On 7/16/12 2:59 PM, Jonathan Crane wrote: > I am trying to model a 2-chain Ab sequence, but I keep getting the > same error. I think it is not reading the chain break '/' correctly, > but not sure.
You have your chains the wrong way round.
You have asked Modeller to read everything from the start of the H chain to the end of the L chain, but Modeller simply reads residues as they are presented to it in the PDB, and 1u6a has the L chain *before* the H chain. So Modeller happily skips all of the L chain to find residue 2:H before it starts reading, and then it reads all the way to the end of the H chain before stopping (since it never finds 215:L). Either swap the chains in your alignment file, or edit the PDB file to put them in the desired order.
Ben Webb, Modeller Caretaker