-0.013 at 1.1 A). The engine is made once, with them. - The bulk-solvent mask on a grid of its own, min(d_min/3, 0.4 A), at most 2^26 points. On the density grid (1.1 A at 3.3 A) gemmi's 0.8 A shrink found no grid offset and was skipped, which put R 0.015-0.03 high at >= 2.5 A. 0.3 and 0.4 A agree to 0.001. - The overall scale and anisotropic B by robust least squares (pseudo-Huber, iteratively reweighted, c = median |residual|) in the fine pass of the k_sol/b_sol grid (ModelScaleBox::robust, refinement only; MR and validation keep the plain fit). Plain least squares on |F| is the exact LS optimum but lets a few badly-fitted strong reflections set the scale (1.1 A set: R 0.1706 against REFMAC's 0.1600). The scale fit of refinement now runs on the CPU (no ModelScaleGPUPool). RefinementSettings::score_only scores the model as given and stops; RefinementResult::score_start carries every term (k, B, anisotropic B, k_sol, b_sol, mask spacing, R in 20 shells, -lnL work/free, the likelihood FOM, hydrogens; per-reflection terms with score_only). GeometryStatistics gains rmsZ. rugnux_refine_test: --score-only, --dump. Measured against REFMAC 5.8.0431 ncyc 0 (refi bref iso) on the same model, data and flags, 14 open-arm sets 1.1-3.6 A: R-work/R-free within 0.002 on 12 (was +0.003..+0.03); 7n2s and 9yl4 score 0.003/0.005 below REFMAC, which a 0.6-0.8 A mask grid reproduces. REFMAC with ANISOU stripped scores identically, so isotropic B is not a parity term. Open: the likelihood's D/FOM (ours 0.01-0.11 higher at high resolution); geometry differs only by REFMAC's metal LINK restraints and residues outside the embedded dictionary. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 4f94b21611874ad9dcf89e6771fe311a0e10bb06) (cherry picked from commit 00db6a6f539ac2da515c0a649474335f4c4b07b8)
Jungfraujoch
Application to receive and analyse data from the PSI JUNGFRAU and EIGER detectors, together with
rugnux, its program for processing stored diffraction data - rotation and serial, macromolecular
and small-molecule - from images to merged reflections.
All documentation is now placed in docs/ subdirectory and for the current version hosted on Jungfraujoch Read The Docs page.