RELION 3.0 particle pose from STAR file

relion30_particle_pose.py

import starfile
from scipy.spatial.transform import Rotation as R

particle_star_file = 'hiv/01_10.00Apx_particles.star'

df = starfile.read(particle_star_file)

# get necessary info from dataframe
xyz = df[['rlnCoordinateX', 'rlnCoordinateY', 'rlnCoordinateZ']].to_numpy()  # (n, 3)
shifts = df[['rlnOriginX', 'rlnOriginY', 'rlnOriginZ']].to_numpy()  # (n, 3)
euler_angles = df[['rlnAngleRot', 'rlnAngleTilt', 'rlnAnglePsi']].to_numpy()  # (n, 3)

# Get absolute position and orientation
particle_positions = xyz - shifts 
rotation_matrices = R.from_euler(
    seq='ZYZ', angles=euler_angles, degrees=True
).inv().as_matrix()  # (n, 3, 3)