Now that, thanks to you, I've got the order of chain/residue number in the pir file fixed, I'm random walking my way through other errors. I had to drop one of my matches because there are differences between the sequence as deposited in the PDB & the pdb file[!]  [At least that has nothing to do with me]. Now another of my matches is giving me fits. It has missing residues 74-85.  I carefully replaced them with -, but I'm still getting the same mismatch error message that I got before I did that. I'm wondering if I have to alter the final residue number in line 2 of the entry for that protein. I have 242, which is the position of the last residue in the sequence, but the pdb file's residue numbers jump from 73 to 86, reflecting the missing residues. I can just drop this entry from the multi-alignment I'm using, which would make the 'casualty rate' 40%, so I'd rather understand better how to fix this issue correctly. I already checked, & this is the only deposited structure for that protein, so it's either fix it or drop it.
Irene Newhouse