Cif use auth

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When loading mmCIF structure files, the cif_use_auth setting (default: on) controls whether the auth_* fields are used or not.

New in PyMOL 1.7.8

With the PDBx/mmCIF format, the PDB introduced new residue and chain numbering schemes. The numbering which is found in PDB files is available in mmCIF files from the auth_* fields. The new numbering, which for example has no insertion codes and strictly increments residue numbers, is available from the label_* fields. For compatibility with PDB files, PyMOL by default will read the auth_* fields (if available, with fallback to label_* fields).

Note that _atom_site.label_asym_id is always loaded into the segi field, independant of the cif_use_auth setting.

Note that non-polymer molecules (e.g. water) are not enumerated by _atom_site.label_seq_id and will appear as a single residue in PyMOL (sequence viewer, when making selections, etc.) with cif_use_auth=off.

Currently affected fields

  • _atom_site.auth_atom_id (ID)
  • _atom_site.auth_comp_id (resn)
  • _atom_site.auth_seq_id (resi)
  • _atom_site.auth_asym_id (chain)
  • _atom_site.pdbx_pdb_ins_code (resi suffix)

Examples

"auth" versus "label" asym_id of 1oky:

PyMOL>set cif_use_auth
PyMOL>fetch 1oky, authon, async=0
PyMOL>get_chains authon
 cmd.get_chains:  ['A']
PyMOL>set cif_use_auth, off
PyMOL>fetch 1oky, authoff, async=0
PyMOL>get_chains authoff
 cmd.get_chains:  ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K']