[3dem] IHRSR++ and SPIDER 21.02

Sun Mar 6 11:31:36 PST 2016

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:

http://www.biomachina.org/courses/structures/download/derosier_handout_02.pdf

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.
Regards,
Ed

On 3/6/16 2:07 PM, Hernando J Sosa wrote:
>
> To clear up definitionsin my book describing a helix asu = X subunits 
> in t = Y turns (per axial repeat) IS the same as providing the 
> selection rule, as these are the only two variables in the selection 
> rule equation l=tn + um that fully describe the helix. With these 
> parameters (u & t) the possible Bessel orders for any layer line 
> number are determined according to the selection rule equation. 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:h=axial_repeat/u, phi=360*t/u.
>
> As discussed the problem with this selection rule definition is that 
> it arbitrarily assumes an integer number of turns and subunits per 
> axial repeat. 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).
>
> 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.Knowing the 'classical' 
> selection would also be necessary if for any reason you want to use 
> 'classical' 3D Fourier-Bessel helical 3D reconstruction packages.
>
> Best
>
> Hernando
>
> ------------------------------------------------------------------------
> *From:* 3dem [3dem-bounces at ncmir.ucsd.edu] on behalf of Edward Egelman 
> [egelman at virginia.edu]
> *Sent:* Saturday, March 05, 2016 10:36 AM
> *To:* Smith, Phillip R.; 3dem at ncmir.ucsd.edu
> *Subject:* Re: [3dem] IHRSR++ and SPIDER 21.02
>
> 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:
>
> doi:10.1088/1478-3975/7/4/045004
>
> Regards,
> Ed
>
> On 3/5/16 9:49 AM, Smith, Phillip R. wrote:
>> 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-
>>
>>> On Feb 29, 2016, at 4:39 PM, Edward Egelman<egelman at virginia.edu>  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:
>>>> 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:
>>>>
>>>>> 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:
>>>>>
>>>>>> 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
>>>>>>
>>>>>>
>>>>>> http://cryoem.ucsd.edu/wikis/software/start.php?id=ihrsr
>>>>>>
>>>>>>
>>>>>> 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.
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>> =================================
>
> -- 
>
>
>
> Edward H. Egelman, Ph.D.
>
> Harrison Distinguished Professor
>
> Dept. of Biochemistry and Molecular Genetics
>
> University of Virginia
>
> phone: 434-924-8210
>
> fax: 434-924-5069
>
> egelman at virginia.edu
>
> http://www.people.virginia.edu/~ehe2n
>

-- 

Edward H. Egelman, Ph.D.

Harrison Distinguished Professor

Dept. of Biochemistry and Molecular Genetics

University of Virginia

phone: 434-924-8210

fax: 434-924-5069

egelman at virginia.edu

http://www.people.virginia.edu/~ehe2n 
<http://www.people.virginia.edu/%7Eehe2n>

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