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Re: [modeller_usage] ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different



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
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