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That depends on what you are using the curve for. Filtering or downsampling (of either the map itself or the rotational average) are both good ways to tidy up the curve. Regarding the "final diameter”, it is up to your judgement where to draw the line - there
may be non-zero background density on the inside/outside of your spherical virus even after rotational averaging. It is probably best to check your diameter value(s) against the high-resolution map without rotational averaging, or against an atomic model if
you have one available.
<div><br>
</div>
<div>Best,</div>
<div>Tom<br>
<div>
<div><br>
<blockquote type="cite">
<div>On 10 Apr 2024, at 06:11, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:</div>
<br class="Apple-interchange-newline">
<div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;"> </span>
<div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; border: 1px solid black; background-color: rgb(255, 235, 156); padding: 0.2em;">
<span style="font-size: 10pt; color: red;"><b>External Sender:</b></span><span class="Apple-converted-space"> </span><span style="font-size: 10pt;">Use caution.</span></div>
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;"> </span>
<div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
<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<span class="Apple-converted-space"> </span><br>
</p>
<pre class="moz-signature" cols="72" style="margin: 0in; font-size: 10pt; font-family: "Courier New";">------------------------------------------------------------------------
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" style="color: blue; text-decoration: underline;">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">
<div class="WordSection1" style="page: WordSection1;">
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; 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></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Georgia, serif;"><o:p> </o:p></span></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; 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></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Georgia, serif;"><o:p> </o:p></span></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Georgia, serif;">David<o:p></o:p></span></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Georgia, serif;"><o:p> </o:p></span></div>
<div>
<div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11.5pt; font-family: Georgia, serif;">=======================================<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: 11pt; font-family: Georgia, serif;"><a href="mailto:David.Belnap@utah.edu" target="_blank" title="mailto:David.Belnap@utah.edu" moz-do-not-send="true" style="color: blue; text-decoration: underline;"><span style="font-size: 11.5pt; color: rgb(5, 99, 193);">David.Belnap@utah.edu</span></a></span><span style="font-size: 11.5pt; font-family: Georgia, serif;"><br>
=======================================</span><span style="font-size: 11pt; font-family: Calibri, sans-serif;"><o:p></o:p></span></div>
</div>
</div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Georgia, serif;"><o:p> </o:p></span></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Georgia, serif;"><o:p> </o:p></span></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Georgia, serif;"><o:p> </o:p></span></div>
<div style="border-width: 1pt medium medium; border-style: solid none none; border-color: rgb(181, 196, 223) currentcolor currentcolor; border-image: none; padding: 3pt 0in 0in;">
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><b><span style="font-family: Calibri, sans-serif;">From:<span class="Apple-converted-space"> </span></span></b><span style="font-family: Calibri, sans-serif;">3dem<span class="Apple-converted-space"> </span><a class="moz-txt-link-rfc2396E" href="mailto:3dem-bounces@ncmir.ucsd.edu" style="color: blue; text-decoration: underline;"><3dem-bounces@ncmir.ucsd.edu></a><span class="Apple-converted-space"> </span>on
behalf of Carlos Oscar Sorzano<span class="Apple-converted-space"> </span><a class="moz-txt-link-rfc2396E" href="mailto:coss@cnb.csic.es" style="color: blue; text-decoration: underline;"><coss@cnb.csic.es></a><br>
<b>Date:<span class="Apple-converted-space"> </span></b>Tuesday, April 9, 2024 at 07:39<br>
<b>To:<span class="Apple-converted-space"> </span></b>Dieter Blaas<span class="Apple-converted-space"> </span><a class="moz-txt-link-rfc2396E" href="mailto:dieter.blaas@meduniwien.ac.at" style="color: blue; text-decoration: underline;"><dieter.blaas@meduniwien.ac.at></a>,
"Ludtke, Steven J."<span class="Apple-converted-space"> </span><a class="moz-txt-link-rfc2396E" href="mailto:sludtke@bcm.edu" style="color: blue; text-decoration: underline;"><sludtke@bcm.edu></a>, Tom Calcraft<span class="Apple-converted-space"> </span><a class="moz-txt-link-rfc2396E" href="mailto:tom.calcraft@crick.ac.uk" style="color: blue; text-decoration: underline;"><tom.calcraft@crick.ac.uk></a><br>
<b>Cc:<span class="Apple-converted-space"> </span></b><a class="moz-txt-link-rfc2396E" href="mailto:3dem@ncmir.ucsd.edu" style="color: blue; text-decoration: underline;">"3dem@ncmir.ucsd.edu"</a><span class="Apple-converted-space"> </span><a class="moz-txt-link-rfc2396E" href="mailto:3dem@ncmir.ucsd.edu" style="color: blue; text-decoration: underline;"><3dem@ncmir.ucsd.edu></a><br>
<b>Subject:<span class="Apple-converted-space"> </span></b>Re: [3dem] determine spherically averaged radial density<o:p></o:p></span></div>
</div>
<div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
