Perhaps necessary preface: I am largely learning as I go, and large parts of Phenix (and the details of refinement data file formats) are still black boxes for me.

My aim is to determine how this refinement procedure has affected the fit to the experimental data--or, really, the subset of the experimental data expected to be relevant for my model.

For obvious reasons,

phenix.model_vs_data chain_A.pdb whole_complex.mtz

are undesirable: they evaluate the model of a single chain against the whole complex's data, and there's obviously a lot of unsatisfied electron density. So, while this command works, it reports an unrepresentative fit. (In theory, one solution to my problem would be to re-combine each chain's refined version, then run model_vs_data on the recombined, refined complex. I'm interested nonetheless in how it would work on the chains separately.

Now, during the refinement procedure, we of course generate .ccp4 density maps for the individual chain models:

phenix.maps chain_A.pdb whole_complex.mtz

which produces the ccp4 file as well as, crucially, chain_A_map_coeffs.mtz. Attempting to employ that resulting .mtz file, i.e.

leads to an evocative error: Sorry_No_array_of_the_required_type: No reflection arrays available.

My highest suspicion is that I need to alter maps.params in a particular way so that reflection arrays are also output to model_map_coeffs.mtz. I could also imagine that I need to be using another program entirely!

Thanks in advance for whatever help you can provide; unfortunately, I can't provide any input files.