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<p>Hi,</p>
<p><br>
</p>
<p> I couldn't agree with Ed more. Although selection rules may initially seem to make the difficult concepts behind helical diffraction (and the image processing that makes use of these concepts) somewhat easier to swallow, in the long run, they cause
more trouble than they are worth. I have found the formalism of DeRosier's (n,Z) net and subunit rise and rotation to be much more satisfactory, and often use the example of a helix built using a subunit rotation of e degrees and a subunit rise of pi Angstroms.
Yes, there are integers that would closely approximate this structure, but that description also loses some of it's beauty!
<br>
</p>
<p><br>
</p>
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-- <br>
<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
David Gene Morgan<br>
Electron Microscopy Center<br>
047D Simon Hall<br>
IU Bloomington<br>
812 856 1457 (office)<br>
812 856 3221 (3200)<br>
http://iubemcenter.indiana.edu</div>
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<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> 3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of Edward Egelman <egelman@virginia.edu><br>
<b>Sent:</b> Sunday, March 6, 2016 2:31 PM<br>
<b>To:</b> Hernando J Sosa; Smith, Phillip R.; 3dem@ncmir.ucsd.edu<br>
<b>Subject:</b> Re: [3dem] IHRSR++ and SPIDER 21.02</font>
<div> </div>
</div>
<div>It depends upon how "classical" you mean! This excellent handout from David DeRosier predates single particle approaches, and from the references must have been written between 1992 and 2000:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.biomachina.org/courses/structures/download/derosier_handout_02.pdf">http://www.biomachina.org/courses/structures/download/derosier_handout_02.pdf</a><br>
<br>
Since David (with Aaron Klug) was the first to use Fourier-Bessel methods in EM (and publish the first 3D reconstruction, he has some authority in this area. The selection rule is introduced in his handout as a parenthetical alternate description, but the entire
Fourier-Bessel formalism presented is in terms of n,Z (where Z is a real number) and not n,l (where l is an integer and arises from an integral selection rule, with u and t being integers). So one does not need (and is hindered by, in my humble opinion) a
selection rule to understand and use the Fourier-Bessel approach. Perhaps I was being picky, but u/t does not "select" anything, while the equation l=tn +um selects what Bessel order n can appear on a layer line l. That is why this equation is called the selection
rule. Of course, any real number can be represented to good approximation as a ratio of two integers, so if some "classical" program requires integers for u and t, one can always approximate them. I may also suffer from a lack of visual imagination (with regards
to Esther's point), as I do not see how saying that a filament twist may range from 13 subunits in 6 turns to 1299 subunits in 600 turns is helpful (a change from 166.15 to 166.28 degrees). I would much rather think in terms of angles. But perhaps that is
just my problem.<br>
Regards,<br>
Ed<br>
<br>
<br>
<div class="moz-cite-prefix">On 3/6/16 2:07 PM, Hernando J Sosa wrote:<br>
</div>
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<p class="MsoNormalCxSpFirst"><font face="Times New Roman"><font size="3">To clear up definitions<span style="">
</span></font><font size="3">in my book describing a helix as</font><span style=""><font size="3">
</font></span><font size="3">u = X subunits </font><span style=""><font size="3"> </font></span><font size="3">in
</font><span style=""><font size="3"> </font></span><font size="3">t = </font><span style=""><font size="3"> </font></span><font size="3">Y turns
</font><span style=""><font size="3"> </font></span><font size="3">(per </font><span style=""><font size="3"> </font></span><font size="3">axial repeat)
</font><span style=""><font size="3"> </font></span><font size="3">IS the same as providing the selection rule, as these are the only two variables in the selection rule equation
</font><span style=""><font size="3"> </font></span><font size="3">l=tn + um that fully describe the helix.
</font><span style=""><font size="3"> </font></span><font size="3">With these parameters (u & t) the possible Bessel orders for any layer line number are determined according to the selection rule equation.
</font><span style=""><font size="3"> </font></span><font size="3">The parameters u and t can be simply converted to the alternative way to describe a helix with the twist (phi) angle and rise (h) per subunit as:</font><span style=""><font size="3">
</font></span><font size="3">h=axial_repeat/u, </font><font size="3"><span style=""> </span><span style=""> </span><span style=""> </span></font><font size="3">phi=360*t/u.</font><font size="3"><span style="">
</span><span style=""> </span></font></font></p>
<p class="MsoNormalCxSpMiddle"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormalCxSpMiddle"><font face="Times New Roman"><font size="3">As discussed the problem with this selection rule definition is that it arbitrarily assumes an integer number of turns and subunits per axial repeat.
