Hi Nat, to compute map CC one needs to define two maps. The source of maps can be PDB files, actual maps (for example, in Xplor or CCP4 or other format), Fourier map coefficients (that need to be FTed to get actual maps), or any combination of the above. To compute maps (as opposed to reading them in from input file), the options for input information are: file(s) with map coefficients or model. In latter case you also need to know which scattering dictionary to use: x-ray or neutron or custom user-defined. Also one needs to define which grid points to use: atom level, residue level or any user-defined (the latter is missing in phenix.real_space_correlation and can be trivially added). phenix.real_space_correlation automatically decides whether to use atom or residue level, depending on resolution (obviously, there is no much sense to compute cc per atom at say 4A resolution, while at 1A resolution cc per atom is justified and more informative than cc computed in any larger scale). Also one needs to handle special cases properly. One of many is (of course) hydrogen atoms, which you need to treat differently given the resolution and data type (x-ray or neutron). Since we already have at least three phenix.*** tools to do more or less the same job (plus phenix.model_vs_data can output it too), adding another awesome one wouldn't probably be that awesome unless you somehow make clear what of the above it can and cannot do (or make it *really awesome* so it figures it all out automatically!). Pavel