Load CIF¶
Loads a CIF/mmCIF structure from a text string and assigns it a user-defined ID. Produces a dictionary mapping the provided ID to the CIF content for use by downstream biotech nodes.
Usage¶
Use this node at the start of workflows where you need to provide a protein structure in CIF/mmCIF format. Paste the CIF text into the input and set a unique ID. The output can be routed into nodes that accept CIF structures or saved/exported.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| cif_string | True | STRING | The full CIF/mmCIF content as a text string. | data_1ABC # _entry.id 1ABC _atom_site.group_PDB ATOM ... |
| cif_id | True | STRING | A unique identifier to associate with this structure. If you also provide a related FASTA elsewhere, use a matching sequence ID. | structure |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| structure.cif | CIF | A dictionary mapping the provided ID to the CIF string. | {'structure': ' |
Important Notes¶
- Unique IDs: Use a unique cif_id for each structure to avoid collisions when handling multiple structures.
- Content format: The node expects raw CIF/mmCIF text, not a file path or URL.
- FASTA alignment: If you plan to use a FASTA sequence corresponding to this structure, ensure the FASTA record ID matches the cif_id.
- Batch handling: The output is a dictionary {id: content}, which fits naturally into nodes that operate on structure dictionaries.
Troubleshooting¶
- Empty output or errors: Ensure cif_string is not empty and contains valid CIF/mmCIF content.
- ID conflicts: If downstream nodes report duplicate IDs, change cif_id to a unique value.
- Invalid format warnings: If other nodes complain about parsing, confirm the CIF text is complete and correctly formatted (no truncated lines or missing data blocks).
- Unexpected downstream behavior: Verify that the receiving node accepts a CIF type and that the output is correctly connected.