<div dir="ltr">Thanks--that certainly makes sense. In that case, I suppose I have a different question: what distinguishes the .mtz file suffixed "map_coeffs," which is output by phenix.maps, from the input .mtz?</div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, May 25, 2016 at 1:28 PM, Christian Roth <span dir="ltr"><<a href="mailto:christianroth034@gmail.com" target="_blank">christianroth034@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<p><font face="Arial">You might look for the Real space correlation
coefficient to see if your model fit that particular map better
than before, but thats probably it.</font></p>
<p><font face="Arial">There is no subset experimental data just influenced
by one chain. The whole complex contributes to each measurement
and vice versa your chain A model contribute to each measurement
you made to generate the maps. Sorry, but that's it<br>
</font></p>
<p><font face="Arial">Christian<br>
</font></p><div><div class="h5">
<div>Am 25.05.2016 um 17:31 schrieb Andy
Watkins:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
<div dir="ltr">
<div>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.</div>
<div><br>
</div>
Suppose I have a model of one chain of a complex and an .mtz
describing the entire complex. I have performed some refinement
procedure altering the model of that single chain.
<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><br>
</div>
<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. (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><br>
</div>
<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><br>
</div>
<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.</div>
</div>
<br>
<fieldset></fieldset>
<br>
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