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? 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?
Any insight that you have to share would be much appreciated.
Best regards, Lillian