I am trying to run a 2d alignment and keep getting a number of errors
that I have been unable to rectify.
When you get a SequenceMismatchError, Modeller also reports in the log
file the sequence you gave in the alignment file and the sequence it
found in the PDB, so you can see where the mismatch occurred. Look in
the log file and change either your alignment or the PDB file so the
sequences match.
In addition to the error message
presented below I've also been getting one that says "Alignment sequence
not found in the pdb file".