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<p class="MsoNormal" style="MARGIN: 0in 0in 10pt"><font size="3" face="Calibri">As I see it both are equivalent descriptions of a helix. Given the rise and turn per subunit a selection rule can be generated and vice versa. An approximate selection rule (expressed
as number of subunits and turns per repeat) can also be generated and from these values the rise and turn per subunit can also be calculated back.</font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 10pt"><font face="Calibri"><font size="3">If you don't know the helical symmetry or your specimen testing tentative selection rules is very useful as they allow to quickly estimate their power spectrums (Bessel orders
and layer line positions) and compare them with the experimental data to find the best match (this could be complicated depending o the quality of the experimental power spectrums and possible multiple near matches). Once you have a matching selection rule
you automatically also have a pretty good estimate of the rise and turn per subunit of your helical specimen (but no handedness).
<span style="mso-spacerun: yes"> Once good estimates of the rise and turn per subunit are available
</span></font><font size="3">you could then forget about selection rules and use iterative refinement methods such as Ed's IRSHR to refine the structure.
</font></font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 10pt"><font size="3" face="Calibri">Best</font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 10pt"><font size="3" face="Calibri">Hernando</font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 10pt"><font size="3" face="Calibri"></font> </p>
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<div id="divRpF772974" style="DIRECTION: ltr"><font color="#000000" size="2" face="Tahoma"><b>From:</b> 3dem [3dem-bounces@ncmir.ucsd.edu] on behalf of Steve Chou [stevezchou@gmail.com]<br>
<b>Sent:</b> Wednesday, March 30, 2016 9:03 PM<br>
<b>To:</b> 3dem@ncmir.ucsd.edu<br>
<b>Subject:</b> Re: [3dem] 3dem Digest, Vol 103, Issue 29<br>
</font><br>
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<div>Dear all,<br>
</div>
<div><br>
My understanding on this topic (could be completely wrong) is described here:<br>
</div>
<div>Suppose there are two "ideal helices": one is 1299 units per 300 turns; the other 13 (1300) units per 3 (300) turns. To describe them using the selection rule, they are l=1299m+300n, and l=13m+3n, respectively.
<br>
</div>
<div>The power spectra (layer line images) of these two ideal helices will be SIMILAR in biological EM conditions [biological molecular building blocks (units) in the EM RESOLUTION RANGE] --- Biology (filaments length, flexibility, etc. usu. the main reason)
introduces ambiguity here. The layer line image of the helix with 1299 units per 300 turns should have more layer lines in a specific height than the other one, but usually not noticeable in biological EM conditions. Bessel orders (n) for each layer line on
these two layer line images are the same, and the heights (Z) of dominant/obvious layer lines change a little bit --- may not be noticeable either, however, the LAYER LINE NUMBERS (l) will be TOTALLY DIFFERENT. I think this is the reason why some people don't
like this (layer line number change). If you don't want be be bothered by the layer number change during the interpretation of the layer line image, then Ed's point is absolutely correct [to use Z instead of l (implying that you are using selection rule)].
<br>
<br>
In real world, it should be fine to describe a helix with 1299 units per 300 turns as 13 (1300) units per 3 (300) turns. This is because the helicity of a helix data set is a range (e.g., between 1297 units per 300 turns and 1301 units per 300 turns).<br>
<br>
</div>
<div>In biological X-ray crystallography, the assemblies of the molecules in the crystals are not perfect either, but crystallographers just force them to be in a specific space group, usually choose the highest reasonable symmetry.<br>
</div>
<div><br>
</div>
<div>Another point: As Ed said, I don't think Fourier-Bessel reconstruction actually needs (relies on) the selection rule.<br>
<br>
Idealists can think filaments using the selection rule (units and turns) and symmetry (non-helical); realists may like to describe them using only rise and rotation, plus symmetry --- this is more practical. Both are fine, especially for easy cases. For complicated
cases, it might take a LONG time (months) to figure out the helical parameters.<br>
<br>
</div>
<div>All the best,<br>
</div>
Steve<br>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Mar 30, 2016 at 11:16 AM, <span dir="ltr"><<a href="mailto:3dem-request@ncmir.ucsd.edu" target="_blank">3dem-request@ncmir.ucsd.edu</a>></span> wrote:<br>
