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<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);"><o:p></o:p> So the default value for the
poor_map_value_threshold is 1, which I assume is 1 sigma.
So if the electron density for a putative water is less than
1 sigma in the 2mFo-DFc map OR if the calculated correlation
coefficient is less than the poor_cc_threshold value
(default 0.7), then the water is removed, right?</span></p>
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<br>
yes.<br>
<br>
<br>
<blockquote
cite="mid:39AF62D77705A347AEAE4226BC2DFF43147AB5B4CA@MBXC.exchange.cornell.edu"
type="cite">
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<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);"> For my own education, what would
be the best way of calculating the correlation coefficient
values for all the waters or ligands in a given model? What
I want to do is get a sense for the relationship between
electron density and correlation coefficient values for
waters in my structure to understand how “strict” the
default poor_cc_threshold value is and whether/how much I
might want to raise it.</span><br>
</p>
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</blockquote>
<br>
You can use <br>
<br>
phenix.model_vs_data model.pdb data.mtz --comprehensive<br>
<br>
and that will list map CC for all atoms or per residue,<br>
<br>
OR<br>
<br>
use <br>
<br>
phenix.real_space_correlation <br>
<br>
if you need more fine-tuning.<br>
<br>
I have to run now - otherwise I miss my flight to London -:)<br>
<br>
All the best!<br>
Pavel.<br>
<br>
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