On 11/18/10 12:28 PM, Irene Newhouse wrote: > 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.
The error message will show you exactly where the mismatch occurs. If it's occurring around residue 74, then you must have put the gap in the wrong place; if it occurs very close to the start of the sequence, it could be similar to your ATOM/SEQRES mismatch you posted about separately.
> 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.
No, the final residue number is just that; Modeller will stop reading the PDB file when it reaches a residue that has that number in the PDB file. It won't stop at the 242nd residue in your case, but at a residue that has the number "242". So missing residues aren't an issue here.
Ben Webb, Modeller Caretaker