On 10/22/12 7:26 AM, Mehdi Talebzadeh Farooji wrote: > I have a template complex (A1:B1); I would like to create a model of > A2:B1 complex, A1 and A2 are similar about 50% and the structure of > the A2 is known. I want to use the known structure (not the template > structure of A1 subunit from complex) for modelling and refinement. I > was wondering if it I could do it with modeller and how?

Sure, this should be straightforward. Just align A2:B1 with A1:B1 and proceed as per usual - it would be very similar to the example at http://salilab.org/modeller/9.11/manual/node28.html

Of course, the alignment for the second subunit will be 100% identical, so the model for B1 will strongly resemble the template. If you want it to be *exactly* the same as the template, just ask Modeller to only model the A subunit: http://salilab.org/modeller/9.11/manual/node23.html

Ben Webb, Modeller Caretaker