last residue no. when there are x-ray invisible residues
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.
Thanks! Irene Newhouse
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
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Irene Newhouse -
Modeller Caretaker