Data sign inversion on local motion correction?

Motion Correction
1

Hi

It’s not that important, but I have a question about Local Motion Correction and pyem

I’m using cryoSPARC v3.3.1+220215 and pyem v0.4

I’ve noticed some differences between the general Motion correction (patch motion, motioncorr2, etc) and Local Motion Correction on cryoSPARC when pyem converts .cs to .star

If I convert the 2D or 3D job from LocalMotion extract particles .cs to .star, relion_reconstruct command gave me a very weird 3D volume. It looks like a inverted density on the positive threshold so I subtract them from box density.

sub2
sub21803×609 147 KB

then, I re-import the .star from pyem on cryoSPARC and 2D class. It seems that the sign is definitely inverted.

(for example)

2d
2d740×316 69.7 KB

This could be solved by changing the data sign on Particle Improt tab

sparc
sparc2000×313 182 KB

Inversion of data sign come from Local Motion Correction or pyem conversion ? I can’t find something about the particle sign in .star file…

What should I do if I want to use the Local Motion Corrected particles from cryoSPARC directly to the RELION classification ?

Thank you!

2

Thank you for the detailed exposition. cryoSPARC Local motion correction outputs particles with a different data sign when compared to other motion correction job types. cryoSPARC tracks the sign information internally in the blob/sign field of “*.cs” files. Inspection and manipulation of “*.cs” files is described in a tutorial. There may be a way to inform Relion about that sign change.

3 Likes
3

Thank you! @wtempel
I will edit the .cs file with python described in the tutorial.

4

Hello @wtempel

I’m sorry for the delay in the feedback due to the busy experimental schedules from the last reply.
Now, I try to edit .cs with python described in a tutorial.

In general motion_correct jobs,
the blob/sign value of particles.cs is array([-1., -1., -1., …, -1., -1., -1.], dtype=float32)

and then, the localmotioncorrected particle.cs has array([1., 1., 1., …, 1., 1., 1.], dtype=float32)

yes, It has a different sign you mentioned above

so, I edit like this
new_sign_array = particle_dataset.data[‘blob/sign’] * -1
particle_dataset.data[‘blob/sign’] = new_sign_array
particle_dataset.to_file(dataset_path)

I checked the blob/sign was converted to +1 sign after this command.
then, I make a .star file with pyem for relion

But, I re-import the sign_inverted.star to cryoSPARC for sign validation, It still looks flipped sign in 2D :frowning:

Need another conversion in particles.cs generated by localmotioncorrected particles ??
thank you!

5

To avoid confusion during further discussion, please can you

  1. post the header plus lines for perhaps one or two particles from sign_inverted.star
  2. describe the last and next-to-last steps that produced sign_inverted.star
  3. post a screen shot of the cryoSPARC re-import job’s Inputs and Parameters tab

Thanks.