Small beta-barrel protein alignment

3D Refinement
11

Yes of course, apologies. You’ll have to use cryosparc-tools to do this. If you haven’t used it before, you can find some guidance on installing and running it here and also here.

Once you have cryosparc-tools working, you can change the value in the fields relatively easily. Here is an example script that should work (using instance-info.json, described in the second link above):

from cryosparc.tools import CryoSPARC
import json
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_number = "P337"
workspace_number = "W14"

project = cs.find_project(project_number)

abinit_1_uid = "J119"
abinit_1_job = project.find_job(abinit_1_uid)
abinit_1_particles = abinit_1_job.load_output("particles_class_0")

aligned_abinit_2_uid = "J121"
aligned_abinit_2_job = project.find_job(aligned_abinit_2_uid)
aligned_abinit_2_particles = aligned_abinit_2_job.load_output("particles_aligned_0")

abinit_1_particles["alignments3D/split"] = 0
aligned_abinit_2_particles["alignments3D/split"] = 1

combined_particles = abinit_1_particles.append(aligned_abinit_2_particles)

external_job_uid = project.save_external_result(
    workspace_uid = workspace_number,
    dataset = combined_particles,
    type = "particle",
    name = "particles",
    title = "Combined particles"
)
project.find_external_job(external_job_uid).log(f"Combined particles from {abinit_1_uid} and {aligned_abinit_2_uid} as half-sets.")

In this case,

  • abinit_1_uid should be the UID (like “J119”) of one of your ab initio jobs
  • aligned_abinit_2_uid should be the UID of the Align 3D Maps job used to align the other abinit map to the first.

This will produce a new job which has the two particle sets, split correctly, as a single “particles” output:

image

You should be able to use these particles in a Local Refinement with one of your maps as the input volume. Be sure that Force re-do GS split is turned off!

I’ll be interested to hear how this technique works out for you!

Also, do you think you could share images of the ab initio results and the homogeneous refinement with an initial lowpass filter of 6 Å? I’m curious if I’ll be able to see anything that might indicate to me why the homogeneous refinement is not able to align the particles.