</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>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">El 09/04/2024 a las 14:39, Dieter Blaas escribió:<o:p></o:p></div>
</div>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<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 style="margin: 0in; font-size: 10pt; font-family: "Courier New";">------------------------------------------------------------------------<o:p></o:p></pre>
<pre style="margin: 0in; font-size: 10pt; font-family: "Courier New";">Dieter Blaas,<o:p></o:p></pre>
<pre style="margin: 0in; font-size: 10pt; font-family: "Courier New";">Max Perutz Laboratories<o:p></o:p></pre>
<pre style="margin: 0in; font-size: 10pt; font-family: "Courier New";">Medical University of Vienna, <o:p></o:p></pre>
<pre style="margin: 0in; font-size: 10pt; font-family: "Courier New";">Inst. Med. Biochem., Vienna Biocenter (VBC), <o:p></o:p></pre>
<pre style="margin: 0in; font-size: 10pt; font-family: "Courier New";">Dr. Bohr Gasse 9/3, <o:p></o:p></pre>
<pre style="margin: 0in; font-size: 10pt; font-family: "Courier New";">A-1030 Vienna, Austria, <o:p></o:p></pre>
<pre style="margin: 0in; font-size: 10pt; font-family: "Courier New";">Tel: 0043 1 4277 61630, <o:p></o:p></pre>
<pre style="margin: 0in; font-size: 10pt; font-family: "Courier New";">Mobile: 0043 699 1942 1659 <o:p></o:p></pre>
<pre style="margin: 0in; font-size: 10pt; font-family: "Courier New";">e-mail: <a href="mailto:dieter.blaas@meduniwien.ac.at" moz-do-not-send="true" class="moz-txt-link-freetext" style="color: blue; text-decoration: underline;">dieter.blaas@meduniwien.ac.at</a><o:p></o:p></pre>
<pre style="margin: 0in; font-size: 10pt; font-family: "Courier New";">------------------------------------------------------------------------<o:p></o:p></pre>
<div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">On 09.04.2024 13:47, Ludtke, Steven J. wrote:<o:p></o:p></div>
</div>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">To add, if your goal is to compute the radial density distribution as a curve rather than the averaged volume, <o:p></o:p></div>
<div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">e2proc3d.py --calcradial 0 map.mrc radial.txt<o:p></o:p></div>
</div>
<div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">(can also calculate min,max)<o:p></o:p></div>
</div>
<div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
</div>
<div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">e2proc3d.py --help<o:p></o:p></div>
</div>
<div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 10.5pt; font-family: "Courier New";">---</span><o:p></o:p></div>
</div>
<div>
<p class="MsoNormal" style="margin: 0in 0in 12pt; font-size: 12pt; font-family: Aptos, sans-serif;">
<span style="font-size: 10.5pt; font-family: "Courier New";">Steven Ludtke, Ph.D.<span class="Apple-converted-space"> </span><a href="mailto:sludtke@bcm.edu" moz-do-not-send="true" style="color: blue; text-decoration: underline;"><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>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><br>
<br>
<o:p></o:p></div>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">On Apr 9, 2024, at 5:34<span style="font-family: Arial, sans-serif;"> </span>AM, Tom Calcraft<span class="Apple-converted-space"> </span><a href="mailto:tom.calcraft@crick.ac.uk" moz-do-not-send="true" style="color: blue; text-decoration: underline;"><tom.calcraft@crick.ac.uk></a>wrote:<o:p></o:p></div>
</div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
<div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 9pt; 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></div>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 9pt; 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" style="color: blue; text-decoration: underline;">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:<span class="Apple-converted-space"> </span><a href="mailto:dieter.blaas@meduniwien.ac.at" moz-do-not-send="true" class="moz-txt-link-freetext" style="color: blue; text-decoration: underline;">dieter.blaas@meduniwien.ac.at</a><br>
------------------------------------------------------------------------<br>
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<pre style="margin: 0in; font-size: 10pt; font-family: "Courier New";">3dem mailing list<o:p></o:p></pre>
<pre style="margin: 0in; font-size: 10pt; font-family: "Courier New";"><a href="mailto:3dem@ncmir.ucsd.edu" moz-do-not-send="true" class="moz-txt-link-freetext" style="color: blue; text-decoration: underline;">3dem@ncmir.ucsd.edu</a><o:p></o:p></pre>
<pre style="margin: 0in; font-size: 10pt; font-family: "Courier New";"><a href="https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem" originalsrc="https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem" shash="zA60HKfJLgMVJPINdI1KDdWEIWzREOrU+FyxUHogii9vQoJXvLysoYG2ao8YoDQ/UvxybD5Lv4IUtVAai+mDrrUwasZ1y996ZUopovI8QqZmbxJg053xkGwlmRxruV8B+pEDwbNlAtT9IJevcLEYy6ykFXPE7SPYeU0xMg+efS4=" moz-do-not-send="true" class="moz-txt-link-freetext" style="color: blue; text-decoration: underline;">https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem</a><o:p></o:p></pre>
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<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">3dem
mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">3dem@ncmir.ucsd.edu</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem</span></div>
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<p style="color:rgb(112,113,115);font-family: 'Trebuchet MS', 'Lucida Grande'; font-style: italic; font-size: 10pt;">
The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT</p>
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