Re: [modeller_usage] last residue no. when there are x-ray invisible residues
To: Irene Newhouse <>
Subject: Re: [modeller_usage] last residue no. when there are x-ray invisible residues
From: Modeller Caretaker <>
Date: Thu, 18 Nov 2010 14:25:32 -0800
Cc:
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.