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