I am starting to learn Rosetta right now and have to relax a structure before I learn more because of a deadline.
After I run the Rosetta Relax successfully when I load the result in Chimera, the pdb seems to be off from the density by a little bit. But when I fit it in, it looks better.
Is this normal? Or am I doing something wrong?
(My structure has multiple repeats of the same unit and I am only fitting one of them)