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

[Modeller Caretaker <>]

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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