[3dem] Anisotropic resolution

[Misha Kudryashev]

Dear Benjamin, Dear colleagues,


I think it is rather simple to estimate resolution anisortopy using Fourier
Shell Correlation within cones in Fourier space pointing to different
directions. For each cone you can estimate the resolution (using an FSC
threshold) and visualize resolutions for each cone on a unit sphere. We had
a bovine respirasome molecule with preferential orientation on an EM grid (
http://www.ncbi.nlm.nih.gov/pubmed/21876144). The resulting structure had
an anisortopic resolution which we estimated in Supplementary Figure 1 of
that paper.


If the two half-maps are statistically independent a lower threshold could
be used. This is easy to program; we did this with an early version of
Dynamo (Daniel Castano-Diez programmed it), but any software or a
validation server may have such functionality.


Best regards,

Misha

2015-08-24 15:44 GMT+02:00 Benjamin Himes <himes.benjamin at gmail.com>:

> Dear colleagues,
>
> I hate to stir the pot on the resolution discussion, however, I have a
> question regarding any progress on analyzing the anisotropy potentially
> present in a 3d em map.
>
> Aside from some discussion on 3d ssnr, particularly by P.P. and a recent
> paper on 3d covariance estimation from J.F. Has anybody tried to implement
> a concrete way of assessing this issue?
>
> I am particularly concerned with maps generated from subTomogram averaging
> and classification: even with an angular distribution that is well sampled,
> I am concerned about the fact that cumulative dose, and increased sample
> thickness on tilting create a situation where the individual projections do
> not have equivalent SNR and therefore a simple plot of angular
> distributions would not accurately reflect the quality of the sampling in
> Fourier space.
>
> It seems a 3d SSNR might work, but the interpretation of such a plot,
> beyond its "potato" like quality, even in terms of the eigenvalues of the
> principle axes is not immediately clear to me.
>
> Many thanks,
>
> Benjamin Himes
>
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>


-- 
Misha Kudryashev, PhD
Biozentrum, University of Basel
Mattenstrasse 26
CH-4058 Basel, Switzerland
tel: +41 61 387 32 32
email:mikhail.kudryashev at unibas.ch
web: www.c-cina.unibas.ch
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