Supported record types

pidibble parses all standard PDB record types. The table below lists them with the container you get in parsed, whether the record is also produced from mmCIF input, and a one-line description. For the exact fields of any record, see the API reference.

Reading the columns

Container is what p.parsed[<key>] holds:

• single — one PDBRecord.

• list — a PDBRecordList of records (a multiple-entry record).

• sub-keys — the record expands into several keys (e.g. JRNL → JRNL.AUTH, JRNL.TITL, …; REMARK → REMARK.<n> and, for tables, REMARK.350.BIOMOLECULE1.TRANSFORM<n>).

• grouping — a structural marker used while parsing multi-model files.

mmCIF marks record types the PDBx/mmCIF parsing path also produces (using author numbering). A record type absent from a given file is simply absent from parsed.

Record	Container	mmCIF	Description
ATOM	list	✓	Atomic coordinates for standard residues.
HETATM	list	✓	Atomic coordinates for heterogens (ligands, ions, waters).
ANISOU	list		Anisotropic temperature factors.
TER	list		Chain terminator.
CONECT	list		Explicit atom-to-atom connectivity.
LINK	list	✓	Covalent and metal-coordination links between residues.
SSBOND	list	✓	Disulfide bonds.
CISPEP	list		Cis-peptide bonds.
SEQRES	list	✓	Primary sequence, one record per chain.
DBREF, DBREF1, DBREF2	list		Cross-references to sequence databases (DBREF1/DBREF2 are the two-line variant).
SEQADV	list	✓	Differences between the entry and its sequence database.
MODRES	list		Modified (non-standard) residues.
HELIX	list	✓	Helix secondary structure.
SHEET	list	✓	β-sheet secondary structure (ranges, sense, registration).
HET	list		Non-standard (heterogen) groups present.
HETNAM	list		Chemical names of heterogens.
HETSYN	list		Synonyms for heterogen names.
FORMUL	list		Chemical formula of each heterogen.
SITE	list		Functionally important sites.
MTRIX1, MTRIX2, MTRIX3	list		Non-crystallographic symmetry transforms.
REVDAT	list		Revision history.
HEADER	single	✓	Classification, deposition date, and PDB id.
TITLE	single	✓	Title of the experiment.
COMPND	single [1]	✓	Description of the macromolecular components (token groups).
SOURCE	single [1]	✓	Biological source of the components (token groups).
KEYWDS	single	✓	Keywords describing the entry.
EXPDTA	single	✓	Experimental technique.
AUTHOR	single		Depositors.
CRYST1	single	✓	Unit-cell parameters and space group.
ORIGX1, ORIGX2, ORIGX3	single		Transformation to the crystallographic origin.
SCALE1, SCALE2, SCALE3	single		Transformation to fractional crystallographic coordinates.
MDLTYP	single		Model-type annotations.
NUMMDL	single		Number of models in the entry.
CAVEAT	single		Warnings about known errors in the entry.
OBSLTE	single		Entries made obsolete by this one.
SPRSDE	single		Entries this one supersedes.
SPLIT	single		Related entries the structure is split across.
MASTER	single		Bookkeeping counts of records in the file.
END	single		End-of-file marker.
JRNL	sub-keys		Primary citation (JRNL.AUTH, JRNL.TITL, JRNL.REF, JRNL.REFN, JRNL.PMID, JRNL.DOI).
REMARK	sub-keys	✓ [2]	Annotation remarks, one key per remark number (REMARK.<n>); tables expand further.
MODEL, ENDMDL	grouping		Model boundaries in multi-model entries.

Notes

[1] (1,2)

From mmCIF input, COMPND and SOURCE are instead flat, per-entity PDBRecordLists rather than token groups — see PDBx/mmCIF parsing.

[2]

For REMARK, the mmCIF path produces the biological-assembly transforms (REMARK 350) and the missing-residue list (REMARK 465).