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P2: tools guide attributes unimplemented BVS and gRMSD to local metal screen #930
Description
Severity: P2 — the guide attributes bond-valence and geometric-fit calculations to a local wrapper that does not implement them.
PR #916, reviewed head 1d760a97efc7b9f9fd80f9d469eadc4409299372.
ref/tools_and_measurements_guide.md:225 says scripts/checkmymetal_local.py computes donor-atom chemistry, bond-valence sums (BVS), and gRMSD without the CheckMyMetal service. The named implementation is a much narrower geometry heuristic: it collects contacts within 3.20 Å, calculates their mean/min/max distances and count, and compares mean distance, count and B-factor with per-element reference values. scripts/checkmymetal_local.py:69–78 returns only z_bond, cn_in_range, and b_in_range; :87–129 shows the complete calculation/output path. Its module documentation explicitly distinguishes it from the canonical service. A hidden/ignored-inclusive search within this named source found no BVS/bond-valence/gRMSD implementation.
Suggested fix: describe only the local outputs and limitations actually implemented, distinguish them from the external service's capabilities, and avoid treating the local heuristic as elemental confirmation. Do not add new scientific calculations merely to satisfy the erroneous description.
Activity
realmarcin commentedon Nov 4, 2026
Acceptance at
169b5e3aefaa160f4b60f2570bf7f95ea911f338: partially corrected, still open.ref/tools_and_measurements_guide.md:225now correctly says the local wrapper does not compute BVS/gRMSD. It still callsb_in_rangea “metal-vs-environment B-factor check” and names_COORDINATION_CUTOFF.The actual
scripts/checkmymetal_local.py:28–39,69–77,108usesINNER_SPHERE_CUTOFF = 3.20.b_in_rangecompares the metal atom's B factor with an absolute per-element interval fromCANONICAL; no neighboring-environment B value is an operand. Contact distance/count and absolute B-range heuristics do not establish elemental identity.Bounded completion: describe those actual operands and limitations, and use the real constant name or omit the implementation name entirely. Do not add new scientific calculations or edit the heuristic to fit the prose. PRIMARY will verify the resulting committed text before acceptance.