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biopython-structure

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Use Bio.PDB to parse and analyze protein structures (PDB/mmCIF) for structural bioinformatics tasks; use when you need structure parsing, geometry calculations, or structural comparison/superposition.

When to use

• You need to parse **PDB** or **mmCIF** files and access the structure hierarchy (model → chain → residue → atom).
• You want to compute **geometric measurements** such as distances, bond angles, and dihedral angles between atoms/residues.
• You need **neighbor searches** (e.g., find residues/atoms within a cutoff) for contact analysis or local environment inspection.
• You want to perform **structural comparison**, including alignment/superposition and RMSD-style evaluation.
• You need to **extract, modify, and save** structures (e.g., subset chains/residues and write back to PDB/mmCIF).

When not to use

• Do not use this skill when the required source data, identifiers, files, or credentials are missing.
• Do not use this skill when the user asks for fabricated results, unsupported claims, or out-of-scope conclusions.
• Do not use this skill when a simpler direct answer is more appropriate than the documented workflow.

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