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Re: [modeller_usage] (no subject)

bestkarollo wrote:

rdabrk__291E> Sequence difference between alignment and  pdb :
                  x  (mismatch at alignment position      1)
 Alignment         IQKVQDDTKT LIKTIVTRIN DI LDFI PGLHPILTLS KMDQTLAVYQ QIL
       PDB        IQKVQDDTKTLIKTIVTRINDILDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRN
Match * * * Alignment residue (UNK) does not match pdb residue I (ILE), 
  for align code 1AX8 (atom file 1AX8), pdb residue number "3", chain " "
You need to remove the spaces from your alignment file, since Modeller considers ' ' to be a valid residue type. As you can see above, the alignment sequence has spaces in, but the PDB sequence does not. 

	Ben Webb, Modeller Caretaker
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