Rotate particle locations

Particle Picking
1

Is there a way to rotate particle locations 90 degrees (falcon4 data) for re-extraction using cryosparc, pyem, or any other tool? Motioncor rotated the output mics and now I want to transform the particle picks for extraction with a different alignment program.
Thanks!

2

Hi @cryofun!

You can rotate particles using cryosparc-tools using the following transformation:

direction = "clockwise" # either clockwise or counterclockwise

if direction == "counterclockwise":
    new_x = 1 - particles["location/center_y_frac"]
    new_y = particles["location/center_x_frac"].copy()
elif direction == "clockwise":
    new_x = particles["location/center_y_frac"]
    new_y = 1 - particles["location/center_x_frac"].copy()

particles["location/center_x_frac"] = new_x
particles["location/center_y_frac"] = new_y

You could then save this dataset with rotated particles as described elsewhere.

As with any time you manipulate particle metadata, I’d recommend double-checking that the results are what you expect, perhaps with a 3D reconstruction of extracted particles. It’s also probably worth ensuring that the micrographs have only been rotated and not reflected in some way.

I hope that helps!