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What you look at is difference density; you see how different is the picture I actually determine from what I would've expected if they were truly just spherical atoms, undistorted.
So that's the difference density.
And there is the electron difference density.
The cryo-EM difference density for the Cor is shown as green mesh.
So this map that I'm showing you here is a difference density map.
For clarity, cryo-EM density for the entire ribosome and mtIF2 has been subtracted from map 2 in Chimera and the difference density is carved 10 Å around our modelled mRNA (contour levels are 10 and 15σ).
One of these subdomains contains a four-cysteine motif that appears to be involved in metal binding as revealed by anomalous difference density.
Difference density maps between gp3 rings containing full-length and C-terminally truncated subunits are consistent with localization of residues 143 152 along the central channel of the nonameric ring.
d f: Phase difference density (see text) for the three oscillators with equivalent PRCs.
From this definition it can be seen that smaller values of Z indicate a larger degree of coherence, and taller, narrow peaks in the phase difference density plot.
A perhaps simpler way to visualize the coherence between the output spike trains comes from the phase difference density, shown in Fig. 3d f.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com