[3dem] How to determine a symmetry of a ring particle?

[Penczek, Pawel A]

Hi,

the method described in the paper mentioned below, while strives to build a statistical test, 
neglects the fact that alignment compromises statistical independence of noise and signal.
As a result, the t-test as proposed in the paper is not applicable.

Regards,
— 
Pawel A. Penczek, Ph.D.
Professor
Structural Biology Imaging Center, Director
The University of Texas
phone: 713-500-5416
fax: 713-500-0652
http://www.uth.tmc.edu/bmb/faculty/pawel-penczek.html




On Jan 14, 2013, at 9:46 AM, Bernard Heymann <bernard_heymann at nih.gov> wrote:

> Dear Alexander 
> 
> Another alternative is the method used in:
> Ultramicroscopy. 1995 Sep;60(2):219-28
> 
> It can handle polymorphism.
> 
> You can find the application here:
> http://lsbr.niams.nih.gov/lsbr/RotaStat.html
> 
> Best
> 
> Bernard
> 
> --------------------------------------------------------------------------------------------------------------------
> J. Bernard Heymann Ph.D.
> LSBR/NIAMS/NIH
> Rm 1515, 50 South Dr, NIH
> Bethesda MD 20892-8025
> Tel. 301-451-8241
> 
> 
> 
> 
> On Jan 14, 2013, at 4:30 AM, Philip Köck <Philip.Koeck at ki.se> wrote:
> 
>> That’s another good idea.
>> You might actually have eigen images already. They could be one of the outputs of the 2D classification
>> you did in Eman.
>> Look at Dube et al. to learn how to interpret the eigen images, if you find them.
>>  
>> From: 3dem-bounces at ncmir.ucsd.edu [mailto:3dem-bounces at ncmir.ucsd.edu] On Behalf Of michael
>> Sent: 14 January 2013 10:23
>> To: 3dem at ncmir.ucsd.edu
>> Subject: Re: [3dem] How to determine a symmetry of a ring particle?
>>  
>> Dear Alexander,
>> 
>> Dube et al. 1993 are using multivariate statistical analysis (MSA) to estimate the symmetry properties by looking at the eigenimages.
>> 
>> A description of the method can be found here: www.singleparticles.org/methodology . You can download the PDF file "Multivariate Statistical Analysis in Single Particle (Cryo) Electron Microscopy". The related chapter is "12. MSA symmetry analysis".
>> 
>> The original paper is: Dube P, Tavares P, Lurz R and van Heel M EMBO J. (1993) 1303-1309.
>> 
>> I also want to refer to Pawel's hint: the method is a symmetry estimation and not a determination.
>> 
>> Regards
>> Michael
>> 
>> 
>> -- 
>> 
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