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