On 6/24/13 1:50 AM, James Starlight wrote: > _modeller.SequenceMismatchError: get_ran_648E> Alignment sequence not > found in PDB file: 1 ./input.pdb (You didn't specify the > starting and ending residue numbers and chain IDs in the alignment, so > Modeller tried to guess these from the PDB file.) Suggestion: put in the > residue numbers and chain IDs (see the manual) and run again for more > detailed diagnostics. You could also try running with > allow_alternates=True to accept alternate one-letter code matches (e.g. > B to N, Z to Q). > > > How I could fix it ?
Did you try doing what the error suggests? You didn't include input.pdb, so I can't be sure, but it's quite possible that it doesn't have a chain with no ID (as you specified in your alignment) but that it has an "A" chain.
Ben Webb, Modeller Caretaker