leonarski_f
bcb71136ab
Metal sites were held only by the 1.9 A metal contact of the repulsions; REFMAC restrains the metal LINKs of the coordinate file (its documentation), which was the one geometry term the 0-cycle comparison did not share (one 2.8 A set: bond rmsd 0.018 against REFMAC's 0.042). - monomers/metals.cif: the Monomer Library's own statistics of metal sites (metals.json, LGPL data as the rest of monomers/), cut by update_monomers.py to the metal ions of its compound list and O, N, S donors: mean distance, spread and number of sites per metal, donor element and coordination number. - AddMetalLinks (before prepare_topology): every LINK / struct_conn record between a metal ion and an O, N or S that no link of the dictionary describes (its ZN-CYS, ZN-HIS, FE-CYS, FE-HIS are taken as they are) gets a link of one bond at EmbeddedMetalDistance for the two elements and the ion's coordination - the number of its donor records, symmetry mates included - from the rows resting on at least 20 sites (the coordination's own row, else the neighbours interpolated), sigma their spread (>= 0.02 A); a His or Cys donor loses the proton the bond replaces (DEL-HD1 / DEL-HE2 / CYSmod1, as the library's links do). Records only, no distance search; records to a symmetry mate count for the coordination but are not restrained (bonds to symmetry mates are not, anywhere). - The metal bonds are a restraint set of their own (RefinementTopology::metal_bonds), evaluated with the geometry and reported apart (GeometryStatistics::rmsd_metal, REFINE_RMSD_METAL_BONDS, REFINE_SCORE_RMSD_METAL_BONDS / _BONDS_ALL): their sigma is the spread of real sites, so they sit further from ideal than covalent bonds, and the weight ladder's 0.02 A bound stays a bound on the covalent ones. refine_parity.py compares REFMAC's bond rmsd (links included) with the combined one, and takes --gpu. Score-only geometry against REFMAC 5.8 0-cycle, all bonds (count): 2.8 A Zn/Fe set 0.0402 (4934) vs 0.042 (4935), was 0.0178; a Zn-Cys set 0.0186 (7102) vs 0.019 (7102); a Ca set 0.0297 vs 0.026 (REFMAC also refines the sugars and uses one Ca-O distance); a Mg set 0.0114 vs 0.017 (REFMAC restrains 8 symmetry links and puts Mg-O at 1.99 A, the library's statistics at 2.07). R of the scored model unchanged (+0.0001 on the first from the removed His/Cys protons). Refined R-free with the links vs without: +0.0016, -0.0002, +0.0005, +0.0004. Test: RefinementRestraints_metal_links (Zn-Cys4 by the dictionary's link, Mg(H2O)6 by the new ones, both back at their distances). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 0fcffc5c71e03e184cff18f07524473462a57b68)
35 lines
1.6 KiB
C++
35 lines
1.6 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 <string>
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#include "gemmi/monlib.hpp"
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// The restraint dictionary refinement uses: the subset of the CCP4 Monomer Library (Vagin et al. 2004,
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// LGPL-3.0) carried in the binary - the standard amino acids and nucleotides, their links and
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// modifications, a few common ligands and additives, water and ions; monomers/update_monomers.py holds
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// the list. Parsed from memory once per process; no file is read.
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const gemmi::MonLib &EmbeddedMonomerLibrary();
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// The ideal distance and its sigma of a bond from a metal ion to a donor atom (O, N, S) at a site of `coordination`
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// donors, from the library's statistics of metal sites (metals.json, embedded as monomers/metals.cif). Only rows
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// resting on at least METAL_MIN_SITES sites count: the row of that coordination number, else the two nearest
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// below and above it interpolated linearly, else the nearest one; the sigma is the row's standard deviation, at
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// least METAL_MIN_SIGMA. False where the pair has no such row.
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constexpr int METAL_MIN_SITES = 20;
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constexpr double METAL_MIN_SIGMA = 0.02; // A
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bool EmbeddedMetalDistance(gemmi::El metal, gemmi::El ligand, int coordination, double &distance, double &sigma);
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// Whether `code` (a residue name) has a description in it.
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bool InEmbeddedMonomerLibrary(const std::string &code);
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// One .cif of monomers/, as CMakeLists.txt embeds it: its name and its text in pieces.
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struct EmbeddedMonomerFile {
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const char *name;
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const char *const *pieces;
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size_t n_pieces;
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};
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