Subject: Re: [modeller_usage] ligand is not generated
From: Modeller Caretaker <>
Date: Wed, 12 May 2021 19:12:24 -0700
On 5/12/21 6:18 PM, MARIANA BRANDI MENDONÇA PINHEIRO wrote:
I am having a problem with ligand generation.
...
The ligand is chain X at 2q3z = /.P.LPF./
The models are created but without chain B/X or any ligand/polypeptide.
In order for the ligand to appear in the model, you must also include
the '.' residue in your target (the 'sequence' entry in the alignment,
P21980 in your case) and align it with the ligand in one of the
templates. See also the example alignment align-ligand.ali at
https://salilab.org/modeller/10.1/manual/node18.html