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Coming from pdb-tools

Most tools have the pdb-tools name with mmcif_ for pdb_ and the same options. The differences:

  • pdb_tocif / pdb_fromcif are mmcif_frompdb / mmcif_topdb.
  • The segment tools (pdb_seg, pdb_selseg, pdb_splitseg) have no counterpart: mmCIF has no segment identifier, and label_asym_id names each molecule (mmcif_selchain --label, mmcif_splitchain --label).
  • pdb_chainbows, pdb_chainxseg and pdb_segxchain have no counterpart: mmCIF has no TER records. mmcif_frompdb uses the TER records of a PDB file to separate molecules and names blank chains, and mmcif_label2auth -chain gives each molecule its own author chain.
  • Where pdb-tools behaves differently (or has a bug), the tool's --help says so.