What — get_expected_heavy_atoms('MSE', present_atom_names=...) returns SD and omits SE for a chemically correct MSE residue; structural repair may then diagnose the wrong atom.
How — Keep sequence-level MSE→MET replacement separate from residue-specific chemical expectations. Use the MSE chemical component or report it unassessed until a chemically faithful template exists.
Why — MSE has a selenium atom named SE; reporting the methionine sulfur atom SD as expected changes element identity in an existing public build path. This is a pre-1.0 scientific correctness defect.
Record — devguide/pending_bugs/mse_heavy_atom_expectations_substitute_met_sulfur_for_selenium.md
Related — #218
Schedule — pre-1.0 defect
What — get_expected_heavy_atoms('MSE', present_atom_names=...) returns SD and omits SE for a chemically correct MSE residue; structural repair may then diagnose the wrong atom.
How — Keep sequence-level MSE→MET replacement separate from residue-specific chemical expectations. Use the MSE chemical component or report it unassessed until a chemically faithful template exists.
Why — MSE has a selenium atom named SE; reporting the methionine sulfur atom SD as expected changes element identity in an existing public build path. This is a pre-1.0 scientific correctness defect.
Record — devguide/pending_bugs/mse_heavy_atom_expectations_substitute_met_sulfur_for_selenium.md
Related — #218
Schedule — pre-1.0 defect