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Hi Jordan,<br>
<br>
Phenix implementation of Fo-Fo map calculation requires the data
sets are isomorphous within some tolerance (which isn't large, I
don't think 6A will be tolerated!). Yes, there is quite involved and
careful scaling happening as part of this procedure, which is
important.<br>
<br>
If you are subtracting real-space maps then you are on your own to
do scaling. I'm guessing in real space scaling can be done more
efficiently by doing it locally.<br>
<br>
I'm curious to know how your or Tim's suggestions worked out in the
end. <br>
<br>
Good luck!<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 3/9/19 01:21, Jordan Luke Pederick
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:ME1PR01MB1059A4208E92C6E8958E92F9AA4E0@ME1PR01MB1059.ausprd01.prod.outlook.com">
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<p style="margin-top:0; margin-bottom:0">Hi,</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">I am trying to generate
a Fo-Fo difference map for two data sets of the same
protein�at ~2.3 angstrom resolution. One dataset is native and
the other�was soaked with a metal ion, so the purpose of the
map is for identifying and visualizing peaks that may
correspond to a bound metal ion.�</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">These datasets differ
by 6�angstroms (~10%) along the A edge -�an isomorphous
difference map generated in Phenix GUI wasn't useful</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">As an alternative I was
planning to make a real-space Fo-Fo difference map making use
of�Superpose Maps in Phenix Gui as follows:</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">Superpose maps would be
used to superimpose (Fobs.metal, PHI.metal) and (Fobs.native,
PHI.native)</p>
<p style="margin-top:0; margin-bottom:0">The superimposed maps
will be opened in Coot and a difference map generated using
"Extensions -> Maps ->� Make a difference map"</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">There were two things I
was unsure about:</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">Does this seem like a
reasonable alternative?�</p>
<p style="margin-top:0; margin-bottom:0">Is scaling of the two
datasets required before generating the difference map?</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">Cheers,�</p>
<p style="margin-top:0; margin-bottom:0">Jordan</p>
<br>
</div>
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