Domask
Switch, deciding if the non-crystal areas in the image should automatically be masked.
Domask is a boolean switch that decides if the script Unbend II should automatically mask the non-crystal areas in the image.
If this switch is set to “yes”, then the Unbend II script will use the program quadserchk_2dx to automatically mask the non-crystal areas in the image, and replace these with the average grey value, leaving the crystal with tapered edges in the image. Unbend II will also change the imagename, by adding the letter “m” at the beginning. After this has been done, the entire image processing needs to be restarted. All steps can now be done better, since the FFT has a higher signal-to-noise ratio. The only step that is done best with the non-masked image is the determination of the defocus, especially of the local defocus in the 7×7 tiles over the image. This step Determine CTF is therefore always done using the image as defined in the variable nonmaskimagename, which always remains at the non-masked image name.