CIF To PDB¶
Converts molecular structures from CIF (mmCIF) format to PDB format using BioPython. Accepts a dictionary of one or more CIF entries and returns a dictionary of PDB strings with the same keys. Skips empty inputs with warnings and raises clear errors for invalid data.
Usage¶
Use this node when you have structures in CIF/mmCIF format and need PDB output for downstream tools that require PDB input (e.g., visualization, chain extraction, sequence fixing). Typically, connect a CIF-producing node or a preloaded CIF dictionary to this node, then pass the resulting PDB to subsequent processing nodes.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| cif | True | CIF | Dictionary of CIF structures to convert. Keys are structure IDs; values are CIF text content. | {'example_dict': {'my_structure': ' |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| structure.pdb | PDB | Dictionary of PDB structures converted from the input CIF entries. Keys mirror the input names. | {'example_dict': {'my_structure': ' |
Important Notes¶
- Input format: The input must be a non-empty dictionary mapping names to CIF strings; otherwise the node raises an error.
- Batch handling: Processes multiple CIF entries in one call; empty strings are skipped with a warning.
- Conversion fidelity: Conversion is performed via BioPython; some mmCIF-specific annotations may not appear in the PDB output.
- Output keys: Output dictionary keys match the input keys, enabling easy mapping in workflows.
- Error behavior: If none of the CIF entries can be converted, the node raises an error.
- Performance: Very large structures may take longer to parse and convert.
Troubleshooting¶
- Error: 'CIF input must be a non-empty dictionary': Ensure you pass a dict like {"id": "
"} rather than a raw string or empty object. - Warning: 'Empty CIF content for
, skipping.' : Provide non-empty CIF text for that entry. - Error: 'Failed to convert CIF
to PDB: ...' : The CIF content may be malformed or unsupported. Validate the mmCIF file or re-export it from the source. - Error: 'No CIF structures could be converted to PDB': All entries were empty or invalid. Verify each input string contains valid CIF content.
- Downstream issues with PDB consumers: If a downstream tool complains about formatting, check that the original CIF parses correctly and consider simplifying or re-generating the structure.