Re: [modeller_usage] Modelling a tetramer from Pentameric NMR structure

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 7/18/17 5:03 AM, Saravanan Parameswaran wrote:
> Is it possible to model the tetramer from  Pentameric NMR structure?

It depends what you mean. If you mean you want to build a model with 
four chains that correspond to four of the five chains in your template, 
then you don't have to do anything special - just add chain breaks to 
your alignment file, as per
https://salilab.org/modeller/9.18/manual/node30.html

If, however, you want to model an entirely different state (for example, 
the pentameric structure has C5 symmetry and you want to build a model 
that has C4 symmetry) then Modeller won't magically do that, since by 
design the monomer-monomer interactions present in your template will 
end up in your model - you would instead need more information on the 
symmetry of the tetramer (e.g. a 3D EM map) and then use a monomer 
assembly tool, for example MultiFit in cyclic symmetry mode:
https://salilab.org/multifit/

	Ben Webb, Modeller Caretaker
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