[3dem] IHRSR++ and SPIDER 21.02

Sun Mar 6 05:25:29 PST 2016

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> 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
Telephone:  617-638-5037
Facsimile:  617-638-4041
http://www.bumc.bu.edu/phys-biophys/faculty/bullitt

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