From 491ff8dedaafb30e8dcdb48836904e111ca507b7 Mon Sep 17 00:00:00 2001 From: Filip Leonarski Date: Tue, 27 Oct 2026 13:32:15 +0100 Subject: [PATCH] SolventSites: the Cat_Wiz credit on its own line, to Naleem et al. The coordination bands are Cat_Wiz's (Naleem, Henning-Knechtel, Kirmizialtin, Auffinger 2026); the distances and the exclusion zone come from the separate surveys of Leonarski et al. 2017, 2019 and 2025. The comment now credits each to its own authors. Co-Authored-By: Claude Opus 5.5 Claude-Session: https://claude.ai/code/session_01HVeDQqN9qRD57vnShzTC37 --- image_analysis/structure_refinement/SolventSites.cpp | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/image_analysis/structure_refinement/SolventSites.cpp b/image_analysis/structure_refinement/SolventSites.cpp index ddabc266b..5b2240e78 100644 --- a/image_analysis/structure_refinement/SolventSites.cpp +++ b/image_analysis/structure_refinement/SolventSites.cpp @@ -17,7 +17,7 @@ namespace { constexpr double PI = 3.14159265358979; -constexpr double SEARCH_RADIUS = 6.0; // A: ion pairs are listed out to it (Cat_Wiz) +constexpr double SEARCH_RADIUS = 6.0; // A: ion pairs are listed out to it, as Cat_Wiz lists them constexpr double SHELL_RADIUS = 3.4; // A: the N and O neighbours listed and typed // A: the ligands bond valences are summed over, following Echols et al. (2014) Acta Cryst. D70, 1104-1114 constexpr double BVS_RADIUS = 3.5; @@ -44,8 +44,9 @@ constexpr double R0_N[BVS_CATIONS] = {1.85, 1.93, 2.26, 2.14}; // and to N with its spread where the papers give one (Mg only: elsewhere the band is all there is, esd 0), the N // and O it cannot have nearer than `too_close`, an exclusion zone [exclude_lo, exclude_hi) it keeps empty (Mg // only), its charge and electrons, and its row in SolventSite::bvs (-1 none). -// Bands following Cat_Wiz, Naleem et al. (2026) Nucleic Acids Res. 54, gkag120; and Leonarski et al. (2017) -// Nucleic Acids Res. 45, 987-1004, (2019) RNA 25, 173-192, (2025) Nucleic Acids Res. 53, gkae1148 +// Coordination bands following Naleem et al. (2026) Nucleic Acids Res. 54, gkag120 (Cat_Wiz) +// Distances and exclusion zone following Leonarski et al. (2017) Nucleic Acids Res. 45, 987-1004, (2019) RNA 25, +// 173-192 and (2025) Nucleic Acids Res. 53, gkae1148 struct SpeciesRule { double lo, hi; double ideal, esd, ideal_n, esd_n;