[3dem] [ccpem] 2D centering of particle images

[Philip Koeck]

Hi.

Another question you might want to think about is what you actually mean by center of geometry, but maybe you have already.
Most views even of symmetric particles will not be symmetric so the only center you can define is the center of gravity, which is very sensitive to noise. If the views are symmetric you can use that symmetry to find the position of the symmetry axis.

All the best,

Philip

-----Ursprungligt meddelande-----
Från: 3dem [mailto:3dem-bounces at ncmir.ucsd.edu] För Marin van Heel
Skickat: den 24 juli 2018 12:34
Till: Wang, Steven; CCPEM at JISCMAIL.AC.UK
Kopia: 3dem at ncmir.ucsd.edu
Ämne: Re: [3dem] [ccpem] 2D centering of particle images



Dear Steven Wang,

Alignment is more of a statistical issue affecting the whole data set than something that should be done on an individual (noisy) particle-by-particle basis.
See, for example, our: "Alignment By Classification" (ABC) paper: 
http://journals.iucr.org/m/issues/2017/05/00/kf5002/index.html

But our IMAGIC-4D software does of course have various options to do it particle-by-particle if that is what you insist you need for testing.

Cheers

Marin van Heel



On 23/07/2018 19:29, Wang, Steven wrote:
> Dear all,
>
> Do you know any software available for aligning the center of geometry of each selected particle to the center of the particle-selection box? I need this centering for testing some algorithms, not for the regular cryo-EM map construction workflows. Thanks.
>
> Steven Wang
>

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