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<p>Hi Andy,</p>
<blockquote
cite="mid:CAKqmowuVHvs+xpj=xqwQWJT90J5b2d2Kc3rqjATxfVaEd3M6-Q@mail.gmail.com"
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<div>Suppose I have a model of one chain of a complex and an
.mtz describing the entire complex. </div>
</div>
</blockquote>
<br>
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"?<br>
<br>
<blockquote
cite="mid:CAKqmowuVHvs+xpj=xqwQWJT90J5b2d2Kc3rqjATxfVaEd3M6-Q@mail.gmail.com"
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<div>I have performed some refinement procedure altering the
model of that single chain.</div>
<div><br>
</div>
<div>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.</div>
</div>
</blockquote>
<br>
Okay. This is what refinement is for. <br>
<br>
<blockquote
cite="mid:CAKqmowuVHvs+xpj=xqwQWJT90J5b2d2Kc3rqjATxfVaEd3M6-Q@mail.gmail.com"
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<div>For obvious reasons,</div>
<div><br>
</div>
<div>phenix.model_vs_data chain_A.pdb whole_complex.mtz</div>
<div>
<div>phenix.model_vs_data chain_A_refined.pdb
whole_complex.mtz</div>
</div>
<div><br>
</div>
<div>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 <i>works</i>,
it reports an unrepresentative fit. </div>
</div>
</blockquote>
<br>
Could you please define "unrepresentative fit" in this context?<br>
<br>
<blockquote
cite="mid:CAKqmowuVHvs+xpj=xqwQWJT90J5b2d2Kc3rqjATxfVaEd3M6-Q@mail.gmail.com"
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<div>(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.</div>
</div>
</blockquote>
<br>
I guess Fobs would not like this as they include contributions from
all atoms, as far as I remember from the theory..<br>
<br>
<blockquote
cite="mid:CAKqmowuVHvs+xpj=xqwQWJT90J5b2d2Kc3rqjATxfVaEd3M6-Q@mail.gmail.com"
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<div>Now, during the refinement procedure, we of course generate
.ccp4 density maps for the individual chain models:</div>
<div><br>
</div>
<div>phenix.maps chain_A.pdb whole_complex.mtz</div>
</div>
</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:CAKqmowuVHvs+xpj=xqwQWJT90J5b2d2Kc3rqjATxfVaEd3M6-Q@mail.gmail.com"
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<div>which produces the ccp4 file as well as, crucially,
chain_A_map_coeffs.mtz. Attempting to employ that resulting
.mtz file, i.e.</div>
<div><br>
</div>
<div>
<div>phenix.model_vs_data chain_A.pdb whole_complex.mtz</div>
<div>phenix.model_vs_data chain_A_refined.pdb
whole_complex.mtz</div>
</div>
<div><br>
</div>
<div>leads to an evocative
error:�Sorry_No_array_of_the_required_type: No reflection
arrays available.</div>
<div><br>
</div>
<div>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!</div>
<div><br>
</div>
<div>Thanks in advance for whatever help you can provide;
unfortunately, I can't provide any input files.<br>
</div>
</div>
</blockquote>
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.<br>
<br>
Cheers,<br>
Pavel<br>
<br>
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