(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?
The PLT that is written out by the cmd line program is a legacy from a long time ago, and is written out in a format that IMAGIC can read. I am pretty sure to do the conversion, you need to do :-
cistem_x_coord = column 2 in plt file.
cistem_y_coord = (image y size in angstroms) - column 1 in plt file
Please let me know if this doesn't work.
thanks for the hint! Indeed converting from Imagic convention solves the problem! The only thing is plt coordinates are in pixels.