PDB Chain Extractor¶
Extracts specific chain(s) from one or more PDB structures. Given a dictionary of PDB contents and a comma-separated list of chain IDs, it filters the ATOM/HETATM records to only those chains while preserving relevant header and annotation lines. Returns a new PDB dictionary with the same keys, containing only the requested chains.
Usage¶
Use this node when you need to isolate particular chains from complex or multimeric PDB structures before downstream steps such as sequence extraction, format conversion, design, or visualization. Connect a PDB dictionary input and specify chain IDs (e.g., A or A,B) to produce a filtered PDB suitable for per-chain analyses.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| pdb | True | PDB | Dictionary of PDB structures to filter, keyed by PDB ID or name. Each value is a full PDB text string. | {'1ABC': 'HEADER ...\\nATOM ... A ...\\nATOM ... B ...\\nEND'} |
| chains | True | STRING | Comma-separated chain IDs to extract. Spaces are ignored and matching is case-insensitive. Each chain ID must be a single alphanumeric character. | A, B |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| filtered_pdb | PDB | Dictionary of filtered PDB structures with only the specified chains kept for each input entry. | {'1ABC': 'HEADER ...\\nATOM ... A ...\\nEND'} |
Important Notes¶
- Chain ID format: Each chain ID must be a single alphanumeric character; input is case-insensitive and whitespace around commas is ignored.
- Batch behavior: Processes all entries in the input PDB dictionary and returns a dictionary with the same keys, filtered by the specified chains.
- Preserved records: Retains common header/annotation lines (e.g., HEADER, TITLE, HELIX, SHEET, CRYST1) and MODEL records, but only includes ATOM/HETATM lines for the requested chains.
- Validation: Raises an error if no valid chain IDs are provided or if none of the specified chains are found; the error lists available chains detected in the input.
- Empty inputs: Skips empty PDB contents with a warning; if all entries are empty or invalid, processing fails.
Troubleshooting¶
- No chains provided: If you see an error that chains cannot be empty, provide at least one chain ID like 'A' or 'A,B'.
- Invalid chain ID: If an error mentions invalid chain ID format, ensure each chain ID is a single alphanumeric character (e.g., 'A', '1').
- Chains not found: If it reports no atoms found for requested chains, verify the chain IDs exist in the source PDB; the error message lists available chains you can use.
- Empty PDB content: If entries are skipped as empty, confirm upstream nodes are producing PDB strings and connections are correct.
- Unexpected output size: If output is missing chains, confirm your 'chains' string has commas between IDs and no accidental characters; spaces are allowed and ignored.