[3dem] IHRSR++ and SPIDER 21.02

Wed Mar 30 08:16:23 PDT 2016

This is an incredibly belated reply. I never responded at the time since 
I did not want to beat a living horse (I had assumed that the horse was 
dead, but I was quite wrong). But a discussion I had yesterday made me 
realize that a response might be useful. Esther has raised that knowing 
that a structure can vary from 13 subunits in 6 turns to 11 subunits in 
5 turns provides a helpful description of the variability. This is only 
a change in twist, which is from 166.15 degrees per subunit (13/6) to 
163.64 degrees per subunit (11/5). But how useful is it describing the 
variability in twist in terms of a repeat either every 5 or 6 turns? A 
structure with 24 subunits in 11 turns would be between these two, and 
have 165.0 degrees rotation per subunit. A structure with 46 subunits in 
21 turns would have 164.35 degrees, also between 13/6 and 11/5. As would 
174/80, 186/85, 291/134, etc. If it is obvious to anyone that all of 
these ratios fall within Esther's range, then I am the one who is 
challenged. Simply stating at the outset that the twist ranges from 
163.64 to 166.15 degrees is much easier, more intuitive and much more 
helpful (in my opinion).
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
>
>
>
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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 
<http://www.people.virginia.edu/%7Eehe2n>

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