Hi Andy,

Suppose I have a model of one chain of a complex and an .mtz describing the entire complex.

I'm struggling making sense of this statement.. MTZ file is just a file format to records some data with labels associated with it in a binary form to make it easier for machines to handle it. So what precisely you mean by ".mtz describing the entire complex"?

I have performed some refinement procedure altering the model of that single chain.

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.

Okay. This is what refinement is for.

For obvious reasons,

phenix.model_vs_data chain_A.pdb whole_complex.mtz
phenix.model_vs_data chain_A_refined.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.

Could you please define "unrepresentative fit" in this context?

(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.

I guess Fobs would not like this as they include contributions from all atoms, as far as I remember from the theory..

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

Well, this is what it seems *you* do as part of *your* protocol, but this is *not* what typical work-flow includes as phenix.refine always reports maps upon completion of refinement; so running phenix.maps seems to be an unnecessary step in this scenario.

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

phenix.model_vs_data chain_A.pdb whole_complex.mtz
phenix.model_vs_data chain_A_refined.pdb whole_complex.mtz

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.
Hm.. I afraid I'm lost now: model vs data tool is not supposed to accept inputs other than original data, Iobs or Fobs, and model files.

Cheers,
Pavel