PDB to CIF Converter
v1.0.0Convert PDB coordinates to mmCIF with model selection and warnings for omitted records.
Convert PDB coordinates to mmCIF with model selection and warnings for omitted records.
Paste fixed-column PDB coordinates, upload a .pdb or .ent file, or fetch a PDB entry from RCSB. Click Convert to produce a PDBx/mmCIF coordinate file. Preview the text, check the atom and model counts, and download the .cif file. Conversion runs locally in the browser.
This excerpt contains the first two atoms of crambin, PDB entry 1CRN:
ATOM 1 N THR A 1 17.047 14.099 3.625 1.00 13.79 N
ATOM 2 CA THR A 1 16.967 12.784 4.338 1.00 10.80 C
ENDWith the default settings, the complete output for this excerpt is:
data_converted_structure
#
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
ATOM 1 N N . THR A ? ? . 17.047 14.099 3.625 1.00 13.79 . 1 THR A N 1
ATOM 2 C CA . THR A ? ? . 16.967 12.784 4.338 1.00 10.80 . 1 THR A CA 1
#The summary reports two atoms, one residue, one chain, and one model. This excerpt is a format example, not the complete crambin structure.
| Input | Accepted content |
|---|---|
PDB input | One structure containing fixed-column ATOM or HETATM coordinate records. Paste text or upload a .pdb or .ent file up to 50 MB. |
| RCSB fetch | Fetch a PDB entry such as 1CRN using the RCSB input control. A bare identifier is not coordinate data. |
PDB columns matter. Keep spaces in the atom records, including blank chain IDs and the alignment of atom names. Windows, Unix, and classic Mac line endings are accepted, as is a leading byte-order mark. Decimal and hybrid-36 atom serials and residue numbers are supported. CIF/mmCIF input is rejected because it is already in the target format.
Missing coordinates, invalid numeric fields, duplicate atom serials within a model, and malformed model numbers produce an error rather than a partial coordinate file. Missing occupancy or B-factor fields are written as unknown (?). An explicit occupancy of 0.00 stays zero.
| Setting | Default | Behavior |
|---|---|---|
Preserve secondary structure | On | Copies HELIX identifiers, endpoints, class, length, and comments, plus SHEET residue ranges. Sheet sense and strand registration are omitted with a warning. Turning this off omits both annotation types. |
Include HETATM records | On | Retains ligands, ions, water, and other HETATM records. Turning this off removes every HETATM record, including modified residues represented that way. |
Preserve temperature factors | On | Retains isotropic B-factors. Turning this off writes unknown values (?), not zeroes. |
Include all models | Off | Converts the first model in file order. Turning this on retains every model and its original model number. Other models omitted by the default are reported in a warning. |
Hydrogens and alternate locations are retained by default. The converter does not choose one alternate conformation or combine coordinates from different models.
| Result | Contents |
|---|---|
| Preview | The mmCIF coordinate text and a summary of converted atoms, residues, chains, and models. Residue counts include heteroatom residues and count each model separately. |
| Files | One primary .cif file. An uploaded structure.ent becomes structure.cif; pasted input becomes converted.cif. |
| Warnings | Omitted records, filtered atoms, omitted models, inferred element symbols, unrecognized formal charges, and connectivity limitations. |
The conversion follows the wwPDB PDB coordinate specification and PDBx/mmCIF syntax. Coordinates remain in angstroms, occupancy retains two decimal places, and B-factors remain in square angstroms. Atom order, residue names, author chain IDs, author residue numbers, insertion codes, alternate-location IDs, and recognized formal charges are retained.
Source atom serials become _atom_site.id. If serials repeat across models, later duplicates receive unused numeric IDs so each output atom has a unique identifier. Missing element symbols are inferred from PDB atom-name alignment and reported for review: a space before CA denotes carbon, whereas left-aligned CA denotes calcium. Unrecognized element symbols are marked as unknown (?) with a warning.
Author residue numbering is stored in _atom_site.auth_seq_id. The converter does not construct polymer sequence or entity tables, so _atom_site.label_seq_id and _atom_site.label_entity_id are unknown (?). PDB author numbering can include negative numbers and insertion codes; it is not interchangeable with the mmCIF sequence identifier.
Explicit CONECT atom pairs are copied without inferring additional bonds or bond orders. Repeated and reciprocal pairs are deduplicated; references to excluded or absent atoms are omitted with a warning. Connections use author identifiers and preserve insertion and alternate-location codes. Model-specific connections that cannot be represented across a selected ensemble are omitted with a warning. Convert those models separately if the connections are needed.
HEADER entry IDs and TITLE text are retained. Other records, including ANISOU, SEQRES, CRYST1, transformation matrices, REMARK, LINK, and SSBOND, are not converted and are listed in warnings. Some viewers may therefore show fewer annotations than the PDB source. Sheet strand pairing and hydrogen-bond registration are not reconstructed.
For a PDB archive entry, its original mmCIF contains sequence, entity, crystallographic, assembly, experimental, and validation information that a coordinate conversion cannot recreate. Use the original archive file for deposition, crystallographic analysis requiring cell or symmetry data, or software requiring complete polymer sequence tables. This converter is useful when only PDB coordinates are available, for example from a structure prediction or modeling program.
| Goal | Tool |
|---|---|
| Obtain an archive structure | PDB download |
| Extract the amino acid sequence from coordinates | PDB to FASTA |
| Convert coordinates to a ligand-oriented format | PDB to MOL2 |
CIF is the general crystallographic information format. PDBx/mmCIF uses that syntax with categories for macromolecular structures. This tool writes PDBx/mmCIF coordinate categories in a file with the .cif extension.
It checks the fields needed to produce readable coordinates. It does not repair missing atoms, change protonation, assign complete ligand chemistry, or validate a structure for deposition. CONECT pairs are labeled as covalent connections for export; inspect metal coordination and ligand bonding before simulation or docking.
Include all models is off by default. Enable it to keep the full ensemble. Original model numbers remain attached to the corresponding coordinates; model 0 is retained with a warning because some software requires numbering from 1.
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