Lost metadata after downsample > csparc2star



I have 3D-refined particles in cryosparc that I want to try refining in relion. In the past I’ve done this, but having trouble this time. Stack comes from 3 datasets: micrographs were imported into cryosparc. Now I’ve combined them and want to export using csparc2star.py. I sent all my particles into a downsample so that it generates a new stack, then I run csparc2star on particles_downsampled.cs.

problem #1: which I seem to get frequently with this script. When I provide the passthrough file it says “a passthrough file may be required”. So I leave the passthrough flag out altogether. This works, but…

problem #2: the output file from above has only pixel size, image name, magnification. No defocus values for example, so I can’t continue to process.

I also tried exporting after a 2D selection, or from the 3D refine, but end up with troubles down the road because the particles come from 3 different datasets.



anyone? Kinda stuck till I can sort this out. Any news on when the proper export feature will be incorporated?


@orangeboomerang I’m going to issue one last patch for csparc2star.py that will allow merging of any number of .cs files based on particle uid.

Proper (database aware) export sounds like it will be in their next release.


thanks, I’ll keep checking back @ your GitHub for latest csparc2star. thanks again!


@orangeboomerang See the new csparc2star.py thread, the current update ought to get you what you want.


thanks Daniel. I appreciate it. I’ll give it a try as soon as I am able.