<span style=""> </span></font><font size="3">However, in practice good approximations can be found assuming a long enough axial repeat or using a more general selection rule expressed in function of the twist and rise (e.g. Moody MF. 1990).</font></font></p>
<p class="MsoNormalCxSpMiddle"><font face="Times
New Roman" size="3"> </font></p>
<p class="MsoNormalCxSpMiddle"><font face="Times New Roman"><font size="3">When trying to determine the symmetry of an unknown helical specimen (or modifications of a known one) I find it useful to go back and forth between these equivalent definitions so I
wouldn't consider unreasonable to talk about selection rules.<span style=""> </span>
</font><font size="3">Knowing the 'classical' selection would also be necessary if for any reason you want to use 'classical' 3D Fourier-Bessel helical 3D reconstruction packages.</font></font></p>
<p class="MsoNormalCxSpMiddle"><font size="3"><font face="Times
New Roman"><span style=""> </span><span style=""> </span><span style=""> </span><span style=""> </span><span style=""> </span></font></font></p>
<p> </p>
<p>Best</p>
<p> </p>
<p>Hernando</p>
<div style="font-size:16px; font-family:Times New Roman; color:#000000">
<hr tabindex="-1">
<div id="divRpF328704" style="direction:ltr"><font face="Tahoma" color="#000000" size="2"><b>From:</b> 3dem [<a class="moz-txt-link-abbreviated" href="mailto:3dem-bounces@ncmir.ucsd.edu">3dem-bounces@ncmir.ucsd.edu</a>] on behalf of Edward Egelman [<a class="moz-txt-link-abbreviated" href="mailto:egelman@virginia.edu">egelman@virginia.edu</a>]<br>
<b>Sent:</b> Saturday, March 05, 2016 10:36 AM<br>
<b>To:</b> Smith, Phillip R.; <a class="moz-txt-link-abbreviated" href="mailto:3dem@ncmir.ucsd.edu">
3dem@ncmir.ucsd.edu</a><br>
<b>Subject:</b> Re: [3dem] IHRSR++ and SPIDER 21.02<br>
</font><br>
</div>
<div>No reasonable person would use selection rules any more. They were formulated in the 1950s and arise from a crystallographic-type formulation where a helix is described by the ratio of integers (units/turn or u/t). For real helices, the best description
is given by two real numbers, a rise (Angstroms) and a rotation (degrees). The description of those tubes (I assume) is given in Parent et al., Physical Biology:<br>
<br>
doi:10.1088/1478-3975/7/4/045004<br>
<br>
Regards,<br>
Ed<br>
<br>
<div class="moz-cite-prefix">On 3/5/16 9:49 AM, Smith, Phillip R. wrote:<br>
</div>
<blockquote type="cite">
<pre>The data and tutorial that you point to is indeed excellent and a nice testbed for software.
But it would be a huge help if someone could provide the selection rule for the F170A tubes in the data provided, p8:
"The values for the symmetry parameters ([Cn], [rise], [deltaphi]) were derived from the diffraction pattern (derivation not shown).”
Hope you can help…
Very best to all!
-Ross Smith-
</pre>
<blockquote type="cite">
<pre>On Feb 29, 2016, at 4:39 PM, Edward Egelman <a class="moz-txt-link-rfc2396E" href="mailto:egelman@virginia.edu" target="_blank"><egelman@virginia.edu></a> wrote:
Hi,
Unfortunately, there are no good tutorials. Also, the more that I learn the more I realize that it is not as simple as I originally assumed. I would suggest reading three papers as a start:
Egelman, E.H. (2010), “Reconstruction of Helical Filaments and Tubes”, Methods in Enzymology 482, 167-183.
Egelman, E.H. (2014). “Ambiguities in helical reconstruction”. eLife 3:e04969 doi:10.7554/eLife.04969.
Egelman, E.H. (2015). “Three-dimensional reconstruction of helical polymers”, Archives of Biochemistry and Biophysics 581, 54-58.
Regards,
Ed
On 2/29/16 2:58 PM, Johannes Haataja wrote:
</pre>
<blockquote type="cite">
<pre>Dear all,
thank you for the replies. I now have an older version of spider.
Regarding IHRSR Prof. Egelman - what would the recommended way/tutorial
for learning to use IHRSR?
My best,
- J.
P.S. I guess ideally one would just read an article about the theory and
unix/linux man-pages of relevant command line tools and then inductively
reason how one must proceed to apply the method to the problem at hand.
Since I lack such a tenacity, I usually look for tutorials in order to
understand how the softwares/black boxes work. Also, I imagine that for
helical reconstruction, like for any inverse problem, there are many
different methods for recovering the quantit(y/ies) of interest and that
people usually are hesitant to openly aside with particular approach may
it be the right one or obviously the wrong one (e.g. Bayesian vs.
Frequentist interpretation of statistics) ;).
ma, 2016-02-29 kello 12:13 -0500, Michael Radermacher kirjoitti:
</pre>
<blockquote type="cite">
<pre>I would contact the people in Albany and also
discuss with them the problem you are having
with your version.
Michael
On 2/29/2016 11:46 AM, Johannes Haataja wrote:
</pre>
<blockquote type="cite">
<pre>Hi,
does anyone know where to obtain old versions of SPIDER, namely v.
21.02? The oldest from download page is 21.11. The reason for asking is
that I need and older SPIDER version to test IHRSR++ v. 1.5 tutorial
<a class="moz-txt-link-freetext" href="http://cryoem.ucsd.edu/wikis/software/start.php?id=ihrsr" target="_blank">http://cryoem.ucsd.edu/wikis/software/start.php?id=ihrsr</a>
to exclude the possibility that the errors I run into (in the final
reconstruction step) have something to do with SPIDER version.
My best,
- J.
</pre>
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<p class="MsoNormal">Edward H. Egelman, Ph.D.</p>
<p class="MsoNormal">Harrison Distinguished Professor</p>
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