It is possible to transfer the heme group from the template to the
target (model) using a "block" residue as suggested by Andras. But as
Christoph pointed out the heme residue type is defined in the Modeller
topology libraries, and the corresponding parameters are present in the
parameter libraries. So (in theory) all you need to know is how to
refer to the HEME residue in the alignment file. This you can figure
out by looking at Modeller's residue type library (restyp.lib) where
you will find the entry:
31 | HEM | h | HEME | heme ligand
this tells you that Modeller uses 'h' as the one-letter code for the
HEME residue. Now all you need to do is add the 'h' residues in the
right places of your template and target sequences in the alignment,
add "SET HETATM_IO = on" to the TOP file, cross you fingers, and re-run
Modeller. If all is fine the heme group will appear in your model.
The difference between this approach and using a block residue is that
the block residue is treated as a rigid object that is just copied from
the template to the model, for example Modeller can not distort the
block residue and the rest of the protein does not "feel" its presence
beyond the protein - block residue distance restraints extracted from
the template. This limitation dissapears when defining the heme group
as a proper residue.
I hope this helps.
Roberto Sanchez, Assistant Professor
Structural Biology Program, Department of Physiology & Biophysics and
Institute for Computational Biomedicine, Mount Sinai School of Medicine
Box 1677, 1425 Madison Avenue, New York, NY 10029
phone +1 (212) 659 8648, fax +1 (212) 849 2456
----- Original Message -----
From: fisera <>
Date: Thursday, February 14, 2002 1:12 am
Subject: Re: Modelling Heme
> please follow instructions from FAQ (Freq. Asked Questions) point 16,
> Modeller manual
> good luck
> Christoph Nimptsch wrote:
> > Dear Modellers,
> > I am trying to model a protein containing a heme group.
> > There is a residue type called heme in top_heav.lib, but I don`t
> know how to
> > utilize it.
> > I am aware of changing my alignment to include HETATMs but I haven`t
> > succeeded yet.
> > Do I have to change the pdb-templates to include the heme
> residue? How can I
> > make it clear that MODELLER 6v1 should use it?
> > Is it possible to receive the model with the heme group in it?
> > Thanks for any suggestions,
> > Christoph Nimptsch