PDB To CIF¶
Converts one or more PDB structures to mmCIF format using BioPython. Accepts a dictionary of PDB IDs to PDB content strings and returns a dictionary of the same IDs mapped to converted mmCIF strings. Includes basic handling to improve chain/entity mappings in the generated mmCIF where possible.
Usage¶
Use this node when you need mmCIF structures for downstream tools that require mmCIF instead of PDB. Typical workflow: load or prepare PDB content, optionally clean/fix it, then convert to mmCIF for analysis, visualization, or as input to other biotech nodes.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| pdb | True | PDB | Dictionary of PDB structures to convert. Keys are structure IDs (names) and values are PDB-formatted strings. | {'example_pdb': 'ATOM 1 N MET A 1 11.104 13.207 8.678 1.00 20.00 N ...'} |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| structure.cif | CIF | Dictionary of converted mmCIF structures. Keys mirror the input IDs; values are mmCIF-formatted strings. | {'example_pdb': 'data_template\n#\nloop_\n_atom_site.group_PDB ...\n'} |
Important Notes¶
- Input format: The input must be a non-empty dictionary mapping IDs to valid PDB text. Invalid or empty strings are skipped and may cause the node to error if no valid entries remain.
- Output mapping: Output keys match input keys, enabling consistent tracking of structures through the workflow.
- Entity/chain mapping: The node attempts to improve entity/chain mappings in the mmCIF output, but results may vary depending on the input structure; verify the output if downstream tools rely on specific entity IDs.
- Error behavior: If no structures can be converted, the node raises an error rather than returning an empty result.
- Content expectation: Provide complete PDB content strings (not file paths). Large structures are supported, but malformed PDB input may fail conversion.
Troubleshooting¶
- Error: 'PDB input must be a non-empty dictionary': Ensure you pass a dictionary with at least one key-value pair where the value is a valid PDB string.
- Conversion failed for specific entry: Validate the PDB text for that entry (formatting, missing headers/records). Try fixing the structure with a PDB repair step before conversion.
- Empty output or missing entries: Inputs with empty or whitespace-only content are skipped. Ensure each value contains valid PDB content.
- Unexpected or missing entity IDs in mmCIF: Check the mmCIF for chain/entity labeling. If downstream tools require precise entity IDs, consider pre-processing/fixing the PDB or manually reviewing the generated mmCIF.
- Downstream tool rejects mmCIF: Confirm that the receiving tool supports the generated mmCIF flavor and that required categories/fields are present. If necessary, re-validate or re-export from another tool after conversion.