Process particles from cryolo

2D Classification
1

Hello,

I’m trying to pick particles in cryolo and importing them into cryoSPARC for further steps. The extraction from micrograph job worked but when performing 2D classifications, it raised errors as following:
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/class2D/newrun.py”, line 57, in cryosparc_master.cryosparc_compute.jobs.class2D.newrun.run_class_2D
AssertionError: CTF parameters must be connected to perform CTF correction.

I use the Patch CTF estimated micrographs as input in Extraction job.

cryosparc version 4.4
cryolo version 1.9.8

Thanks a lot.

2

Hi @Lai,

How are you getting the particles/picks into CS? Are you using crYOLO in a standalone setting and importing a .star file or are you using CS-tools to pick particles in crYOLO as described here?

Best,
Kye

3

Hi,

I use crYOLO GUI to pick particles and it generated four outputs, one of them is CRYOSPARC/cryosparc.star. The result looks like :

data_

loop_
_rlnMicrographName #1
_rlnCoordinateX #2
_rlnCoordinateY #3
_rlnAutopickFigureOfMerit #4
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 490.93841552734375 3937.248825073242 0.35988849401474
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 1771.45556640625 3947.5416717529297 0.5496110320091248
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 2919.79345703125 3952.607681274414 0.3419470489025116
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 3558.08447265625 3927.53369140625 0.7469070553779602
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 3787.430419921875 3940.988815307617 0.6527037620544434
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 3420.403564453125 3877.25341796875 0.729738175868988
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 2337.649658203125 3808.981689453125 0.2347775101661682
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 2644.262939453125 3810.0367126464844 0.20469319820404053
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 3181.429931640625 3800.4844970703125 0.2900577187538147
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 3681.886962890625 3805.6930236816406 0.3370276093482971
………………

Thanks

4

Hi @Lai,

Did you perform the steps for importing particles from crYOLO following the ones outlined in this post?

Best,
Kye

5

Hi @kstachowski ,

Thanks very much! It works now.
I did check the “ignore raw data” and “ignore pose data” as in the post you mentioned. I did not give the microscope parameters. And it finally works after giving those parameters. Those parameters ensure it use micrograph CTF as particle CTF when extracting as I only give the coordinates.

Thanks again.

Best,
Lai

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