Processing an individual image
With parameters set appropriately you are ready to begin image processing.
The scripts on the left represent individual processing steps which need to be performed to fully process an image.
Calculate FFT begins image processing by calculating the initial Fourier transform of a tapered version of your original image. Additionally it alters any parameters, which are obviously incorrect in the database. In particular the image side length will be automatically corrected to the correct length and the non-masked image name will be changed to match up to an appropriate value if the specified file can’t be found. To begin processing select any number of scripts via the shift key to select contiguous blocks, or the control (command on Mac) key to additionally select individual scripts. While Get Defocus & Tilt, Get Lattice & Tilt and Get Spotlist are optional in order to generate a final map, the rest of the standard scripts are not. The former merely automate the process of automatically determining parameters relevant to unbending and CTF correction as well as determining the underlying reciprocal lattice.
Whether or not these scripts are run, users always have the option to manually refine any of these parameters including the determined CTF. Automatically determined lattices then often provide a good starting point for manual lattice determination.
Any script may be run and rerun any number of times, with the results files simply overwriting previous ones.