Load PDB¶

Loads a Protein Data Bank (PDB) structure provided as a raw text string and packages it into a structured output for downstream biotech nodes. You assign an identifier to the PDB, and the node emits a mapping from that ID to the provided PDB content. The node does not modify or validate the PDB format.

Usage¶

Use this node at the start of workflows when you already have PDB content (e.g., pasted text or preloaded data) and need to pass it to structure-processing or visualization nodes. It is commonly paired with nodes that consume PDB structures or with sequence nodes where the PDB ID should match a corresponding FASTA record.

Inputs¶

Field	Required	Type	Description	Example
pdb_string	True	STRING	The full PDB file content as text. This should be a valid PDB-formatted string.	HEADER EXAMPLE PDB ATOM 1 N MET A 1 20.154 34.198 27.447 1.00 20.00 N ATOM 2 CA MET A 1 21.560 34.560 27.800 1.00 20.00 C TER END
pdb_id	True	STRING	An identifier to associate with this PDB entry. Must be unique within the workflow. If you also provide a FASTA record for this structure elsewhere in the workflow, its sequence ID should match this value.	pdb

Outputs¶

Field	Type	Description	Example
structure.pdb	PDB	A dictionary mapping the provided PDB ID to the PDB string content.	{'my_structure': 'HEADER EXAMPLE PDB\nATOM 1 N MET A 1 20.154 34.198 27.447 1.00 20.00 N\nEND\n'}

Important Notes¶

ID uniqueness: Use unique pdb_id values to avoid collisions when working with multiple structures.
FASTA alignment: If you include a corresponding FASTA record, ensure its sequence ID exactly matches the pdb_id.
No validation: The node does not validate PDB formatting; malformed content may cause downstream nodes to fail.
Pass-through behavior: The node does not alter the PDB content; it wraps your input into a keyed structure for workflow compatibility.

Troubleshooting¶

Downstream errors when parsing PDB: Verify pdb_string is valid PDB format; correct formatting or regenerate the structure.
Unexpected overwriting or missing entries: Ensure each pdb_id is unique across the workflow to prevent key collisions.
Empty or truncated output: Check that the entire PDB text was provided (including END/TER records where applicable) and that there are no hidden characters removed during copy/paste.
Mismatch with FASTA-based steps: Align the pdb_id with the sequence ID used in related FASTA inputs.