[phenixbb] Appropriate model_vs_data usage over part of a structure
Pavel Afonine
pafonine at lbl.gov
Wed May 25 17:16:51 PDT 2016
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
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