Boltz Template Builder¶
Builds template entries for Boltz YAML configurations from a provided PDB structure. Supports selecting specific chain IDs, mapping them to template IDs, optionally enforcing the template during modeling, and applying an interatomic distance threshold.
Usage¶
Use this node when you want to provide a structural template (PDB) to guide Boltz modeling. Typical workflow: supply a PDB file, optionally specify which chains to use and how to map them to template IDs, then connect the output to a list-combiner and finally into a Boltz YAML combiner before prediction.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| structure_content | True | PDB | PDB structure content to use as a template. Provide a file-like input containing the text of a PDB file. | {'example.pdb': 'ATOM ... PDB CONTENT ...'} |
| chain_ids | False | STRING | Comma-separated chain identifiers from the structure to use as templates (e.g., A,B). If left empty, chain selection is not constrained. | A,B |
| template_ids | False | STRING | Comma-separated template chain IDs to pair 1:1 with chain_ids (e.g., A,B). The number of entries must match chain_ids when provided. | X,Y |
| force | False | BOOLEAN | If true, adds a flag to enforce use of the template during modeling. | True |
| threshold | False | FLOAT | Distance threshold in Angstroms to constrain template application. 0 means no limit. | 3.5 |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| templates | * | A list containing one template object built from the PDB and options. This list can be combined with other items and fed into a Boltz YAML combiner. | [{'pdb': 'ATOM ... PDB CONTENT ...', 'chain_id': ['A', 'B'], 'template_id': ['X', 'Y'], 'force': True, 'threshold': 3.5}] |
Important Notes¶
- Chain-ID mapping: If chain_ids are provided, template_ids (if set) must contain the same number of entries to ensure correct 1:1 mapping.
- Single vs multiple chains: When a single chain ID is provided, it may be recorded as a single value; multiple chains are recorded as a list.
- Threshold behavior: A threshold of 0 applies no distance limit; any positive value will be included in the template.
- Force flag: Enabling force adds a directive to more strongly enforce the template during modeling.
- Input validity: The PDB content must be non-empty and valid text; empty or missing structure content will cause an error.
Troubleshooting¶
- Error: 'Structure content is required': Ensure you connected a valid PDB input and it contains text (not empty).
- Error: 'Structure file content cannot be empty': The PDB file is present but empty. Provide a proper PDB file.
- Warning: 'Number of template IDs must match number of chain IDs': Check that template_ids has the same number of items as chain_ids. Use comma-separated lists with matching counts.
- Unexpected result: No chain filtering applied: If chain_ids is left blank, the template won’t be limited to specific chains.
- Downstream combine issues: If the Boltz YAML combiner expects a list, connect this node’s output directly or via a list combiner without altering its list structure.