Hi,
 
Quick question.  I am trying to refine occupancy of a ligand and was attempting to do this using the method outlined under the CCI Apps documentation for phenix.refine. 
 

  • Refinement of one occupancy factor per selected group of atoms (group occupancy refinement):

    % phenix.refine data.hkl model.pdb strategy=group_occupancies \
  refine.occupancies.group="chain A and resid 1"
    • Yet, when I type the commands, I keep getting an error saying that something is wrong with my commands: strategy, group, etc.  I have not (at least I don't recall) loading the updated CCI Apps and only have what was installed with Phenix 1.24b installation. 
     
    Am I doing something wrong here or do I need to update the CCI Apps?
     
    Thanks in advance for all feedback!
     
     
     
    Cheers,
    Nick
     
     
     
     
     
    ________________________________________
     
    Nicholas Noinaj
    University of Kentucky School of Medicine
    Department of Molecular and Cellular Biochemistry
    Biomedical Biological Sciences Research Building, Rm 236
    741 S. Limestone
    Lexington, Ky 40536
    Lab:  859-323-8183
    Home:  859-228-0978
    [email protected]
    www.noinaj.com