Boltz Template Builder¶
Builds a template object for Boltz YAML, wrapping a PDB structure and optional chain mapping. You can specify which target chain(s) to template, optionally map them to template chain IDs, and control enforcement with a distance threshold and a force flag.
Usage¶
Use this node when you want to guide structure prediction with a known PDB template. Connect a PDB structure source to structure_content, optionally set chain_ids (and matching template_ids) to map template chains to target chains, then combine its output with sequences/constraints/properties using a Boltz list combiner and a Boltz YAML combiner for prediction.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| structure_content | True | PDB | PDB structure content to use as a template. Expects a file-like mapping where the first entry's content is the PDB text. | {'my_template.pdb': 'HEADER ...\\nATOM ...\\nEND'} |
| chain_ids | False | STRING | Target chain IDs to apply the template to. Comma-separated list (e.g., A,B). If one ID is provided, a single chain is targeted; multiple IDs target multiple chains. | A,B |
| template_ids | False | STRING | Template chain IDs corresponding to chain_ids, comma-separated. Must be the same count as chain_ids to be applied. Maps which chain(s) from the PDB serve as the template for each target chain. | A,B |
| force | False | BOOLEAN | If true, adds a potential to enforce adherence to the template during modeling. | True |
| threshold | False | FLOAT | Distance threshold in Angstroms. Values > 0 limit deviations from the template to within this threshold; 0 means no limit. | 2.0 |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| templates | * | A list containing one template object ready to be merged into a Boltz YAML configuration. | [{'pdb': 'ATOM ...', 'chain_id': ['A', 'B'], 'template_id': ['A', 'B'], 'force': True, 'threshold': 2.0}] |
Important Notes¶
- Structure content format: The input must be a mapping of filename to PDB text; the first entry's content is used.
- Chain and template mapping: chain_ids sets the target chain(s). template_ids is only applied if it contains the same number of entries as chain_ids.
- Single vs multiple chains: A single chain ID becomes a scalar in the output; multiple become a list.
- Threshold semantics: A threshold of 0 disables distance limiting; any positive value adds a 'threshold' field.
- Force behavior: Enabling force adds a 'force' field to strengthen adherence to the template during modeling.
- No chain mapping: If chain_ids is left empty, the template is included without explicit chain mapping.
Troubleshooting¶
- Error: 'Structure content is required': Ensure structure_content is connected and is a mapping with at least one PDB entry.
- Error: 'Structure file content cannot be empty': The PDB text in structure_content must not be blank.
- Template mapping not applied: If template_ids count doesn't match chain_ids, the mapping is skipped. Provide equal-length, comma-separated lists.
- Unexpected behavior with spaces: Trim spaces around chain IDs and template IDs; use plain comma-separated values like 'A,B'.
- No effect from threshold: A threshold of 0 disables limiting; set a positive value to apply a distance threshold.