Bio Structural Biology Structure Io

About this skill

Reads, writes, downloads, and converts macromolecular structures with Biopython Bio.PDB. Use when choosing a format (mmCIF/PDBx vs legacy PDB vs BinaryCIF) for a structure that may exceed PDB's ~62-chain / 99,999-atom limits; when residue numbers do not match the paper because of auth vs label numbering (MMCIFParser defaults authresidues=True); when metadata (resolution, method, R-free) is missing because Bio.PDB drops it and MMCIF2Dict is needed; when the deposited coordinates are the asymmetric unit and the biological assembly must be downloaded separately; when downloading from RCSB (files.rcsb.org, PDBList); and when a legacy MMTF path is dead (RCSB retired MMTF July 2024, use BinaryCIF).

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Original listing metadata

Original name

bio-structural-biology-structure-io

Original description

Reads, writes, downloads, and converts macromolecular structures with Biopython Bio.PDB. Use when choosing a format (mmCIF/PDBx vs legacy PDB vs BinaryCIF) for a structure that may exceed PDB's ~62-chain / 99,999-atom limits; when residue numbers do not match the paper because of auth_* vs label_* numbering (MMCIFParser defaults auth_residues=True); when metadata (resolution, method, R-free) is missing because Bio.PDB drops it and MMCIF2Dict is needed; when the deposited coordinates are the asymmetric unit and the biological assembly must be downloaded separately; when downloading from RCSB (files.rcsb.org, PDBList); and when a legacy MMTF path is dead (RCSB retired MMTF July 2024, use BinaryCIF).

About this listing

Category: Science & research
Reported license: Not specified
Listing language (estimated): English
Review status: Not individually reviewed
Agent compatibility: Atlas installation supports Claude Code, Codex, and Cursor. Skill-specific dependencies and features are checked during setup.