[3dem] IHRSR++ and SPIDER 21.02

Sun Mar 6 05:34:28 PST 2016

But what you wrote is not a selection rule! What you wrote is a 
description of a helix in terms of u/t, where u (units) and t (turns) 
are both forced to be integer. The "selection rule" is l=tn + um. The 
problem with the integer ratios is that they do not simply provide 
visual meaning. From my 2007 J. Structural Biology review about IHRSR:

"Consider an example with actin. For “u/t=13/6”, the helical repeat is 
355Å, and
the angle between subunits is 166.1538°. But now change the twist 
between subunits by 0.128°, so the angle is
166.2818°. The symmetry is now most simply expressed as
u/t=1299/600, and the helical repeat changes from 355Å to
35,463Å! This argues that the classical formalism generates
an ill-conditioned problem."

So it is worth getting into this.
Regards,
Ed

On 3/6/16 8:25 AM, Bullitt Esther wrote:
> Are we really going to get into this?
>
> I am in general a reasonable person, and I still find selection rules 
> to be a good way to get an intuitive feeling for the structure of a 
> helical filament.
>
> Is it the be-all, end-all?  Of course not.
> Is it a useful approximation as a start for understanding the biology? 
>  Yes, it  is.
> For example, if one determines that filaments you analyze range from 
> 13 u/ 6 t    to  11u / 5 t, that gives a visual meaning to how much 
> the filament tightens/loosens while performing its functions. 
>  Necessary for structure determination?  Not really.  Helpful?  In my 
> opinion, yes.
>
> In addition to the references Ed suggested, I am a fan of Murray 
> Stewart's 1988 article, 'Computer Image Processing of Electron 
> Micrographs of Biological Structures with Helical Symmetry' , in J 
> Electron Microscopy Technique 9:325-358
>
> Sincerely,
> Esther
>
> On Mar 5, 2016, at 10:36 AM, Edward Egelman <egelman at virginia.edu 
> <mailto:egelman at virginia.edu>> wrote:
>
>> 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
>>
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>
> ---
> Esther Bullitt, Ph.D.
> Dept. of Physiology & Biophysics
> Boston University School of Medicine
> 700 Albany Street, Room W302
> Boston, MA  02118-2526
>
> Email: bullitt at bu.edu <mailto:bullitt at bu.edu>
> Telephone:  617-638-5037
> Facsimile:  617-638-4041
> http://www.bumc.bu.edu/phys-biophys/faculty/bullitt
>

-- 

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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