Import of particle coordinates (v2)

Import and Export
1

Hi,

Is there a way to import particle coordinates (not stacks) into cryoSPARCv2 in order to do particle extraction/local motion correction within cryoSPARCv2? If not, are you planning to incorporate this feature? Thanks.

Simon

2

Using Import Particle Stack, you can import the particles.star (from RELION extraction job) or other data.star to cryoSPARC. Just remember to check the option “Ignore raw data” and let cryoSPARC know the “Source Micrographs”.

-Xing

3

Hi Xing,

thanks a lot for the info!

Simon

4

Hi,

I’m also trying to import particles from RELION to do local refinement. But the rlnAngleRot, rlnAngleTilt, rlnAnglePsi, rlnOriginX, rlnOriginY were not imported from the .star file, and the local refinement had the following error:

Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 49, in cryosparc2_compute.run.main
File “cryosparc2_compute/jobs/runcommon.py”, line 325, in check_default_inputs
assert False, 'Non-optional inputs from the following input groups and their slots are not connected: ’ + missing_inputs + ‘. Please connect all required inputs.’
AssertionError: Non-optional inputs from the following input groups and their slots are not connected: particles.blob, particles.alignments3D. Please connect all required inputs.

I’m wondering how to get around this problem? I tried the “Ignore raw data” above for the import particle stack jobs, but the alignment information was still missing.

Best regards,
Yuxi

5

Hi Xing,

Can we import .box coordinate files into cryosparc?
Import particle stack might do this job but I can’t figure out what input files I should put into which input box.

Detailed instruction would be greatly helpful.
Thank you.

Uhnsoo

1 Like
6

Dear Xing,
How do I ‘let cryoSPARC know the “Source Micrographs”’? Which option do I need to check? Thanks!
Dijun Du

2 Likes
7

Hello,
I am also having some trouble importing relion particle locations. I get the following:

Traceback (most recent call last): File “cryosparc2_master/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main File “cryosparc2_compute/jobs/imports/run.py”, line 180, in run_import_particles assert qname in inv_index_source, “Could not find match for %s” % qname AssertionError: Could not find match for FoilHole_16503757_Data_16504323_16504324_20181116_1111_Fractions.mrc

I assume I have a path wrong (probably the source like mentioned earlier)?

Thank you for your time!

8

I also would like to know this. I imported the star file from relion (corresponding to relion-aligned images) but now I’m wanting to re-extract from cryosparc-aligned images. I get the error “slot particles.location must be connected”.

I even tried going back to the relion star file and changing the micrograph locations to point to the cryosparc “…rigid.align.mrc” microgaphs.

Have been struggling for a while with this, any help appreciated.

9

Closing as solved here: How to import particles from relion