Re: [modeller_usage] Including ligand from template
To: James Starlight <>, modeller_usage <>
Subject: Re: [modeller_usage] Including ligand from template
From: Modeller Caretaker <>
Date: Tue, 15 Apr 2014 12:03:07 -0700
On 4/15/14, 2:05 AM, James Starlight wrote:
I've followed 1st modeller tutorial making alignment of my target
against 1 template (with the inclusion of hetatm from the template). As
the result I've obtained the below alignment
As pointed out already, you haven't told Modeller to put the ligand in
the model. Is it possible that you modified the 2rh1.pdb file? Your
template sequence doesn't match the one in 2rh1 from PDB (there's an
extra sequence in the official PDB from residue 1002:A to 1161:A that
isn't in yours). Maybe you removed the ligand by mistake too.