leonarski_fandClaude Opus 5.5
1420908885
The model scale searched b_sol only over 10-80 A^2. That is the range
Fokine & Urzhumtsev report for models at ordinary B, but on low-resolution
entries whose deposited B is 200-400 A^2 the fit sat on the 80 A^2 ceiling
(and k_sol on its 0.1 floor): a solvent edge far sharper than the atoms it
lies against, reaching too deep in resolution. R-free came out 0.05-0.10
above REFMAC (0 cycles) and phenix.model_vs_data on the same MTZ, model
and flags.
The ceiling is now max(80, 2 x the model's mean atomic B) (SolventBMax),
for the reported fit and for the rigid-body placement's per-zone solvent
(CPU, GPU and the host fallback alike). The grid keeps eight b_sol values
across a wider box, so it costs no more points; the default box, and so
every model with mean B <= 40 A^2, is bit-identical to before.
Measured (10 open-arm sets with --model, GPU build, vs the same base):
high-B set, 7.0 A: R-free 0.462 -> 0.364, b_sol 80 -> 379 (REFMAC 0.366,
REFMAC's own b_sol ~371; model_vs_data 0.291);
the rigid-body step now commits
high-B set, 3.9 A: 0.410 -> 0.331, b_sol 80 -> 388, k_sol 0.10 -> 0.225
(REFMAC 0.328, model_vs_data 0.314); null 10.1 -> 14.2 sigma
B~200 set, 3.2 A: 0.408 -> 0.402, b_sol 80 -> 120; enantiomorph label
decision unchanged (27.2 -> 25.8 sigma)
7 other sets (mean B 16-57): bit-identical R, k_sol, b_sol, placement.
p.hkl md5 and the MTZ reflection data are identical to the base on all 10.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
49 lines
2.5 KiB
C
49 lines
2.5 KiB
C
// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#pragma once
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#include <cstddef>
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#include "gemmi/model.hpp"
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#include "gemmi/scaling.hpp"
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// Fit the overall scale, the anisotropic B and the flat bulk solvent of a model to observed
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// amplitudes, writing the answer into `scaling` (k_overall, b_star, k_sol, b_sol) so that
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// gemmi's own scale_data() can then apply it.
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//
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// The caller decides which reflections are fitted: FitModelScale reads scaling.points, which
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// prepare_points() filled. Pass the WORKING set to keep the free reflections out of the scale
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// model - that is a property of the call site, not of this function.
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//
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// Replaces gemmi's fit_isotropic_b_approximately() + fit_parameters(), which is an unbounded
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// Levenberg-Marquardt: nothing there stops k_sol and b_sol reaching values a flat solvent model
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// is meaningless at (b_sol of 1707 A^2 was measured on this corpus). Here k_sol and b_sol come
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// from a grid search over the physical ranges, so an unphysical answer cannot be represented.
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// The box the solvent parameters are searched in. The defaults are the physically reasonable
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// range reported by Fokine & Urzhumtsev and adopted as phenix's default grid: k_sol in (0.1, 0.8)
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// and b_sol in (10, 80) A^2, of which phenix searches b_sol 10-80 in steps of 5. A model with high
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// atomic B gets a higher b_sol ceiling (SolventBMax).
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struct ModelScaleBox {
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double k_lo = 0.10, k_hi = 0.60;
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double b_lo = 10.0, b_hi = 80.0;
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};
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// The b_sol ceiling for `model`: 80 A^2, or twice the model's mean atomic B where that is higher.
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// b_sol is how far the solvent's edge is smeared, and the edge can be no sharper than the atoms it
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// lies against: a model at B of 300 A^2 beside a solvent held at 80 gets a solvent term that reaches
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// far too deep in resolution, which only a too-small k_sol can then offset. Fokine & Urzhumtsev's
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// 10-80 A^2 is for models at the B of ordinary entries (their mean b_sol 46 A^2), where the ceiling
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// stays at 80.
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double SolventBMax(const gemmi::Model &model);
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struct ModelScaleReport {
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int n_points = 0; // reflections the fit actually used
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int n_grid = 0; // grid points evaluated
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double r_work_fit = 1.0; // R on the fitted reflections, at the chosen solution
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};
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// nthreads: the grid points are fitted in parallel on up to this many threads; the answer does not
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// depend on it.
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ModelScaleReport FitModelScale(gemmi::Scaling<float> &scaling, ModelScaleBox box = {}, size_t nthreads = 1);
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