Re: [modeller_usage] Problem in oligomer modelling
To: Soong Jiaxin <>,
Subject: Re: [modeller_usage] Problem in oligomer modelling
From: Modeller Caretaker <>
Date: Tue, 29 Sep 2015 13:45:39 -0700
On 09/28/2015 07:05 PM, Soong Jiaxin wrote:
I'm modelling a dodecamer. Somehow, there seems to be a problem for some
of the monomers to connect to the other monomers. The oligomer template
I used has interdimeric contacts. However, the way my model connects
among the monomers is different from the template I used. The tail for
the monomer in concern goes in and out of the beta strands of the
neighbour monomer instead of connecting by touching the C-terminal
region interface of the next monomer. Is there a way to fix this or is
this normal for a protein model?
This sounds like a problem with your alignment to me - probably a shift
in one or more of your templates. Try writing out the alignment in PAP
format (or viewing it in something like Chimera) so you can see more
clearly which residues are aligned.
I have attached a copy of my modelling script as well.
This looks fine to me (assuming that your subunits are supposed to be
symmetric, of course). You could certainly try it without the symmetry
restraint to see if that helps.