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<p>Dear all,</p>
<p> thank you very much for your suggestions! We finally made it
with Eman2. I have just two last questions: 1) The curves are
extremely noisy - probably because of the high resolution and
sharpening. Is it legitimate to remove the very central density
data and to filter the volumes to lower resolution and/or to
smoothen the curves (e.g. Bezier). 2) Is it correct that the final
diameter corresponds to the value where the curve passes zero
density?</p>
<p>Thanks, best, Dieter <br>
</p>
<pre class="moz-signature" cols="72">------------------------------------------------------------------------
Dieter Blaas,
Max Perutz Laboratories
Medical University of Vienna,
Inst. Med. Biochem., Vienna Biocenter (VBC),
Dr. Bohr Gasse 9/3,
A-1030 Vienna, Austria,
Tel: 0043 1 4277 61630,
Mobile: 0043 699 1942 1659
e-mail: <a class="moz-txt-link-abbreviated" href="mailto:dieter.blaas@meduniwien.ac.at">dieter.blaas@meduniwien.ac.at</a>
------------------------------------------------------------------------</pre>
<div class="moz-cite-prefix">On 09.04.2024 19:38, David Michael
Belnap wrote:<br>
</div>
<blockquote type="cite"
cite="mid:FFFCA937-0744-429D-B2D3-ED9E0038764F@utah.edu">
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<div class="WordSection1">
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Georgia",serif">Another
option is bradial in the Bsoft package (website, bsoft.ws).
Here is an example command:<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Georgia",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Georgia",serif">bradial
-verbose 7 -subtractbackground -radial -origin 142,142,142
-minmax 0,150 -step 0.5 run_class001.mrc<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Georgia",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Georgia",serif">David<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Georgia",serif"><o:p> </o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span
style="font-size:11.5pt;font-family:"Georgia",serif;color:black">=======================================<br>
David M. Belnap<br>
Electron Microscopy Core Laboratory<br>
Department of Biochemistry<br>
School of Biological Sciences<br>
2501 SMBB<br>
University of Utah<br>
Salt Lake City, Utah 84112 USA<br>
Phone 801.585.1242<br>
FAX 801.587.3077<br>
</span><span
style="font-size:11.0pt;font-family:"Georgia",serif;color:black"><a
href="mailto:David.Belnap@utah.edu" target="_blank"
title="mailto:David.Belnap@utah.edu"
moz-do-not-send="true"><span
style="font-size:11.5pt;color:#0563C1">David.Belnap@utah.edu</span></a></span><span
style="font-size:11.5pt;font-family:"Georgia",serif;color:black"><br>
=======================================</span><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Georgia",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Georgia",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Georgia",serif"><o:p> </o:p></span></p>
<div
style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span
style="font-family:"Calibri",sans-serif;color:black">From:
</span></b><span
style="font-family:"Calibri",sans-serif;color:black">3dem
<a class="moz-txt-link-rfc2396E" href="mailto:3dem-bounces@ncmir.ucsd.edu"><3dem-bounces@ncmir.ucsd.edu></a> on behalf of Carlos
Oscar Sorzano <a class="moz-txt-link-rfc2396E" href="mailto:coss@cnb.csic.es"><coss@cnb.csic.es></a><br>
<b>Date: </b>Tuesday, April 9, 2024 at 07:39<br>
<b>To: </b>Dieter Blaas
<a class="moz-txt-link-rfc2396E" href="mailto:dieter.blaas@meduniwien.ac.at"><dieter.blaas@meduniwien.ac.at></a>, "Ludtke, Steven J."