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1. Re: IHRSR++ and SPIDER 21.02 (Edward Egelman)<br>
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----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 30 Mar 2016 11:16:23 -0400<br>
From: Edward Egelman <<a href="mailto:egelman@virginia.edu" target="_blank">egelman@virginia.edu</a>><br>
To: <a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a><br>
Cc: "Smith, Phillip R." <<a href="mailto:smithp01@nyumc.org" target="_blank">smithp01@nyumc.org</a>><br>
Subject: Re: [3dem] IHRSR++ and SPIDER 21.02<br>
Message-ID: <<a href="mailto:56FBEDC7.7030904@virginia.edu" target="_blank">56FBEDC7.7030904@virginia.edu</a>><br>
Content-Type: text/plain; charset="utf-8"; Format="flowed"<br>
<br>
This is an incredibly belated reply. I never responded at the time since<br>
I did not want to beat a living horse (I had assumed that the horse was<br>
dead, but I was quite wrong). But a discussion I had yesterday made me<br>
realize that a response might be useful. Esther has raised that knowing<br>
that a structure can vary from 13 subunits in 6 turns to 11 subunits in<br>
5 turns provides a helpful description of the variability. This is only<br>
a change in twist, which is from 166.15 degrees per subunit (13/6) to<br>
163.64 degrees per subunit (11/5). But how useful is it describing the<br>
variability in twist in terms of a repeat either every 5 or 6 turns? A<br>
structure with 24 subunits in 11 turns would be between these two, and<br>
have 165.0 degrees rotation per subunit. A structure with 46 subunits in<br>
21 turns would have 164.35 degrees, also between 13/6 and 11/5. As would<br>
174/80, 186/85, 291/134, etc. If it is obvious to anyone that all of<br>
these ratios fall within Esther's range, then I am the one who is<br>
challenged. Simply stating at the outset that the twist ranges from<br>
163.64 to 166.15 degrees is much easier, more intuitive and much more<br>
helpful (in my opinion).<br>
Regards,<br>
Ed<br>
<br>
On 3/6/16 8:25 AM, Bullitt Esther wrote:<br>
> Are we really going to get into this?<br>
><br>
> I am in general a reasonable person, and I still find selection rules<br>
> to be a good way to get an intuitive feeling for the structure of a<br>
> helical filament.<br>
><br>
> Is it the be-all, end-all? Of course not.<br>
> Is it a useful approximation as a start for understanding the biology?<br>
> Yes, it is.<br>
> For example, if one determines that filaments you analyze range from<br>
> 13 u/ 6 t to 11u / 5 t, that gives a visual meaning to how much<br>
> the filament tightens/loosens while performing its functions.<br>
> Necessary for structure determination? Not really. Helpful? In my<br>
> opinion, yes.<br>
><br>
> In addition to the references Ed suggested, I am a fan of Murray<br>
> Stewart's 1988 article, 'Computer Image Processing of Electron<br>
> Micrographs of Biological Structures with Helical Symmetry' , in J<br>
> Electron Microscopy Technique 9:325-358<br>
><br>
> Sincerely,<br>
> Esther<br>
><br>
> On Mar 5, 2016, at 10:36 AM, Edward Egelman <<a href="mailto:egelman@virginia.edu" target="_blank">egelman@virginia.edu</a><br>
> <mailto:<a href="mailto:egelman@virginia.edu" target="_blank">egelman@virginia.edu</a>>> wrote:<br>
><br>
>> No reasonable person would use selection rules any more. They were<br>
>> formulated in the 1950s and arise from a crystallographic-type<br>
>> formulation where a helix is described by the ratio of integers<br>
>> (units/turn or u/t). For real helices, the best description is given<br>
>> by two real numbers, a rise (Angstroms) and a rotation (degrees). The<br>
>> description of those tubes (I assume) is given in Parent et al.,<br>
>> Physical Biology:<br>
>><br>
>> doi:10.1088/1478-3975/7/4/045004<br>
>><br>
>> Regards,<br>
>> Ed<br>
>><br>
>> On 3/5/16 9:49 AM, Smith, Phillip R. wrote:<br>
>>> The data and tutorial that you point to is indeed excellent and a nice testbed for software.<br>
>>><br>
>>> But it would be a huge help if someone could provide the selection rule for the F170A tubes in the data provided, p8:<br>
>>><br>
>>> "The values for the symmetry parameters ([Cn], [rise], [deltaphi]) were derived from the diffraction pattern (derivation not shown).?<br>
>>><br>
>>> Hope you can help?<br>
>>><br>
>>> Very best to all!<br>
>>><br>
>>> -Ross Smith-<br>
>>><br>
>>>> On Feb 29, 2016, at 4:39 PM, Edward Egelman<<a href="mailto:egelman@virginia.edu" target="_blank">egelman@virginia.edu</a>> wrote:<br>
>>>><br>
>>>> Hi,<br>
>>>> 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:<br>
>>>><br>
