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<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>
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<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>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Georgia",serif">David<o:p></o:p></span></p>
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<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"><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>
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<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 <3dem-bounces@ncmir.ucsd.edu> on behalf of Carlos Oscar Sorzano <coss@cnb.csic.es><br>
<b>Date: </b>Tuesday, April 9, 2024 at 07:39<br>
<b>To: </b>Dieter Blaas <dieter.blaas@meduniwien.ac.at>, "Ludtke, Steven J." <sludtke@bcm.edu>, Tom Calcraft <tom.calcraft@crick.ac.uk><br>
<b>Cc: </b>"3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br>
<b>Subject: </b>Re: [3dem] determine spherically averaged radial density<o:p></o:p></span></p>
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<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>
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<p class="MsoNormal">El 09/04/2024 a las 14:39, Dieter Blaas escribió:<o:p></o:p></p>
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<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">dieter.blaas@meduniwien.ac.at</a><o:p></o:p></pre>
<pre>------------------------------------------------------------------------<o:p></o:p></pre>
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<p class="MsoNormal">On 09.04.2024 13:47, Ludtke, Steven J. wrote:<o:p></o:p></p>
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<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>
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<p class="MsoNormal">e2proc3d.py --calcradial 0 map.mrc radial.txt<o:p></o:p></p>
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<p class="MsoNormal">(can also calculate min,max)<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">e2proc3d.py --help<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Courier New"">---</span><o:p></o:p></p>
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<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"><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>
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<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"><tom.calcraft@crick.ac.uk></a> wrote:<o:p></o:p></p>
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<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">
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</span><o:p></o:p></p>
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<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">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">dieter.blaas@meduniwien.ac.at</a><br>
------------------------------------------------------------------------<br>
<br>
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