I’m writing a guide for my lab on how to get cryosparc extracted particles into RELION. I managed to get it working, but I wanted to know what exactly each restacked particle and passthrough file is doing. So far, I’ve gotten 2D classification to work with the particles and all passthrough files except for 2D and 3D alignments.
I’m tempted to just get people to include all 6 files when converting to star, but first I wanted to understand what exactly each of these .cs files are storing. Thanks!
The files were referenced by the cryosparc web interface as follows: blob, ctf, alignments 3D, filament, alignments2D, pick_stats and location.
From the institution’s directory for cryoSPARC processing, the .blob file’s path is: ./cryosparc/CS-six6so1-mutants/J539/restacked_particles.cs
All of the other files have the following path: ./cryosparc/CS-six6so1-mutants/J539/J539_passthrough_particles.cs
I identifed the files through the output tab of a “Restack Particles” on the CryoSPARC web interface. I’ve just found the csg file in the exports directory, though. It’s called J539_particles_exported.csg. The content goes as follows:
Are all of the non-blob files in the cryosparc interface just the same file?
If I wanted to export content to relion, would the csg file help with this? I’m currently using csparc2star and manually moving the restack files between cryosparc and relion project. The process works, but it’s quite involved.
For further context on the workflow before particle restacking:
The output was produced using these cryosparc jobs in the following order: import as tiff, patch motion correction, CTF correction w/ CTFFIND4, exposure curation, reference-free filament tracing, junk detector, pick inspection, particle extraction, multiple rounds of refinement by 2D classification, and ab initio reconstruction, and then particle restacking
Please can you post a screenshot of what you are looking at, including some context (active tab in the job viewer, for example) so we can ensure we are (literally and figuratively) on the same page.
Of course. Here’s the screenshot of one of the restack particles jobs that I’ve used to export particles to RELION. I highlighted the files that I downloaded from the web interface in red. I highlighted the button that I used to acquire the csg file in blue (clicking the button gave me the pathway for the csg file).
@G-ED1 For each group under a job’s Outputs tab, there is a corresponding csg file in the job directory. Your Restack Particles job has one group. The metafile: key inside the corresponding csg file indicate that all items, blob, ctf, _etc., are stored in a single file J539_particles_exported.csin this case. For other job types, the metafile: keys inside a specific csg file may refer to diffent cs files for the various items. For example, the Particles Selectedcsg file for a Select 2D job indicates that blob items are stored inside one cs file and ctf items in another.
Keep in mind that the blob information inside a cs file are meta data, such as file paths. The actual data are store outside the *.cs file, at the paths recorded inside the blob-associated *.cs file.
csg files are machine readable YAML files and may be useful in some data conversion tasks, but I am not sure whether they are useful for your specific use case.
