---

name: input-data-formats description: "Author, validate, and debug Chai FASTA input records for proteins, ligands, DNA, RNA, modified residues, entity names, and chain naming." disable-model-invocation: true metadata: disco-role: operating license: Apache 2.0

Input Data Formats

Use this sub-skill when an agent needs to create or repair Chai input FASTA records before folding. It covers entity headers, sequences, ligand SMILES, modified residues, entity names, and the chain-name consequences of fasta_names_as_cif_chains / entity_name_as_subchain.

Route First

• Need to run chai-lab fold or chai_lab.chai1.run_inference after the FASTA is valid? Use ../cli-inference/SKILL.md.
• Need .aligned.pqt, A3M conversion, MSA server, or template hit files? Use ../msa-templates/SKILL.md.
• Need contact/pocket/covalent restraint CSVs or glycan bond details? Use ../restraints-glycans/SKILL.md.
• Need only basic glycan|name FASTA routing? This sub-skill covers the header; glycan string semantics belong to ../restraints-glycans/SKILL.md.

Fast Authoring Rules

• Write one FASTA record per Chai entity: >protein|name, >protein|name=receptor, >ligand|name=atp, >dna|name=primer, >rna|name=guide, or >glycan|name=n_linked.
• Always provide an entity name; Chai rejects headers without a label and inference requires names to be unique.
• Use explicit entity types instead of relying on sequence heuristics; short A/C/G/T records are ambiguous across DNA, RNA, and protein.
• Encode modified polymer residues as bracketed multi-character residue names, such as AAA(SEP)AAA or (MSE)G, not as unbracketed three-letter text.
• Encode ligands as SMILES strings; use bracketed ions such as [Mg+2] or [Zn+2], because bare ion text can pass header parsing but fail ligand tokenization.
• Preserve entity order intentionally: automatic chain IDs are assigned from the accepted chain order, while fasta_names_as_cif_chains=True uses entity names as parsing/output chain IDs.

Validate Before Folding

Run the bundled helper before expensive inference:

python scripts/validate_chai_fasta.py input.fasta
python scripts/validate_chai_fasta.py --tokenize --entity-names-as-subchains input.fasta

The first command checks Chai header parsing, required names, duplicate names, type heuristics, and polymer modified-residue syntax. The optional tokenization check catches malformed SMILES and chain-name issues that only appear when Chai builds chains.

References

• references/fasta-and-entities.md — format grammar, entity tables, naming rules, and chain-name implications.
• references/api-reference.md — validation and parsing APIs useful for scripts and diagnostics.
• references/troubleshooting.md — common parser, sequence, ligand, duplicate-name, and chain-name failures.