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The missing wedge effect leads to distortions of the density maps in real spaces.
The missing wedge effect leads to distortions of the density maps along the tilt-axis.
Our simulated subtomograms therefore contain a wedge-shaped region in reciprocal space for which no structure factors have been measured (i.e. the missing wedge effect), resulting in distortions in the density map as observed in the experimental measurements.
Besides the low resolution and SNR of subtomograms, distortions due to missing data (ie, the missing wedge effect) make subtomogram alignment challenging, and these effects must be explicitly considered in the alignment process.
In general, is not possible to definitively assign the fringe of density to a specific number of glycoprotein spikes, given the low signal-to-noise levels, lack of complete density information because of the missing wedge effect, and the likely non-canonical HA spike morphology.
WMD-corrected PCA, which attempts to compensate for the missing wedge effect in the electron cryotomogram, and k-means clustering was performed using PEET.
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As a result our data contains a wedge-shaped region in Fourier space for which no data has been measured (missing wedge effects), similar to experimental measurements.
We test our approach on realistically simulated cryo electron tomograms including low resolution, high levels of noise and distortions due to missing wedge effects and electron optical factors.
DOI: http://dx.doi.org/10.7554/eLife.03600.008 The orientation of our crystals prevented the full sampling of reciprocal space leading to systematic incompleteness (missing wedge or missing cone).
This amplitude decrease with N should not be interpreted as a real effect: artifacts from the missing wedge induce a deceptive contrast into the reconstructions, with for instance white fringes around the darker features in the XY view (Fig. 4A, FBP N = 1).
Despite the recent progress in the field of reconstruction and regularization techniques, the missing wedge artefacts remain untreated in most current reconstruction workflows in structural biology.
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