PDB Combiner¶
Merges up to five PDB dictionaries into a single PDB output. Optionally prefixes chain IDs per input to avoid collisions and ensures unique chain IDs by auto-suffixing when duplicates occur.
Usage¶
Use this node when you need to assemble a multi-chain PDB input from multiple PDB sources, such as combining separate structures or subunits into one complex. Connect one or more PDB inputs; enable chain prefixing to systematically keep chain IDs distinct across inputs.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| pdb_1 | False | PDB | First PDB dictionary to merge. Expects a mapping of chain IDs to PDB content. | PDB with chains like A, B |
| pdb_2 | False | PDB | Second PDB dictionary to merge. Expects a mapping of chain IDs to PDB content. | PDB with chain C |
| pdb_3 | False | PDB | Third PDB dictionary to merge. Expects a mapping of chain IDs to PDB content. | PDB with chain A |
| pdb_4 | False | PDB | Fourth PDB dictionary to merge. Expects a mapping of chain IDs to PDB content. | PDB with chain D |
| pdb_5 | False | PDB | Fifth PDB dictionary to merge. Expects a mapping of chain IDs to PDB content. | PDB with chain E |
| prefix_chains | False | BOOLEAN | If true, adds per-input prefixes to chain IDs (PDB1_, PDB2_, etc.) to avoid chain ID collisions. Duplicate IDs are further resolved with numeric suffixes. | true |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| combined_pdb | PDB | A single PDB dictionary containing all chains from the provided inputs with unique chain IDs. | PDB with chains like PDB1_A, PDB2_A, C |
Important Notes¶
- At least one input required: The node raises an error if no PDB inputs are provided.
- Chain ID uniqueness: With prefix_chains enabled, chain IDs are prefixed per input and any remaining conflicts are auto-resolved by adding numeric suffixes (e.g., _1, _2).
- Without prefixing: If prefix_chains is false and a chain ID collision occurs, a warning is generated and numeric suffixes are still added to ensure uniqueness.
- Input order matters for prefixes: The prefix for each input is determined by its slot (PDB1_, PDB2_, ...).
- Maximum inputs: Supports up to five PDB inputs.
Troubleshooting¶
- Error: 'At least one PDB input is required': Connect at least one valid PDB input.
- Unexpected chain renaming: If you see suffixes like _1 or _2, it means a chain ID conflict occurred. Enable prefix_chains to systematically separate chain spaces by input.
- Missing chains in output: Ensure each provided PDB input is a valid PDB dictionary (mapping chain IDs to content) and not empty.
- Confusing chain IDs after merge: Turn on prefix_chains to make the source of each chain explicit (PDB1_, PDB2_, etc.).