Lucas Bleicher wrote: > I want to model a heterotrimer consisting of proteins A, B and C, > where the structure of the A:B complex is already known, and C should > be modelled. There is a known structure of another structure made of > proteins D, E and F, where D and E are homologous to A:B (and can be > easily spatially superposed) and F is homologous to C. > > Do I have to work with restraints or is there a way to set a PIR file > using the A:B and D:E:F complexes as "knowns" so that Modeller can > assume that it must build an A:B:C complex so that A:B would be in > the equivalent positions to D:E (but should of course be nearly > identical to the A:B x-ray structure more than the D:E structure, > since A:B is the real thing) and C must be modelled using F as > template and be in the position it would occupy in the D:E:F > structure?
I can't think of an easy way to do this with a Modeller alignment. Probably the easiest thing to do is to make a structural superposition of your A:B and D:E:F templates, then make a new PDB file (e.g. by simple cut and paste) containing A:B:F in their superposed orientations. Then you can simply use this A:B:F pseudo-template to build your model.
Ben Webb, Modeller Caretaker