Re: [modeller_usage] Getting a ligand to work in homology models
To: Casey Becker <>,
Subject: Re: [modeller_usage] Getting a ligand to work in homology models
From: Modeller Caretaker <>
Date: Mon, 4 Jan 2021 15:04:52 -0800
On 1/3/21 5:07 PM, Casey Becker via modeller_usage wrote:
I'm currently trying to model a hemoglobin monomer that has a heme group
as a ligand. If I run Modeller through the chimera interface, the ligand
carries over to the models. However, if I run through IDLE, which I
prefer to do because I'm using parallel jobs, the ligand does not carry
over. Any help appreciated.
The only explanation I can think of is that you're using a different
alignment file in the two cases (which you didn't post here). Ligands
are specified there, not in your Python script (you just need to tell
Modeller in your Python script to read HETATM residues from your
template by setting env.io.hetatm=True, which you are doing).