Import particles from Relion

Import and Export
1

Dear all,

I am using cryosparc 2.4.6 and have trouble importing particles from relion3.
I extracted particles in relion and imported the particles and the star file to cryosparc v2.
Particles where extracted as black-on-white and are depicted with inversion contrast in cryosparc. So that seems to work fine.

But, I would rather like to import white-on-black since that is the usually way for other software packages. I played around with the option dark-on-light / light-on-dark and differntly inverted particles, but it seems like cryosparc really requires black-on-white particles and does the inversion internally. Could it be that the option dark-on-light / LoD is not properly working?

However, once I use these particles for either 2D or ab-initio I recieve the following error:

Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main
File “cryosparc2_worker/cryosparc2_compute/jobs/class2D/run.py”, line 148, in cryosparc2_compute.jobs.class2D.run.run_class_2D
File “cryosparc2_compute/particles.py”, line 119, in get_prepared_fspace_data
return fourier.resample_fspace(fourier.fft(self.get_prepared_real_data()), self.dataset.N) File “cryosparc2_compute/particles.py”, line 114, in get_prepared_real_data return (self.dataset.prepare_normalization_factor * self.dataset.prepare_data_sign) * (self.dataset.prepare_real_window * (self.get_original_real_data() - self[‘prepare/float_value’]))
File “cryosparc2_compute/particles.py”, line 109, in get_original_real_data
return self.blob.view().copy() # TODO!!! All the particle code assumes x is slow axis! WRONG!
File “cryosparc2_compute/blobio/mrc.py”, line 101, in view
return self.get()
File “cryosparc2_compute/blobio/mrc.py”, line 98, in get
data = n.fromfile(file_obj, dtype=self.dtype, count= n.prod(self.shape)).reshape(self.shape)
ValueError: total size of new array must be unchanged

I realized that this problem only exists when several mrcs stacks are used. Once I assembled of particles into one large mrcs stack (using particle_preproc) I can perform the the processing in cryo sparc. However, I would rather keep the organization of mrcs-stack per micrograph for bookkeeping reasons.

To sum up:
Is it possible to import mrcs stacks with white-on-black contrast
What is the problem with this error.

I realize that it is a long post, but I assumed that both problems are related.
All the best
Ferdinand

2

I am now using one large stack instead of several small ones and everything works now. The contrast is also correctly recognized.

3

Dear FerdKrupp,

Would you mind to show me how to assemble particles into one large mrcs stack using particle_preproc? Thanks!

Dijun Du

4

This should not be necessary - I routinely import from star files with per-mic stacks

However, making a single stack/star is useful sometimes for portability:
relion_preprocess --operate_on in.star --operate_out output_rootname

Cheers
Oli

5

It works for me now. Thank your very much!
Dijun Du