I am trying to work through the protein-protein docking driven by cryo-EM tutorial published in Methods of Molecular Biology (EMD1884 & PDB 2YKR) to dock subunits F & R with restraints from a masked map around the two subunits. In the first part (docking subunit F into the map using PowerFit) I get results from the submitted job and produced images of solutions. Although the images show fitting inside the map subvolume; when I check the downloaded results I see the docked solution outside the used map. Not sure what am I missing?
Your comment is appreciated!