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.