PDB Fixer¶
Replaces the residue identities of a specific chain in one or more PDB structures using a provided FASTA sequence. Coordinates, atom counts, and residue numbering are preserved; only the residue three-letter codes in the target chain are changed. If the FASTA length differs from the chain length, it replaces as many residues as possible and leaves the rest unchanged.
Usage¶
Use this node when you need to retarget a designed backbone (e.g., a glycine-only chain from backbone generation) with a desired amino-acid sequence for downstream design or scoring workflows. Typical flow: load or create PDB(s) → prepare a FASTA sequence for the replacement chain → run PDB Fixer with the target chain ID → pass the fixed PDB(s) to subsequent nodes.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| pdb | True | PDB | Dictionary of PDB structures to modify: {pdb_name: pdb_content}. The node will update only the specified chain in each entry. | {'design_1': 'ATOM ...\nATOM ...\nEND\n'} |
| fasta | True | FASTA | FASTA text containing the replacement amino-acid sequence. Headers (lines starting with '>') are allowed and ignored; the final sequence is taken as the concatenation of non-header lines. | >target_chain ACDEFGHIKLMNPQRSTVWY |
| target_chain | True | STRING | Single-character chain ID to replace (e.g., 'A', 'B'). | B |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| fixed_pdb | PDB | Dictionary of updated PDB structures with the target chain’s residues replaced according to the FASTA sequence. Other chains are unchanged. | {'design_1': 'ATOM ... (with updated residue names in chain B) ...\nEND\n'} |
Important Notes¶
- Residue mapping: The FASTA sequence (1-letter codes) is mapped to 3-letter residue names (e.g., A→ALA, G→GLY). Unknown letters are skipped and original residue names are kept.
- Length mismatches: If FASTA length differs from the number of residues in the chain, only the overlapping positions are replaced; extra residues on either side remain unchanged.
- Scope of change: Only the residue names in ATOM/HETATM records of the target chain are modified. Coordinates, atom order, residue numbering, and other chains are preserved.
- Chain requirement: The specified chain ID must exist in each PDB. If a chain is missing, processing for that PDB fails.
- FASTA parsing: Headers are ignored and all non-header lines are concatenated (whitespace removed) to form the sequence.
- Allowed codes: Supports standard amino acids (including SEC 'U' and PYL 'O'). 'X' maps to UNK; any unrecognized character leaves the original residue unchanged.
- Input format: The PDB input must be a non-empty dictionary: {pdb_name: pdb_content}.
Troubleshooting¶
- Error: 'PDB input must be a non-empty dictionary': Ensure you pass a dictionary with keys as names and values as PDB strings.
- Error: 'Target chain ID cannot be empty': Provide a single-character chain ID (e.g., 'A').
- Error: 'Chain 'X' not found in PDB': Confirm the chain exists in the PDB. Check chain IDs by inspecting ATOM/HETATM records (column 22).
- FASTA parsed as empty: Verify the FASTA contains sequence lines beneath any header and that there are no non-amino characters.
- Sequence length mismatch warning: This is expected if the FASTA and chain lengths differ. The node will replace only the overlapping residues.
- Unexpected characters in FASTA: Non-standard letters are ignored for replacement at those positions; the original residue is kept.
- Malformed PDB lines: If the file lacks standard ATOM/HETATM formatting, replacement may fail. Use a validated PDB or convert/clean the structure before running.