PDB Chain Extractor¶
Extracts specified chains from one or more PDB structures. It retains relevant header/metadata lines and all ATOM/HETATM records for the selected chains, producing a new PDB that contains only those chains. Chain selection is case-insensitive and whitespace-tolerant.
Usage¶
Use this node when you need to isolate specific protein chains from PDB structures for focused analysis or downstream tasks (e.g., per-chain sequence extraction, modeling, or visualization). Connect a PDB dictionary input and specify one or more chain IDs (e.g., A, A,B). The output preserves the original PDB IDs while filtering contents to the requested chains.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| pdb | True | PDB | Dictionary of PDB structures to filter, mapping {pdb_id: pdb_content}. Each value is a PDB text string. | {"1abc": "HEADER ...\nATOM ... A ...\nATOM ... B ...\nEND"} |
| chains | True | STRING | Comma-separated list of chain IDs to extract. Single-character, alphanumeric chain IDs only. Spaces are ignored and case-insensitive. | A, B |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| filtered_pdb | PDB | Dictionary of PDB structures filtered to contain only the specified chains. Keys are the original PDB IDs; values are PDB strings that include the chosen chains and end with an END record. | {"1abc": "HEADER ...\nATOM ... A ...\nATOM ... A ...\nEND"} |
Important Notes¶
- Chain IDs: Must be single alphanumeric characters (e.g., A, B, 1). Input is case-insensitive and ignores spaces.
- Multiple PDBs: Input may contain a batch of PDBs; each will be filtered independently while preserving its original ID.
- Metadata lines: Common header and annotation records (e.g., HEADER, TITLE, REMARK, HELIX, SHEET) are preserved. ATOM/HETATM lines are kept only for selected chains.
- End of file: The output PDB string includes a terminal END line.
- Validation: If no atoms are found for the requested chains in a PDB, the node raises an error listing available chains detected in that PDB.
- Empty entries: Empty PDB contents are skipped; if all are empty or invalid, the node raises an error.
Troubleshooting¶
- Error: Chains parameter cannot be empty: Provide at least one chain ID, e.g., "A" or "A,B".
- Error: Invalid chain ID 'X': Ensure each chain ID is a single alphanumeric character with no extra symbols.
- Error: No atoms found for chains [...]: Verify the requested chains exist in the PDB. The error message includes available chains detected; adjust your selection accordingly.
- Output is empty or missing expected chains: Confirm the chain list formatting (comma-separated), check for typos, and ensure the original PDB actually contains those chains.
- Batch input issues: If some PDBs are empty or malformed, they will be skipped. Ensure at least one valid PDB remains; otherwise, the node will raise an error.