Re: [modeller_usage] Modeling ligands in the binding site
To: Qinghua Liao <>
Subject: Re: [modeller_usage] Modeling ligands in the binding site
From: Modeller Caretaker <>
Date: Tue, 03 Nov 2009 08:25:24 -0800
Cc: modeller mailing list <>
Qinghua Liao wrote:
my question is what the differences of alignment between that of with
and without ligand! Is it just the value of env.io.hetatm? And how to
set the atoms with restraint? Could somebody share the all python
scripts used during the entire process of Modeling ligands in the
binding site? Any response will be highly appreciated!
You can find a full working example in the examples/automodel/
directory. The Python script is model-ligand.py and the alignment is
align-ligand.ali. The alignment differs in that extra '.' residues are
added for each HETATM residue that should be copied from template to target.
Creating restraints on ligand atoms is done in exactly the same way as
protein atoms. If you can't figure out the numbering, first build a
model without any additional restraints and look at the output PDB file
to see the residue numbers and chain IDs.