Contents

• Introduction
• Required software
  • ModelMaker
  • Rosetta
  • MODELLER
  
  
• Folding protein termini using ModelMaker
  • Structure prediction
  • Interactive fitting to a cryo-EM density with iMDFF and QwikMD
  
  
• Modeling amino acid insertions
  • Structure prediction with Rosetta
  • Interactive fitting to a cryo-EM density with iMDFF
  
  
• Model fit to mid-resolution EM density
  • MDFF run
  • Cross correlation coloring
  • Mid-resolution refinement
  • Structure check
  
  
• Homology model
  • Building a homology model with MODELLER
  • Rigid body docking to the Rpn11 human density
  • Interactive MDFF run to the human Rpn11 density
  
  
• High-resolution real-space refinement