Add one box per chain: Protein, Ligand, DNA, or RNA. Ligands take a SMILES string (Chai-1 does not accept CCD codes). A modification applies a CCD residue code at a given position. Chai-1 does not support cyclic chains.
One protein chain sequence per line.
One DNA chain sequence per line.
One RNA chain sequence per line.
JSON list of {"type": "protein"|"dna"|"rna", "chain": "A", "sequence": "..."}.
One ligand SMILES per line.
JSON list, e.g. [{"chainA":"A","res_idxA":1,"chainB":"B"}] (any residue on chainB near residue res_idxA on chainA).
JSON list, e.g. [{"chainA":"A","res_idxA":1,"chainB":"B","res_idxB":1}].
JSON list, e.g. [{"chainA":"A","res_idxA":1,"covalentAtomA":"C","chainB":"B","res_idxB":1,"covalentAtomB":"C"}]. Chai-1 was not trained on intra-chain bonds; use inter-chain pairs.