Hi Yarrow,
I am going to deposit a structurein the pdb but noticed that all of the mtz files from phenix.refine only contain coeficients and not reflection info.
this is expected. I'm not sure why you need a separate tool to create a data file for PDB deposition if you already have that file... The reflection data file that contains your Fobs (or Iobs), as well as free-R flags (and may be HL coefficients, if available) and that you used to run the refinement is what you should deposit to PDB.
Is it as simple as running another refinement with write_maps = true instead of false?
"write_maps = true " will output CNS/X-plor formatted electron density maps.
Will this right out an mtz with structure factors instead of just coeficients.
No.
Ideally, I would like to create an mtz with structure factors as well as a map for CNS.
Regarding an MTZ with structure factors -- see above. For the maps in X-plor/CNS format use "write_maps=true" keyword or whatever is equivalent in the GUI. Let me know if you have questions or need help with this. Pavel.