Re: [modeller_usage] Reg: Ligand HETATM atoms missing in model
To: Samdani A <>,
Subject: Re: [modeller_usage] Reg: Ligand HETATM atoms missing in model
From: Modeller Caretaker <>
Date: Tue, 4 Jan 2022 11:13:33 -0800
On 1/3/22 7:50 AM, Samdani A wrote:
I am trying to model an ion, water and ligand from a template and below
is my alignment file.
...> The modelled structure generated without any error containing ion and
water. But only two atoms were observed in the modelled structure but
the ligand in the template contains 38 atoms. The atoms in ligand were
not retained in the model from the template.
I would need to see your PDB file to be sure, but Modeller copies ligand
atoms from templates based on their names, so if multiple atoms have the
same name, you will only get one atom in the output file. This can
sometimes happen if your input PDB file is not in the correct format,
e.g. you have the atom names in the wrong columns in the file.