(1) I ran find_particles from cmdline and got plt file out with coordinates presumably in Angstroms. If I import them in cisTEM GUI and display, they do not make sense at all.
However, if I run find particles with the exact same parameters through cisTEM GUI, it displays nicely picked particles (but this doesn't produce any plt). The cordinates are completely different inside the sqlite compared to (1). Any ideas what I'm missing?