>>>> Egelman, E.H. (2010), ?Reconstruction of Helical Filaments and Tubes?, Methods in Enzymology 482, 167-183.<br>
>>>><br>
>>>> Egelman, E.H. (2014). ?Ambiguities in helical reconstruction?. eLife 3:e04969 doi:10.7554/eLife.04969.<br>
>>>><br>
>>>> Egelman, E.H. (2015). ?Three-dimensional reconstruction of helical polymers?, Archives of Biochemistry and Biophysics 581, 54-58.<br>
>>>><br>
>>>> Regards,<br>
>>>> Ed<br>
>>>><br>
>>>><br>
>>>> On 2/29/16 2:58 PM, Johannes Haataja wrote:<br>
>>>>> Dear all,<br>
>>>>> thank you for the replies. I now have an older version of spider.<br>
>>>>><br>
>>>>> Regarding IHRSR Prof. Egelman - what would the recommended way/tutorial<br>
>>>>> for learning to use IHRSR?<br>
>>>>><br>
>>>>> My best,<br>
>>>>> - J.<br>
>>>>><br>
>>>>> P.S. I guess ideally one would just read an article about the theory and<br>
>>>>> unix/linux man-pages of relevant command line tools and then inductively<br>
>>>>> reason how one must proceed to apply the method to the problem at hand.<br>
>>>>> Since I lack such a tenacity, I usually look for tutorials in order to<br>
>>>>> understand how the softwares/black boxes work. Also, I imagine that for<br>
>>>>> helical reconstruction, like for any inverse problem, there are many<br>
>>>>> different methods for recovering the quantit(y/ies) of interest and that<br>
>>>>> people usually are hesitant to openly aside with particular approach may<br>
>>>>> it be the right one or obviously the wrong one (e.g. Bayesian vs.<br>
>>>>> Frequentist interpretation of statistics) ;).<br>
>>>>><br>
>>>>><br>
>>>>><br>
>>>>> ma, 2016-02-29 kello 12:13 -0500, Michael Radermacher kirjoitti:<br>
>>>>><br>
>>>>>> I would contact the people in Albany and also<br>
>>>>>> discuss with them the problem you are having<br>
>>>>>> with your version.<br>
>>>>>><br>
>>>>>> Michael<br>
>>>>>><br>
>>>>>> On 2/29/2016 11:46 AM, Johannes Haataja wrote:<br>
>>>>>><br>
>>>>>>> Hi,<br>
>>>>>>> does anyone know where to obtain old versions of SPIDER, namely v.<br>
>>>>>>> 21.02? The oldest from download page is 21.11. The reason for asking is<br>
>>>>>>> that I need and older SPIDER version to test IHRSR++ v. 1.5 tutorial<br>
>>>>>>><br>
>>>>>>><br>
>>>>>>> <a href="http://cryoem.ucsd.edu/wikis/software/start.php?id=ihrsr" rel="noreferrer" target="_blank">
http://cryoem.ucsd.edu/wikis/software/start.php?id=ihrsr</a><br>
>>>>>>><br>
>>>>>>><br>
>>>>>>> to exclude the possibility that the errors I run into (in the final<br>
>>>>>>> reconstruction step) have something to do with SPIDER version.<br>
>>>>>>><br>
>>>>>>> My best,<br>
>>>>>>> - J.<br>
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>>> =================================<br>
>><br>
>> --<br>
>><br>
>><br>
>><br>
>> Edward H. Egelman, Ph.D.<br>
>><br>
>> Harrison Distinguished Professor<br>
>><br>
>> Dept. of Biochemistry and Molecular Genetics<br>
>><br>
>> University of Virginia<br>
>><br>
>> phone: <a href="tel:434-924-8210" target="_blank" value="+14349248210">434-924-8210</a><br>
>><br>
>> fax: <a href="tel:434-924-5069" target="_blank" value="+14349245069">434-924-5069</a><br>
>><br>
>> <a href="mailto:egelman@virginia.edu" target="_blank">egelman@virginia.edu</a><br>
>><br>
>> <a href="http://www.people.virginia.edu/~ehe2n" rel="noreferrer" target="_blank">
http://www.people.virginia.edu/~ehe2n</a><br>
>><br>
>> _______________________________________________<br>
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><br>
> ---<br>
> Esther Bullitt, Ph.D.<br>
> Dept. of Physiology & Biophysics<br>
> Boston University School of Medicine<br>
> 700 Albany Street, Room W302<br>
> Boston, MA 02118-2526<br>
><br>
> Email: <a href="mailto:bullitt@bu.edu" target="_blank">bullitt@bu.edu</a> <mailto:<a href="mailto:bullitt@bu.edu" target="_blank">bullitt@bu.edu</a>><br>
> Telephone: <a href="tel:617-638-5037" target="_blank" value="+16176385037">617-638-5037</a><br>
> Facsimile: <a href="tel:617-638-4041" target="_blank" value="+16176384041">617-638-4041</a><br>
> <a href="http://www.bumc.bu.edu/phys-biophys/faculty/bullitt" rel="noreferrer" target="_blank">
http://www.bumc.bu.edu/phys-biophys/faculty/bullitt</a><br>
><br>
><br>
><br>
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<br>
--<br>
<br>
<br>
<br>
Edward H. Egelman, Ph.D.<br>
<br>
Harrison Distinguished Professor<br>
<br>
Dept. of Biochemistry and Molecular Genetics<br>
<br>
University of Virginia<br>
<br>
phone: <a href="tel:434-924-8210" target="_blank" value="+14349248210">434-924-8210</a><br>
<br>
fax: <a href="tel:434-924-5069" target="_blank" value="+14349245069">434-924-5069</a><br>
<br>
<a href="mailto:egelman@virginia.edu" target="_blank">egelman@virginia.edu</a><br>
<br>
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