A protein consists of a chain of amino acids joined by peptide bonds. The protein here is seen as an extended chain, as at the start of most design and de-novo puzzles.
At the lowest level, a protein consists of a long chain of amino acids held together by peptide bonds, also known as a polypeptide.
A chain always starts with an N terminal with an unbonded amino group group, and ends with C terminal with an unbonded carboxyl group. In between the terminals, the carboxyl group of one amino acid is joined to the amino group of the next amino acid by a peptide bond.
Although it's rare in Foldit, proteins may consist of multiple chains, each with its own N terminal and C terminal. Each chain can be a different length with a different primary structure. In puzzles involving this type of protein, all the usual Foldit tools are available on each chain.
Puzzle 1448: Classroom Puzzle: Amyloid Protein is one example of a puzzle with multiple chains. Puzzle 1448 had 120 segments, consisting of three identical copies of a 40-segment chain.
Puzzle 58: Insulin Mutant is another example, with two different chains. This puzzle has been presented as a revisiting puzzle several times, most recently as 1501: Revisiting Puzzle 58: Insulin Mutant.
Symmetry puzzles are another case involving multiple chains. These puzzles involve oligomers, multiple identical copies of a single chain or monomer. In this type of puzzle, there's an active copy of the chain or monomer, and one or more "shadow" copies. Many Foldit tools only act or report on the active copy, but any changes are automatically applied to each shadow copy.
Symmetry puzzles are different than other Foldit puzzles involving multiple chains. In puzzle 1448, each one of the three chains had identical primary structure, but each could take on a different shape. In symmetry puzzles, each chain automatically has the same primary structure and shape at all times.
In the Protein Data Bank (PDB) and other sources, different chains are designated A, B, C and so on. Foldit does not assign a specific identifier to different chains. In outside sources, the residues in each chain are numbered separately, starting with the N terminal as number 1.
In Foldit, all segments are numbered continuously, without regard to chains.
For example, in puzzle 58: Insulin Mutant, the solution is available in the PDB as 1A7F. Segments 1 to 21 in Foldit correspond to residues 1 to 21 in chain A of 1A7F. Segments 22 to 50 in Foldit correspond to residues 1 to 29 in chain B of 1A7F. For chain B, adding 21 to the residue number gives the corresponding Foldit segment number. (Chain A contains 21 residues.)
In Foldit, the only way to detect different chains in a recipe is to look at the results of structure.GetAtomCount. For a given amino acid, a N terminal at the start of a chain will have two additional atoms (two extra hydrogens), while the C terminal at the end of a chain will have one additional atom (an extra oxygen), compared to the same amino acid in the middle of a chain. (For cysteine residues, the presence of a disulfide bridge also changes the atom count. Each cysteine loses one hydrogen atom when a disulfide bridge forms, changing the atom count from 11 to 10 for a non-terminal segment.)