Cat_Wiz: A stereochemistry-guided toolkit for locating, diagnosing and annotating Mg ²⁺ ions in RNA structures

Misassigned Mg ²⁺ ions are pervasive in RNA structural databases, obscuring mechanistic interpretation, undermining comparative analyses and compromising machine-learning training sets. We present Cat_Wiz , a Coot -integrated and stereochemistry-guided toolkit that automates the diagnosis, correction and annotation of Mg ²⁺ binding sites. Cat_Wiz combines three modules: MG_diagnosis validates and regularizes existing assignments, MG_detect identifies unmodeled ions, MG_clamp classifies recurrent clamp motifs. Cat_Wiz includes also a precise binding site annotation system. The implemented stereochemical principles that provide a robust experimental foundation for characterizing Mg ²⁺ binding sites were derived from an analysis of the 1.55 Å resolution Escherichia coli ribosome and from surveys of the Cambridge Structural Database. Applications to ribosomes, hammerhead ribozymes, group I introns, and quaternary RNA assemblies demonstrate that Cat_Wiz rapidly recovers missing ions, corrects misassignments, and improves stereochemical fidelity in minutes rather than days. Beyond refinement, Cat_Wiz generates curated data that can seed diverse machine-learning and AI models. This transparent, cost-effective framework establishes reproducible standards for RNA ion assignments and will drive progress in the automatic design of RNA 3D architectures through the description of unique Mg ²⁺ -dependent backbone folds.