Hi Joel,
    
    
      What is the command to report the average ADP for protein main
      chain and side chains (Similar to the CNS model_stats function)?
      Is there also an easy command to report average ADP of protein,
      solvent and ligands separately? 
    
    phenix.model_vs_data model.pdb data.mtz
    
    More information:
    
    J. Appl. Cryst. (2010). 43, 669-676 
    phenix.model_vs_data: a high-level tool for the calculation of
    crystallographic model and data statistics
    P. V. Afonine, R. W. Grosse-Kunstleve, V. B. Chen, J. J. Headd, N.
    W. Moriarty, J. S. Richardson, D. C. Richardson, A. Urzhumtsev, P.
    H. Zwart and P. D. Adams
    
    You probably need to use a recent version of PHENIX.
    
    Pavel.