I'm refining tubulin based on this tutorial here: https://www.rosettacommons.org/demos/latest/public/electron_density_structure_refinement/structure_refinement
I save the nucleotides and separate pdb files, convert them into mol2 and generate params file that I pass to Rosetta.
It seems, however, that Rosetta completely flips the orientation of the nucleotides.
I attached screenshots of both the starting model nucleotides and the refined nucleotides fitted into the density.
On a side note, what article is this atomic refining based on? I want to learn more about how the structures are refined into density.