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

Philip Köck Philip.Koeck at ki.se
Mon Jan 14 01:05:33 PST 2013

Maybe the staining doesn't actually deform the particles that much. Another reason for the lack of
obvious symmetry in your class averages could be that you don't actually have very many top views.
Maybe most of you particles are slightly tilted.
If you have side views as well you might want to record more particles and attempt a 3D-reconstruction.
You could do this without applying symmetry and then see what it looks like.
Or you test all symmetries that are possible either individually (and then compare results) or in
a multirefinement procedure. For the latter you need many more particles than 1000. 7000 might do
for seven different symmetries.
Of course none of this proves anything, as Pavel points out, but it might give you indications.


-----Original Message-----
From: 3dem-bounces at ncmir.ucsd.edu [mailto:3dem-bounces at ncmir.ucsd.edu] On Behalf Of Penczek, Pawel A
Sent: 11 January 2013 21:23
To: Alexander Aleshin
Cc: <3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] How to determine a symmetry of a ring particle?

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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> 3dem at ncmir.ucsd.edu
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