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

[Bernard Heymann]

Pawel is right - in an anal retentive way. However, the alignment is just translational and does not change the nature of the noise. Also, the amount of shift is dependent on how well the particle was picked. So if you want to leave out the alignment, you just have to pick the particle very carefully. So in practice, it is splitting hairs to call it statistically invalid.

I applaud the people who had positive suggestions. I would suggest that you try different methods and see whether you get reasonable results. The RotaStat program did produce useful results and is worth a try.

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 10:55 AM, "Penczek, Pawel A" <Pawel.A.Penczek at uth.tmc.edu> wrote:

> 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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