<a class="moz-txt-link-rfc2396E" href="mailto:sludtke@bcm.edu"><sludtke@bcm.edu></a>, Tom Calcraft
<a class="moz-txt-link-rfc2396E" href="mailto:tom.calcraft@crick.ac.uk"><tom.calcraft@crick.ac.uk></a><br>
<b>Cc: </b><a class="moz-txt-link-rfc2396E" href="mailto:3dem@ncmir.ucsd.edu">"3dem@ncmir.ucsd.edu"</a>
<a class="moz-txt-link-rfc2396E" href="mailto:3dem@ncmir.ucsd.edu"><3dem@ncmir.ucsd.edu></a><br>
<b>Subject: </b>Re: [3dem] determine spherically averaged
radial density<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p>Same here, I am afraid you would need to update the Xmipp if
you still want to use it.<o:p></o:p></p>
<p>Kind regards, Carlos Oscar<o:p></o:p></p>
<div>
<p class="MsoNormal">El 09/04/2024 a las 14:39, Dieter Blaas
escribió:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p>Dear Tom and Steven,<o:p></o:p></p>
<p> thanks for the quick answer! But I also need to install
the entire Eman2 package for it work?<o:p></o:p></p>
<p>Best, Dieter<o:p></o:p></p>
<pre>------------------------------------------------------------------------<o:p></o:p></pre>
<pre>Dieter Blaas,<o:p></o:p></pre>
<pre>Max Perutz Laboratories<o:p></o:p></pre>
<pre>Medical University of Vienna, <o:p></o:p></pre>
<pre>Inst. Med. Biochem., Vienna Biocenter (VBC), <o:p></o:p></pre>
<pre>Dr. Bohr Gasse 9/3, <o:p></o:p></pre>
<pre>A-1030 Vienna, Austria, <o:p></o:p></pre>
<pre>Tel: 0043 1 4277 61630, <o:p></o:p></pre>
<pre>Mobile: 0043 699 1942 1659 <o:p></o:p></pre>
<pre>e-mail: <a href="mailto:dieter.blaas@meduniwien.ac.at"
moz-do-not-send="true" class="moz-txt-link-freetext">dieter.blaas@meduniwien.ac.at</a><o:p></o:p></pre>
<pre>------------------------------------------------------------------------<o:p></o:p></pre>
<div>
<p class="MsoNormal">On 09.04.2024 13:47, Ludtke, Steven J.
wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">To add, if your goal is to compute the
radial density distribution as a curve rather than the
averaged volume,
<o:p></o:p></p>
<div>
<p class="MsoNormal">e2proc3d.py --calcradial 0 map.mrc
radial.txt<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">(can also calculate min,max)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">e2proc3d.py --help<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span
style="font-size:10.5pt;font-family:"Courier New"">---</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-bottom:12.0pt"><span
style="font-size:10.5pt;font-family:"Courier New"">Steven
Ludtke, Ph.D.
<a href="mailto:sludtke@bcm.edu"
moz-do-not-send="true"><sludtke@bcm.edu></a> Baylor
College of Medicine<br>
Charles C. Bell Jr., Professor of
Structural Biology Dept. of
Biochemistry <br>
Deputy Director, Advanced
Technology Cores and
Molecular Pharmacology<br>
Academic Director, CryoEM Core<br>
Co-Director CIBR Center</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On Apr 9, 2024, at 5:34<span
style="font-family:"Arial",sans-serif"> </span>AM,
Tom Calcraft
<a href="mailto:tom.calcraft@crick.ac.uk"
moz-do-not-send="true"><tom.calcraft@crick.ac.uk></a>
wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal"><span
style="font-size:9.0pt;font-family:Helvetica">Hi
Dieter,<br>
<br>
The math.rotationalaverage function in EMAN2’s
e2proc3d.py should do what you are looking for:<br>
<br>
e2proc3d.py --process=math.rotationalaverage
input.mrc output.mrc<br>
<br>
Best,<br>
Tom<br>
<br
style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;text-align:start;-webkit-text-stroke-width: 0px;word-spacing:0px">
<br>
</span><o:p></o:p></p>
<blockquote
style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"><span
style="font-size:9.0pt;font-family:Helvetica">On
9 Apr 2024, at 10:33, Dieter Blaas <<a
href="mailto:dieter.blaas@meduniwien.ac.at"
moz-do-not-send="true"
class="moz-txt-link-freetext">dieter.blaas@meduniwien.ac.at</a>>
wrote:<br>
<br>
<br>
External Sender: Use caution.<br>
<br>
<br>
Dear all,<br>
<br>
we need to determine the spherically averaged
radial density of a<br>
symmetric virus. Long ago, we used for this
xmipp_operate but my old<br>
scipion3 and xmipp installs do not work any
more. Is there any other<br>
piece of software that can easily do this
without too much ado?<br>
<br>
Thanks for hints, Dieter<br>
<br>
------------------------------------------------------------------------<br>
Dieter Blaas,<br>
Max Perutz Laboratories<br>
Medical University of Vienna,<br>
Inst. Med. Biochem., Vienna Biocenter (VBC),<br>
Dr. Bohr Gasse 9/3,<br>
A-1030 Vienna, Austria,<br>
Tel: 0043 1 4277 61630,<br>
Mobile: 0043 699 1942 1659<br>
e-mail: <a
href="mailto:dieter.blaas@meduniwien.ac.at"
moz-do-not-send="true"
class="moz-txt-link-freetext">dieter.blaas@meduniwien.ac.at</a><br>
------------------------------------------------------------------------<br>
<br>
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