Hi Rasmus,
First:
Thank you for sharing your question on the forum!
Yes that is the case it seems with around 3Å and 1.5Å resolution. But it’s considering nominals only, and while you may have less than average signal transfer around these resolutions, deviation from nominal target defocus should lift these up a bit.
It’s also important to note that as long as it is not truly so close to zero, if it is measured correctly, the CTF correction will restore this amplitude because this curve is used to divide the power spectrum of the raw average structure.
So the third graph, the one titled “Resolution Threshold for Aliasing”, shows for a given field of view (given in box size (px) assuming the selected pixel size) what resolution the CTF has a frequency above Nyquist (starts to alias). If the circle is above the exponential falloff or to the right of where the curve falls to zero, then you have no aliasing concerns for the selected resolution. In your attached case you don’t have any aliasing even to Nyquist (if you imagine bringing the open circle straight down).
If the open circle is below the exponential fall-off part of the curve and to the left of where the curve falls to zero then you have aliasing at the selected resolution. This is shown in the picture below where for a box size of 128 and a pixel size of 1Å the CTF is only faithful out to around 2.9Å and is undergoing aliasing at the selected 2Å resolution:
The fourth graph, the one titled “Minimum Boxsize to Avoid Aliasing” shows for a given pixel size what box size you need to avoid aliasing at Nyquist, so again its is similar to imagining the third graph with the open circle fixed at Nyquist. If the open circle is above (or outside to the left) of the hump of the curve then the CTF is correct all the way out to Nyquist as is true in the case you have shown.
If the open circle is below the hump as in the photo below then I need to increase my box size to preserve the CTF. In the photo below I need a box size of at least 168px to avoid aliasing out to Nyquist, or if I don’t expect around 3Å resolution I could decrease the magnification a step and as long as it is larger than 1.2Å pixel size then I’d be in the clear.
Yes, if you have a fixed pixel size then you can only interpret the graph vertically by increasing box size to affect the aliasing. However if you are not fixed to a particular magnification you can adjust your position laterally by changing the mag.
No, you don’t have any aliasing for this box size and pixel size at all, as the open circle is above all of the curves.
Yes you are losing some signal on the edges due to delocalisation, however you are only losing half of the power (as delocalisation moves the signal in opposite directions) since the delocalisation is less than the box size. It just means you need more particles than if all of the signal fit in the box. However, boxes are rarely large enough to fit all of the signal as this graph lets you appreciate, and we just make up for it with more particles.
Discord has some restrictions when you first start using the forum to prevent things like spam, but I will look into changing the number of images that can be posted.
Hope all of that is helpful, and if anything was unclear let me know and I am happy to explain further or to try again in another manner.