Extraction of old particle set after Patch motion and Patch CTF

Particle Picking
1

Hello

I am using version 2.13.2
I previously selected particles from averaged images.
then I ran patch motion correction and patch CTF refinement on the corresponding movies and
I am trying to re-extract the set of particles with patch_ctf_extract, but I get an error message:

License is valid.
Running job on master node
[CPU: 93.9 MB] Project P1 Job J277 Started
[CPU: 93.9 MB] Master running v2.13.2, worker running v2.13.2
[CPU: 94.0 MB] Running on lane default
[CPU: 94.0 MB] Resources allocated:
[CPU: 94.0 MB] Worker: xxx
[CPU: 94.0 MB] --------------------------------------------------------------
[CPU: 94.0 MB] Importing job module for job type patch_ctf_extract...
[CPU: 191.5 MB] Job ready to run
[CPU: 191.5 MB] ***************************************************************
[CPU: 1.47 GB] Traceback (most recent call last): File "cryosparc2_master/cryosparc2_compute/run.py", line 78, in cryosparc2_compute.run.main File "cryosparc2_master/cryosparc2_compute/jobs/ctf_estimation/run.py", line 411, in cryosparc2_compute.jobs.ctf_estimation.run.run_extract AssertionError: Missing exposure with uid 510393884642721793

Outputs
particles
particleCount: 0

is this a problem of file naming? if yes, is there a way to change this?
Thanks

2

Hey @valbibpc,

So if I’m understanding correctly, you had particles in cryoSPARC that you wanted to re-extract. You then did patch motion correction which created new averaged micrographs, and did Patch CTF Estimation on those. If you already have the particle locations, you can use the “Extract from Micrographs” job, connect the micrographs from the Patch CTF Estimation job and connect your particles, and it should extract them. Let me know if I got that right.

3

hi sarulthasan

in fact I want to improve the particles in a similar way to polishing in Relion.
I have already tried Extract from micrographs and here is what it says:

[CPU: 683.1 MB] Starting multithreaded pipeline …

[CPU: 692.2 MB] Started pipeline

[CPU: 960.2 MB] GPU 0 using a batch size of 512

[CPU: 960.7 MB] – 0.0: processing J272/motioncorrected/FoilHole_1856804_Data_1852382_1852383_20191004_0236-3160_patch_aligned_doseweighted.mrc

[CPU: 960.7 MB] – 0.1: processing J272/motioncorrected/FoilHole_1856804_Data_1852468_1852469_20191004_0235-3158_patch_aligned_doseweighted.mrc

[CPU: 692.3 MB] (1 of 3503) Finished processing micrograph 0. It had no particles in it.

[CPU: 1.71 GB] – 0.0: processing J272/motioncorrected/FoilHole_1856804_Data_1852475_1852476_20191004_0235-3159_patch_aligned_doseweighted.mrc

[CPU: 692.3 MB] (2 of 3503) Finished processing micrograph 1. It had no particles in it.

[CPU: 1.71 GB] – 0.1: processing J272/motioncorrected/FoilHole_1856804_Data_1852482_1852483_20191004_0232-3153_patch_aligned_doseweighted.mrc

[CPU: 692.3 MB] (3 of 3503) Finished processing micrograph 2. It had no particles in it.

[CPU: 1.71 GB] – 0.0: processing J272/motioncorrected/FoilHole_1856804_Data_1852488_1852489_20191004_0233-3155_patch_aligned_doseweighted.mrc

[CPU: 692.3 MB] (4 of 3503) Finished processing micrograph 3. It had no particles in it.

[CPU: 1.71 GB] – 0.1: processing J272/motioncorrected/FoilHole_1856804_Data_1852495_1852496_20191004_0234-3156_patch_aligned_doseweighted.mrc

[CPU: 692.3 MB] (5 of 3503) Finished processing micrograph 4. It had no particles in it.

[CPU: 1.71 GB] – 0.0: processing J272/motioncorrected/FoilHole_1856804_Data_1852500_1852501_20191004_0234-3157_patch_aligned_doseweighted.mrc

…

it doesn’t find any particles and it goes on forever like this.
maybe I am not using the right procedure.
Best