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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>
<blockquote
cite="mid:F0E461AAE34D0448B6EE7D31E433B708011AEE0430@AEWEXCPM21.yuad.uds.yu.edu"
type="cite">
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<p class="MsoNormalCxSpFirst"><font face="Times New Roman"><font
size="3">To clear up definitions<span style="mso-spacerun:
yes">
</span></font><font size="3">in my book describing a helix
as</font><span style="mso-spacerun: yes"><font size="3">
</font></span><font size="3">u = X subunits </font><span
style="mso-spacerun: yes"><font size="3"> </font></span><font
size="3">in
</font><span style="mso-spacerun: yes"><font size="3"> </font></span><font
size="3">t =
</font><span style="mso-spacerun: yes"><font size="3"> </font></span><font
size="3">Y turns
</font><span style="mso-spacerun: yes"><font size="3"> </font></span><font
size="3">(per
</font><span style="mso-spacerun: yes"><font size="3"> </font></span><font
size="3">axial repeat)
</font><span style="mso-spacerun: yes"><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="mso-spacerun: yes"><font size="3"> </font></span><font
size="3">l=tn + um that fully describe the helix.
</font><span style="mso-spacerun: yes"><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="mso-spacerun: yes"><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="mso-spacerun: yes"><font size="3">
</font></span><font size="3">h=axial_repeat/u, </font><font
size="3"><span style="mso-spacerun: yes"> </span><span
style="mso-spacerun: yes"> </span><span
style="mso-spacerun: yes"> </span></font><font size="3">phi=360*t/u.</font><font
size="3"><span style="mso-spacerun: yes">
</span><span style="mso-spacerun: yes"> </span></font></font></p>
<p class="MsoNormalCxSpMiddle">
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<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="mso-spacerun: yes"> </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"><o:p><font size="3" face="Times
New Roman"> </font></o:p></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="mso-spacerun:
yes">
</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="mso-spacerun: yes"> </span><span
style="mso-spacerun: yes"> </span><span
style="mso-spacerun: yes"> </span><span
style="mso-spacerun: yes"> </span><span
style="mso-spacerun: yes"> </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
color="#000000" size="2" face="Tahoma"><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 moz-do-not-send="true" 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 moz-do-not-send="true" 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"><span><br>
<br>
</span><span></span></p>
<p class="MsoNormal">Edward H. Egelman, Ph.D.</p>
<p class="MsoNormal">Harrison Distinguished Professor</p>
<p class="MsoNormal">Dept. of Biochemistry and
Molecular Genetics</p>
<p class="MsoNormal">University of Virginia</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"><span class="GramE">phone</span>:
434-924-8210</p>
<p class="MsoNormal"><span class="GramE">fax</span>:
434-924-5069</p>
<p class="MsoNormal"><a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:egelman@virginia.edu" target="_blank">egelman@virginia.edu</a></p>
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</xml><![endif]-->Edward H. Egelman, Ph.D.<u5:p></u5:p></p>
<p class="MsoNormal">Harrison Distinguished Professor<u5:p></u5:p></p>
<p class="MsoNormal">Dept. of Biochemistry and Molecular
Genetics<u5:p></u5:p></p>
<p class="MsoNormal">University of Virginia<u5:p></u5:p><o:p></o:p></p>
<p class="MsoNormal"><u5:p> </u5:p></p>
<p class="MsoNormal"><span class="GramE">phone</span>:
434-924-8210<u5:p></u5:p></p>
<p class="MsoNormal"><span class="GramE">fax</span>:
434-924-5069<u5:p></u5:p></p>
<p class="MsoNormal"><a class="moz-txt-link-abbreviated" href="mailto:egelman@virginia.edu">egelman@virginia.edu</a><u5:p></u5:p></p>
<p class="MsoNormal"><a
href="http://www.people.virginia.edu/%7Eehe2n"><a class="moz-txt-link-freetext" href="http://www.people.virginia.edu/~ehe2n">http://www.people.virginia.edu/~ehe2n</a></a><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:Times;mso-fareast-font-family:
"Times New
Roman";mso-bidi-font-family:"Times New
Roman""><o:p> </o:p></span></p>
</div>
<u5:p></u5:p></div>
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