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<p class="MsoNormal"><span lang="EN-US">Hello,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">my apologies if this is a recurring (and potentially trivial) question that does not directly concern Chimeras functionalities.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I am wondering how to properly set the value of the contour level to visualize a Coulomb potential map.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">When I use the approximation of 1 Da = 1.2
</span><!--[if gte msEquation 12]><m:oMath><i><span lang=EN-US style='font-family:"Cambria Math",serif'><m:r>Å</m:r></span></i></m:oMath><![endif]--><![if !msEquation]><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;position:relative;top:2.5pt;mso-text-raise:-2.5pt;mso-fareast-language:EN-US"><img width="9" height="18" style="width:.0937in;height:.1875in" id="_x0000_i1025" src="cid:image003.png@01D7C06B.AA8F9850"></span><![endif]><span lang="EN-US">³
to adjust the displayed volume in the Volume viewer dialog<em><span style="font-family:"Calibri",sans-serif;font-style:normal"> almost no secondary structure, but a lot of dust is visible.</span></em><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">The same problem occurs when I’d like to visualize, for example, an
</span>α<span lang="EN-US">-helix of a subunit rigid-body fitted to the density. I use the “zone” command to trim the density at a pre-defined 2
<em><span style="font-family:"Calibri",sans-serif;font-style:normal">Å</span></em> around the
</span>α<span lang="EN-US">-helix. <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">But is there any general guideline on how to properly set the contour level? I often find values between 1 </span><span lang="EN-US" style="font-family:GreekC">σ</span><span lang="EN-US"> to 3 </span><span lang="EN-US" style="font-family:GreekC">σ.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I assume this is the standard deviation of the map. If so, can it be measured via the “Volume Mean, SD, RMS” command?
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Kind regards<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Phil<o:p></o:p></span></p>
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