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.

Ben Webb, Modeller Caretaker