Subject: Re: [modeller_usage] modeling an oligomer
From: Modeller Caretaker <>
Date: Thu, 07 Aug 2008 12:14:33 -0700
Cc:
Douglas Kojetin wrote:
I would like to create an oligomeric (hexamer) model. I have a Ca-
only hexameric model (chains A-F) to use for the template and an
experimentally determined monomer structure I would like to use for
the target.
If you have a multimer template, and want to build a multimer model,
that's straightforward. Just use the regular modeling scripts, and add
chain breaks (/) in your alignment file accordingly. See
http://www.salilab.org/modeller/9v4/manual/node28.html for an example.
Your alignment would look like
If you also want to use your monomer structure, just align it with one
of the chains of the other template and build a model using both
templates. In principle you could use 6 copies of your monomer
structure, each aligned with a different chain, e.g.
You could also build a monomer model (aligned to just one chain of your
template - just change the sequence for the model, leaving the templates
unchanged, and replace all but one chain with gaps) but then you have to
figure out how to fit your 6 monomer models together after modeling.
That sort of protein-protein docking is outside the scope of the
Modeller package.
I've attempted to do
this using the "model-myini.py" script as described here:
No, don't do that. That just sets the starting point for the
optimization - not the final structure - and so is only useful in cases
where the optimizer needs a 'helping hand' to build the model (for
example, you may manually correct serious problems, such as knots in the
protein chain, that the optimizer wouldn't be able to fix itself). If
you want to influence the *final* structure, include it as a template.