Q : I have done a few eotests on different reconstructions. Do you know how the information in the fsc.eotest output file relates to the bold black EOTEST line that shows up in the FSC curve? I could be wrong, but they don't seem to be the same in my reconstructions. A colleague seemed to think it could be something to do with the A/pix in the .mrc file being different to the one I am entering in EMAN to create the convergence plot and bring up the FSC curve...
A : They are one and the same, but the x-axis (s axis) is rescaled when plotted from inside eman in the convergence plot. In the fsc.eotest file, the 1st column is expressed in pixels in Fourier space. Since Nyquist frequency corresponds to 1/2 the box size and is 2*A/pix, the conversion factor is column 1 /(apix * box size).