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Re: [modeller_usage] Introducing HETATM ligands into models based on multiple templates

On 07/20/2009 05:25 PM, Violetta Kivovich wrote:
I am trying to create a model of a protein using 3 different templates.
The first template covers about 1/3 of the protein, the second covers
the central part of the model protein and the third overlaps with the
second with an additional extension to cover the c-terminus of the
protein. The templates' crystal structures have incorporated metal ions
and other ligands, which i would like to transfer into the model.
Unfortunately i cannot seem to make this work using the script for
introducing HETATM ligands into the model. I have created the alignment
file and added '.' into both the template and into the sequence
alignment. The PDB has the HETATM ligands at the end of the sequence, so
i have added them at the end of the alignment file, as suggested in the
manual. However, since three different templates are being used, only
parts of which overlap, introducing '.' at the end of the model sequence
does not work, because it does not align with the template. On the other
hand adding '.' into the model sequence, the way it would align with the
template, disturbs the structure, disrupting the alignment with the
other templates and causing a break in the peptide. I tried adding gaps
for each ligand in the other templates, but this does not help. I have
tried creating part of the model with just one template and the aligning
sequence from my protein of interest. In that situation the ligands are
easily added. Is there any remedy to my problem in modeller that i have
not considered?

If I understand you correctly you have an alignment that looks like

template1   AAAAAAAAA..----------
template2   -----------BBBBBBBBBB
model       aaaaaaaaa..bbbbbbbbbb

This won't work because Modeller assumes that an amino acid chain corresponds to the primary sequence in the alignment, and ligands break the chain. So you'll end up with a chain break at the end of 'aaa'.

A fix for the alignment above would be something like

template1   AAAAAAAAA----------..
template2   ---------BBBBBBBBBB--
model       aaaaaaaaabbbbbbbbbb..

Modeller does not care where gaps are placed in your template sequences, as long as the residues come in the same order as in the PDB file, so this is essentially the same alignment.

If your ligands are placed very awkwardly in the PDB file, you could certainly edit the PDB file in a text editor to reorder them or remove ligands you don't want, rather than editing your alignment.

You also imply that all of your templates contain ligands. In most cases it only makes sense for each ligand in the model to be aligned with precisely one template ligand, since Modeller will just copy the coordinates from the template. Modeller will allow you to align a model ligand with ligands in multiple templates, but what you'll end up with is a ligand containing uniquely-named atoms from all of the templates, which is usually not what you want.

here is the script i am using for introducing HETATM ligands into the model

Your script looks fine to me. As you have probably already seen, the only change needed to include ligands is to turn on env.io.hetatm, which you have done already in your script. All of the hard work is done by the alignment.

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage