[3dem] IHRSR++ and SPIDER 21.02

[Edward Egelman]

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

President

Biophysical Society

phone: 434-924-8210

fax: 434-924-5069

egelman at virginia.edu

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

icture

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