Hi All,
I ran a Local Refinement job with the option “minimize over per-particle scale” enabled, and I obtained an image showing the distribution of per-particle scale factors in the results, as shown in the attached picture. However, after converting the particles.cs and passthrough_particles.cs files into a STAR file using pyem, I noticed that the resulting file does not contain any information about these scale factors. Initially, I thought the rlnCtfBfactor column might correspond to this parameter, but the values in this column are all zero.
Is there a way to extract this information?
Thank you!
Hi @Wayne – if you are just trying to export the per-particle scale values, you can get those using cryosparc tools. For example, the script below saves them in a .txt file (but any number of other formats are also possible).
from cryosparc.tools import CryoSPARC
import json
import numpy as np
from pathlib import Path
with open(Path('~/instance-info.json').expanduser(), 'r') as f:
instance_info = json.load(f)
cs = CryoSPARC(**instance_info)
assert cs.test_connection()
project_uid = "P345"
project = cs.find_project(project_uid)
job_uid = "J15"
job = project.find_job(job_uid)
particles = job.load_output("particles")
per_particle_scale = particles["alignments3D/alpha"]
with open(f"{project_uid}-{job_uid}_per-particle-scale.txt", "w") as f:
f.write("\n".join(str(s) for s in per_particle_scale))
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