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Hi Andy,<br>
<br>
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<div class="WordSection1"><span style="font-size: 11pt;
font-family: "Calibri","sans-serif";
color: rgb(31, 73, 125);"> I’m looking for a
description of how the “secondary_map_and_map_cc_filter”
parameter operates. The default is set to be a
2mFobs-DFmodel, and I assume it’s calculating a correlation
coefficient as the basis for filtering waters that are present
in the mFobs-DFmodel maps (i.e. primary map) but not in the
2mFo-DFc map. However, I’d like to confirm my assumption is
true and also learn whether the cutoff value for whether or
not a putative water molecule gets culled can be changed. I
haven’t found the information in the online documentation or
the Phenixbb archives. </span></div>
</blockquote>
<br>
yes, the second map, 2mFo-DFc is used to computed map CC
(poor_cc_threshold<span style="color: blue;"></span>). Also, it is
used to filter waters by the absolute value of the 2mFo-DFc map
computed at water oxygen center (poor_map_value_threshold).<br>
<br>
The default values are good for most of cases (I hope).<br>
<br>
Pavel.<br>
<br>
<br>
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