On 07/29/2013 12:02 PM, Kelly Tran wrote:

The error I receive is:

---
   File "/Library/modeller-9.10/modlib/modeller/coordinates.py", line
298, in _indxres
     raise KeyError("No such residue: %s" % indx)
KeyError: 'No such residue: 1:B'
---

I separate the chains with '/' in my alignment file.

See http://salilab.org/modeller/9.12/manual/node29.html

Modeller numbers residues in the entire protein starting at 1 by default; it doesn't reset the numbering to 1 when it starts a new chain.

        Ben Webb, Modeller Caretaker
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