Re: [modeller_usage] Treading onto known PDB template

To: Modeller Caretaker <>

Subject: Re: [modeller_usage] Treading onto known PDB template

From: Geoffrey Woollard <>

Date: Mon, 6 Jul 2020 19:00:12 -0400

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Cc:

Thanks! As a proof of concept, I modelled the full length sequence onto the structure (ie I filled in the missing densities from loops etc).

I did this proof of concept with one protomer. However the channel is a homotetramer with C4 symmetry.

The structure of the tetramer is known (ie chains ABCD, with C4 symmetry). However, I can't just duplicate the protomer and align it with the each chain in the tetramer because some of the new modelled density clashes with where the tetramer contacts are. This included the ion pore, which interests me, and which I want to get right.

Can I do the modelling in the context of the tetramer? Otherwise I would have to just do it with the protomer, and then delete out parts that were clashing.

Are there options for applying symmetry during modelling? Or at least telling modeller that other density is present and to avoid clashing (in this case the new density of one protomer might clash with the missing density of the rest of the tetramer).

On Wed, Jun 10, 2020 at 1:34 PM Modeller Caretaker <">> wrote:

On 6/10/20 5:45 AM, Geoffrey Woollard via modeller_usage wrote:
> I'm studying a transmembrane ion channel (protein 1). There are
> structures of protein 1 in a closed conformation, and I am interested in
> the open conformation. There is a very similar protein in an open
> conformation (protein 2). So I am trying to thread the sequence of
> protein 1 onto the atomic model of protein 2. I know the template.

This should be very straightforward to do with Modeller. See the simple
example at https://salilab.org/modeller/9.24/manual/node16.html

Ben Webb, Modeller Caretaker
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