CIF To PDB¶
Converts one or more macromolecular CIF (mmCIF) structures into PDB format. Accepts a dictionary of CIF name-to-content mappings and returns a dictionary of PDB name-to-content mappings, preserving the original keys.
Usage¶
Use this node when you have structures in mmCIF format and need PDB format for downstream tools or visualization. Typically placed after a loader or generator that outputs CIF and before nodes that expect PDB input.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| cif | True | CIF | Dictionary of CIF structures to convert. Keys are structure identifiers (e.g., filenames without extension), and values are the full mmCIF text content. | {'1abc': ' |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| structure.pdb | PDB | Dictionary of converted PDB structures. Keys mirror the input CIF keys; values are the full PDB text content. | {'1abc': ' |
Important Notes¶
- Input format: The input must be a non-empty dictionary mapping names to valid mmCIF text content.
- Key preservation: Output keys match the input keys for easy alignment with upstream and downstream nodes.
- Conversion constraints: Invalid or malformed CIF content will cause the node to raise an error for that entry.
- Batch behavior: Processes all provided entries and returns all successful conversions; the node fails if none can be converted.
Troubleshooting¶
- Error: 'CIF input must be a non-empty dictionary': Ensure you pass a dictionary with at least one entry. The keys should be strings and values should be the full mmCIF text.
- Error converting a specific entry: Verify the mmCIF content is complete and well-formed. Try validating the CIF or removing non-standard or corrupted lines.
- Empty output for some keys: The node skips entries with empty or whitespace-only CIF content. Confirm your source provides actual structure text.
- Memory or performance issues on large files: Convert in smaller batches or reduce input size if encountering resource constraints.