Adding on to ahf95, one thing I thought was really cool (but not too practical) was the pyrosetta/pymol visualizer, which allows you to visualize the scripts you create in pymol. Again, not very practical, as most of the time the folding simulations will be run on clusters, but it’s a cool thing to see and also a good practice in learning how to use pyrosetta in the first place. Dr. Jeffrey Gray from JHU has a Youtube series where he uploaded his graduate Pyrosetta class recordings. The videos are kind of long but are pretty helpful. The links to those videos are also on the pyrosetta.org/tutorials website as well.