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<p>Two more nuances about map comparison and scaling:</p>
<p>- one you will find here:</p>
<p><a class="moz-txt-link-freetext" href="https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2012_07.pdf#page=16">https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2012_07.pdf#page=16</a></p>
<p>- and another one is.. 'sigma' (rmsd) scaled maps appear to be of
the two kinds where in one case rmsd is calculate using the whole
unit cell volume and in the other case using only macro-molecular
region. The latter is clearly better making it solvent content
independent. Which one of the two modern programs use isn't well
documented.</p>
<p>Pavel<br>
</p>
<div class="moz-cite-prefix">On 3/30/22 07:30, Alexandre OURJOUMTSEV
wrote:<br>
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cite="mid:b499be8914cd4e009810defa72ebaac1@igbmc.fr">
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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>
<div>
<div style="border:none;border-top:solid #E1E1E1
1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b>From:</b>
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>
<a class="moz-txt-link-rfc2396E" href="mailto:phenixbb-bounces@phenix-online.org"><phenixbb-bounces@phenix-online.org></a>
<b>On Behalf Of </b>Vatsal Purohit<br>
<b>Sent:</b> Wednesday, March 30, 2022 4:01 PM<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> [phenixbb] Question about RMSD vs e/A^3<o:p></o:p></p>
</div>
</div>
<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
style="font-size:10.0pt;color:black" lang="EN-IN">Post-doctoral
fellow, Davis Lab, Emory University</span><span
style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222"
lang="EN-IN"><o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt;background:white"><span
style="color:black" lang="EN-IN"><a
href="mailto:vatsal.purohit@emory.edu" target="_blank"
moz-do-not-send="true"><span style="font-size:10.0pt">vatsal.purohit@emory.edu </span></a></span><span
style="font-size:10.0pt;color:black" lang="EN-IN">|
346-719-9409</span><span
style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222"
lang="EN-IN"><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>
</div>
<br>
<fieldset class="moz-mime-attachment-header"></fieldset>
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