Re: [modeller_usage] SequenceMismatchError when adding missing residues in LoopModel()
To: Steven Truong <>
Subject: Re: [modeller_usage] SequenceMismatchError when adding missing residues in LoopModel()
From: Modeller Caretaker <>
Date: Mon, 5 Apr 2021 18:02:47 -0700
Cc: "" <>
On 4/5/21 5:42 PM, Steven Truong wrote:
I think I have the template sequence alignment matching exactly to the
PDB file, in the same way the second entry “1qg8_fill” has a full
sequence. However, I am indicating missing residues with “1qg8.”
Should I fill in those dashes with missing residues? I’m likely
misunderstanding how AutoModel/LoopModel works then. When you refer to
“template sequence,” is that “1qg8” or “1qg8_fill” in the align.pir file
on the tutorial?
The template is the known structure, i.e. the PDB file, 1qg8 in the example.
Well, this simply isn't correct. The "missing" glycine here isn't
missing in the 6z43 PDB file - it is there (residue 35 in chain A). What
are you trying to accomplish here?