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<p style="margin-top:0;margin-bottom:0">Also, I am interested if anyone knows of any publications that have included a real-space difference map?</p>
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<p style="margin-top:0;margin-bottom:0">Cheers,</p>
<p style="margin-top:0;margin-bottom:0">Jordan</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Jordan Luke Pederick<br>
<b>Sent:</b> Monday, 11 March 2019 1:25:57 PM<br>
<b>To:</b> Eric Montemayor; Pavel Afonine; Philip Kiser; Tim Gruene; phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] Fo-Fo difference map for non-isomorphous datasets</font>
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<p style="margin-top:0; margin-bottom:0">Thank you all for the prompt responses and suggestions.</p>
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<p style="margin-top:0; margin-bottom:0"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">My metal ion of interest is Cesium in
this case, so I guess I am more interested in using this approach for visualization rather than peak identification - the strong density of Cs is fairly obvious</span><br>
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<p style="margin-top:0; margin-bottom:0">I have attached a few images of the superimposed (Fo, Phi) maps and resulting difference map using either Superpose maps in phenix or transform_map in coot following Tim's suggestions.</p>
<p style="margin-top:0; margin-bottom:0">I also tried using maprot (CCP4) to apply the rotation/translation operator from the LSQ superpose but the resulting map was not superposed correctly (not sure why).</p>
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<p style="margin-top:0; margin-bottom:0">Both results seem kind of reasonable - I have shown one of the difference peaks for what is likely to be a bound Cs. For both approaches the peak was very obvious at a 3 sigma level, and could still be observed to around
10 sigma in both cases. I am still unsure about differences in scaling, so although strong positive peaks can be identified, I wouldn't be confident using the map to interpret smaller differences.</p>
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<p style="margin-top:0; margin-bottom:0">In response to Eric - I checked the anomalous signal, which was fairly weak. The resulting anomalous difference map did show positive peaks up to a level of ~10 sigma that matched those observed in the above real-space difference
maps, with a 3 sigma level corresponding to 0.0137 e/A^3. The CCanom was also low (1-5% between shells), so I was thinking that another approach might be more suitable for this data?</p>
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<p style="margin-top:0; margin-bottom:0">Cheers,</p>
<p style="margin-top:0; margin-bottom:0">Jordan</p>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Eric Montemayor <montemayor.eric@gmail.com><br>
<b>Sent:</b> Sunday, 10 March 2019 4:50:21 AM<br>
<b>To:</b> Jordan Luke Pederick<br>
<b>Subject:</b> Re: [phenixbb] Fo-Fo difference map for non-isomorphous datasets</font>
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<div dir="auto">Why not just look for peaks in the anomalous difference Fourier for just the derivative dataset? If there�s even a weak anomalous signal, you won�t need to mess with non-isomorphism between multiple datasets.... the information you need is
already contained alone in the derivative dataset.</div>
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<div dir="auto">What is the metal? The above approach won�t work for something like magnesium, but should work for almost any transition metal.</div>
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<div dir="auto">Eric</div>
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<div dir="ltr" class="x_x_gmail_attr">On Sat, Mar 9, 2019 at 3:23 AM Jordan Luke Pederick <<a href="mailto:jordan.pederick@adelaide.edu.au">jordan.pederick@adelaide.edu.au</a>> wrote:<br>
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<p style="margin-top:0; margin-bottom:0">Hi,</p>
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<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>
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<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>
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<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>
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<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>
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<p style="margin-top:0; margin-bottom:0">There were two things I was unsure about:</p>
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<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>
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<p style="margin-top:0; margin-bottom:0">Cheers, </p>
<p style="margin-top:0; margin-bottom:0">Jordan</p>
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