Volume reconstruction

3D Reconstruction
1

Dear colleagues,

Is there a way to reconstruct the volume using the particles with different box size from where the initial 3D refiment was perfomed without need to repeat the 3D refinement?

Thank you.

Kind regards,
Dmitry

2

Hi @Dmitry,

Are you looking to reconstruct the volume in a different pixel size? If you haven’t tried, you might wanna try changing Reconstruction box size (voxels) in Homogeneous Reconstruction Only.

If you would like to crop/pad the particles while keeping the pixel size consistent, I’d set up a downsample job and change Crop / pad to box size (pix) to your desired box size. Don’t forget to set Fourier crop to box size (pix) to the new box size for cropping/padding to work. After the downsample job, run Homogeneous Reconstruction Only for the reconstruction.

Best,
Kookjoo

2 Likes
3

Hello @kookjookeem,
Thank you for your answer.

Could you please clarify.

  1. I need to extract the correspondent particles with desirable new box size.
  2. Run the Homogenious Reconstruction Only with the particles from 1.
    Is that correct?

But how can I be sure that the alignment information was applied to the newly extracted particles?
Some programs proposing to apply the alignment on the newly extracted dataset. I am not sure I know how to perform that in the CS.

I tried to run the Homogenious Reconstruction Only right away specifying the larger box size in the settings

image
image438Ă—896 98.1 KB

But the program failed with the following error.

Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 95, in cryosparc_master.cryosparc_compute.run.main
File “cryosparc_master/cryosparc_compute/jobs/refine/newrun.py”, line 1152, in cryosparc_master.cryosparc_compute.jobs.refine.newrun.run_homo_reconstruct
File “cryosparc_master/cryosparc_compute/engine/newengine.py”, line 3267, in cryosparc_master.cryosparc_compute.engine.newengine.reconstruct
File “cryosparc_master/cryosparc_compute/engine/newengine.py”, line 3274, in cryosparc_master.cryosparc_compute.engine.newengine.reconstruct
File “cryosparc_master/cryosparc_compute/engine/newengine.py”, line 378, in cryosparc_master.cryosparc_compute.engine.newengine.EngineThread.setup_comparison
AssertionError

Thank you.

Kind regards,
Dmitry

4

I don’t think homogeneous reconstruction will do box padding.

Correct.

If you re-extract using the output from the 3D refinement, the 3D alignments will be passed through so a homogeneous reconstruction will work immediately.

2 Likes