Hi, I looked into the discussion forum but I might have missed this topic if exists already. For making a figure for the supplementary, which includes a micrograph and its relative CTF fit, how one would do it with cryosparc ? I have taken the two images from a curate exposure job. How one would get to the scales of both micrograph and fit ? Can one crop the picture of the CTF fit to match the size of a K3 micrograph ? Many thanks !
If your micrograph is P pixels wide, and the calibration is A Å/pixels, then the micrograph is P x A angstroms wide. If you put your micrograph into whatever you use to make figures (eg Powerpoint or Illustrator), you can make the micrograph as big or small as you like, and note the final size, S, in figure inches (or whatever units). To make a 100-Å scale bar, draw a line of length L = 100 x S / (P x A).
Other may chime in and correct me if I’m wrong, but I believe you are free to make the FFT/CTF correction whatever size you like to make your figure look nice and it generally does not need a scale bar. For anyone who actually cared about the scale of the FFT, they would probably know that the half-width = 1/2A, so the FFT has a built in scale bar (provided you report A somewhere, which you should do in the methods, and provided you have not cropped the FFT).
If you do crop the FFT, you probably should add a marker, because the outer edge will no longer indicate Nyquist (1/2A). Just bear in mind that FFTs are in 1/distance units. So if you crop the FFT 1/2 as wide, the outer edge now corresponds to 1/2 x 1/2A = 1/4A.
Many thanks for your help and nice explanation @rj.edwards