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

Penczek, Pawel A Pawel.A.Penczek at uth.tmc.edu
Fri Jan 11 12:23:10 PST 2013

Dear Alexander,

while there are many packages that would allow you to analyze symmetry of a particle imaged by TEM,
there is no method that would allow you to "determine" its symmetry.  I assume by determine you
mean a "proof" or a statistical test that would allow you to claim that the particle has certain symmetry.
So far, no satisfying method was developed that would be solely based on computational analysis of imaged data
and which would allow you to make such claim.

Pawel A. Penczek, Ph.D.
Structural Biology Imaging Center, Director
The University of Texas
phone: 713-500-5416
fax: 713-500-0652

On Jan 11, 2013, at 2:14 PM, Alexander Aleshin <aaleshin at sanfordburnham.org> wrote:

> Could anybody advice me about a way/software to analyze a symmetry of a ring particle imaged by negative staining TEM. The actual symmetry (number of subunits in a ring) is not known, but appears to be within a range of 14-20 subunits per a particle. The number of subunits may also vary  from a particle to  particle. I've got about a thousand projections  with a symmetry axis being perpendicular to the image, but the staining appears to deform particle shapes. As a result, the symmetry of class averages is not obvious.
> I am an EM novice, just learned EMAN2 workflow, but I have some experience in structure analysis by Xray crystallography.
> Regards,
> Alexander Aleshin
> Sanford-Burnham Medical Research Institute
> Infectious & Inflammatory Disease Center
> 10901 North Torrey Pines Road
> La Jolla, California 92037
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