Hi Nick, thanks for your question!
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.
Yes, with the latest CCI Apps you can do group or/and individual occupancy refinement. Please note, that older versions of PHENIX or CCI Apps may not support occupancy refinement. So, make sure you are using the latest CCI Apps!
% phenix.refine data.hkl model.pdb strategy=group_occupancies \ refine.occupancies.group="chain A and resid 1"
Make sure you don't type "\" in your example above -:)
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.
Please check if you are using the documentation for the right version of PHENIX or CCI Apps. If you are using phenix.refine from the latest CCI Apps, then you should look at the Documentation at: http://www.phenix-online.org/download/cci_apps/ However, if you are using phenix.refine from the complete PHENIX installation, then you should look at structure refinement documentation supplied with that installation. Please look at "Quick Facts" to understand the difference between phenix.refine in PHENIX and in CCI Apps. If none above helped, please send me the phenix.refine log file or error message so I can do some diagnostics. Thanks! Pavel.