I've been using the iterative local rebuilding approach based on this tutorial:
In a recent publication titled "Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta", the following was mentioned:
While previously we have developed an iterative local rebuilding tool that is capable of refining homology models into near-atomic-resolution cryo-EM maps (DiMaio et al., 2015), several advances were required to extend this tool so that it can successfully refine hand-built models. Our new approach includes a method for automatically detecting and correcting problematic residues in hand-built models without overfitting, a model-selection method for identifying models with good agreement to the density data and with physically realistic geometry, a voxel-size refinement method for correcting errors in calibrating the magnification scaling factor of a microscope, an improved sidechain-optimization method to correct sidechain placement errors in very large systems, and a way to estimate uncertainty in a refined model.
I wonder though how I can use the new method, because I couldn't find the XML scripts for the described protocol in the supplementary as quoted below. Also every .gz archive in the supplementary contain only 1 file with no extension, I'm not sure how to use that! Lastly, the link to the pdf below seems to be down.
All methods described are available as part of Rosetta Software Suite, using weekly releases after week 35, 2016. The Rosetta XML files and flags for running all the refinements discussed in this manuscript are included as Supplementary files 1–3. The scripts and the tutorial used for running the method described here is available at the website of the corresponding author (https://faculty.washington.edu/dimaio/files/density_tutorial_sept15_2.pdf).
I would appreciate your input.