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

Carlos Oscar Sorzano coss at cnb.csic.es
Mon Jan 14 00:32:51 PST 2013

Dear Alexander,

in Xmipp you may try two different ways (not exclusive):
- CL2D to see if the clustering alone is already able to separate the 
different classes and clearly show the symmetry of each one.
- Align all particles, and then perform a rotational spectra analysis 
(the peaks of the spectra will tell you the rotational symmetry of the 
images). Note that this rotational spectra analysis can be performed on 
any of the classes that comes out of CL2D.

Kind regards, Carlos Oscar

El 11/01/2013 21:14, Alexander Aleshin escribió:
> 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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Carlos Oscar Sánchez Sorzano                  e-mail:   coss at cnb.csic.es
Biocomputing unit                             http://biocomp.cnb.csic.es
National Center of Biotechnology (CSIC)
c/Darwin, 3
Campus Universidad Autónoma (Cantoblanco)     Tlf: 34-91-585 4510
28049 MADRID (SPAIN)                          Fax: 34-91-585 4506

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