PDB Fixer¶
Rewrites residue identities in a specified chain of one or more PDB structures to match a provided FASTA sequence. It parses the FASTA, maps 1-letter amino acids to 3-letter residue names, and updates the residue names for the target chain in-place, preserving coordinates and atom records. If sequence length differs from the chain residue count, it replaces as many residues as possible and warns about the mismatch.
Usage¶
Use this node after loading PDB files and a target FASTA sequence when you need a PDB chain's residue identities to match a designed or target sequence (e.g., workflows involving structure generation then sequence design). Typical flow: Load PDB -> Load/prepare FASTA -> PDB Fixer (set target_chain) -> downstream design/refinement or export.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| pdb | True | PDB | Dictionary of PDB structures to modify, keyed by name. Each value is the full PDB file content as a string. | {'1abc_fixed': 'ATOM 1 N ALA A 1 ...', 'design_model': 'ATOM 1 N GLY B 1 ...'} |
| fasta | True | FASTA | FASTA content containing the target amino acid sequence (1-letter codes). Header lines starting with '>' are supported; the sequence can span multiple lines. | >target_chain ACDEFGHIKLMNPQRSTVWY |
| target_chain | True | STRING | Chain identifier in the PDB to rewrite (e.g., "A" or "B"). | B |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| fixed_pdb | PDB | Dictionary of PDB structures with the specified chain's residue names updated to match the FASTA sequence. Keys mirror the input names. | {'design_model': 'ATOM 1 N ALA B 1 ...\nATOM 2 CA ALA B 1 ...\n...'} |
Important Notes¶
- Residue identity only: This node updates residue names (3-letter codes) for atoms in the target chain; it does not change coordinates, atom counts, backbone, or numbering.
- Sequence length mismatch: If the FASTA length differs from the number of residues detected in the chain, only the overlapping positions are replaced. A warning is issued.
- Chain detection: The chain must exist in ATOM/HETATM records with a standard chain ID character at column 22 (index 21). If not found, processing fails for that PDB.
- Unknown residues: Any 1-letter code not in the supported set is left unchanged at that position and triggers a warning.
- Multiple inputs supported: Accepts a dictionary of multiple PDBs and processes each independently.
- Standard residues expected: Works best when the chain is composed of standard amino acids; non-protein residues are skipped for identity inference.
- Case handling: FASTA amino acids are case-insensitive; they are normalized to uppercase for mapping.
Troubleshooting¶
- Error: 'PDB input must be a non-empty dictionary': Ensure you pass a dictionary mapping names to PDB file contents and that strings are non-empty.
- Error: 'Target chain ID cannot be empty' or 'Chain
not found in PDB' : Confirm the chain ID exists in the PDB (check the chain column in ATOM records) and matches exactly. - Error: 'FASTA content cannot be empty' or 'No sequence found in FASTA data': Provide valid FASTA with at least one non-header sequence line.
- Sequence length mismatch warnings: This is expected if the target chain length differs from the FASTA. Verify you chose the correct chain or adjust the sequence.
- Unexpected amino acid warnings (e.g., 'Unknown amino acid X'): Replace unsupported characters in the FASTA (e.g., X, B, Z) with standard 1-letter amino acid codes.
- No changes observed: Verify that the specified chain matches the chain in the PDB, the FASTA length overlaps the residue count, and the sequence uses standard amino acid letters.