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<p class="MsoNormal"><span lang="FR">Dear Vatsal,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR"><o:p> </o:p></span></p>
<p class="MsoNormal">You can find some useful comments here :<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:12.0pt">"</span><span style="font-size:12.0pt">Metrics for comparison of crystallographic maps".
</span><i><span style="font-size:12.0pt">Acta Cryst., </span></i><span style="font-size:12.0pt">D<b>70</b></span><i><span style="font-size:12.0pt">,</span></i><i>
</i><span style="font-size:12.0pt">2593-2606 (2014)<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">With best regards,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Sacha Urzhumtsev<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b>From:</b> phenixbb-bounces@phenix-online.org <phenixbb-bounces@phenix-online.org>
<b>On Behalf Of </b>Vatsal Purohit<br>
<b>Sent:</b> Wednesday, March 30, 2022 4:01 PM<br>
<b>To:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> [phenixbb] Question about RMSD vs e/A^3<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-IN">Hi all,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-IN"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-IN">I had a question about comparing structures based on RMSD comparisons vs e<sup>-</sup>/A^3. While the former seems to be more frequently used in structural studies with a standard value of 1.0 rmsd for 2Fo-Fc and 3.0
rmsd for Fo-Fc, there are differences in RMSD based on resolution. Hence, I wanted to ask if e<sup>-</sup>/A^3 could be a more appropriate comparison for looking at differences in electron density in a ligand-binding site between 2 structures of the same enzyme?
So, here you would try and set e<sup>-</sup>/A^3 of all the maps (2Fo-Fc and Fo-Fc) to the same value.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-IN"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-IN">The structures I’m referring to are between 2-2.5 angstroms in resolution.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-IN"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-IN">I have also worked with the map sigma level comparison tool on PHENIX and wanted to know if that might be an alternate way to compare maps in 2 structures accordingly.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-IN"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-IN">Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-IN">Vatsal<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-IN"><o:p> </o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt;background:white"><span lang="EN-IN" style="font-size:10.0pt;color:black">Post-doctoral fellow, Davis Lab, Emory University</span><span lang="EN-IN" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222"><o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt;background:white"><span lang="EN-IN" style="color:black"><a href="mailto:vatsal.purohit@emory.edu" target="_blank"><span style="font-size:10.0pt">vatsal.purohit@emory.edu </span></a></span><span lang="EN-IN" style="font-size:10.0pt;color:black">|
346-719-9409</span><span lang="EN-IN" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-IN"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-IN"><o:p> </o:p></span></p>
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