Lillian chong wrote: > I have two questions about using Modeller to build a chimera protein > based on two known structures (as in #1 of the FAQ): > 1. How does Modeller determine the initial relative orientations of the > two structures?

The initial structure is the target sequence threaded onto the template(s) backbone, so the initial relative orientation will be essentially that of your input PDB files.

> 2. Is there a way to extensively sample the relative orientations of > the two structures? Perhaps through randomization of dihedral angles, > loop modeling, or some other approach?

Since you have no domain-domain restraints, Modeller will not be able to do a good job of optimizing the structure. So you should impose some sort of orientation restraint (maybe an angle between the mass centers of the two domains and a central point). Then you could perhaps vary that angle and build models to sample the orientation, but there are many ways to do this.

Ben Webb, Modeller Caretaker