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structure-navigation

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Navigate the Bio.PDB SMCRA hierarchy (Structure-Model-Chain-Residue-Atom) safely, surfacing the heterogeneity it hides by default. Use when deciding how to handle altloc/DisorderedAtom conformers before a distance or RMSD, indexing residues insertion-code-safe with the full (hetflag, resseq, icode) tuple, choosing the ATOM/observed vs SEQRES/canonical vs UniProt sequence, selecting the right Model for an NMR ensemble, filtering waters/hetero/metals correctly, and reconciling auth vs label numbering. Keywords SMCRA, altloc, DisorderedAtom, insertion code, SEQRES, PPBuilder, auth_seq_id.

When to use

• handling altloc/DisorderedAtom conformers
• indexing residues with insertion codes
• choosing ATOM vs SEQRES vs UniProt sequence
• selecting NMR ensemble models
• filtering waters/hetero/metals
• reconciling auth vs label numbering

When not to use

• aligning to UniProt/MSA by string position
• assuming every SEQRES residue has coordinates
• assuming construct equals canonical sequence
• using resname to classify water vs ligand

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