Dear modeller users,
I have the following problem:
I have to model a homo-dimer. There is no template of dimer (there are several templates that cover just some parts of the monomer and thus I do use multiple templates to get a descent model of the monomer). I have an alignment file that looks something like this:
>P1;proteintomodel A—AABB-BC—CC / A—AABB-BC—CC*
>P1;template1_1 ———BB-BC-CC / ————————*
>P1;template1_2 ———————— / ———BB-BC-CC*
>P1;template2_1 A-AABB———— / ————————*
>P1;template2_2 ———————— / A-AABB————*
On the positive side I have a list of constraints, so I want to rely on the constraints when I model the dimer interface.
The problems is that since the templates for each of the monomers have the same coordinates (modelling each of the monomers of my dimer) i do obtain a model of my dimer with the 2 monomer chains basically inter-twisted (so there is no any kind of interface in between the chains because the chains are nested one in another). Also i can’t understand why, but one of the chains has secondary structure while the other doesn’t. I hoped the constraints file will push and orient the chains in the right possible way but it doesn’t seem the case.
Please suggest me any ideas to overcome this problem. Thanks in advance. Expecting reply from you guys.
On 1/21/16 4:36 AM, Anouk wrote: > The problems is that since the templates for each of the monomers have > the same coordinates (modelling each of the monomers of my dimer) i do > obtain a model of my dimer with the 2 monomer chains basically > inter-twisted (so there is no any kind of interface in between the > chains because the chains are nested one in another).
Modeller only uses internal coordinates for the restraints, so is independent of the relative orientations of your templates, but your initial model (.ini file) is probably bad to start with. One solution would be to manually translate one monomer in the .ini file so they don't overlap, and then provide that as your starting model.
> Also i can’t understand why, but one of the chains has secondary > structure while the other doesn’t.
This sounds like a problem with your alignment (most likely the "bad" chain isn't aligned with any template), but I'd need to see the real alignment file to be sure.
Ben Webb, Modeller Caretaker
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Anouk -
Modeller Caretaker