Workaround to use particle subsets - ValueError: cannot reshape array of size 0 into shape

Does anyone know how to get around the following error? “ValueError: cannot reshape array of size 0 into shape” - I have seen this discussed in the past year but with no definitive answer.

I encounter this error when I import and refine a particle subset of a large extraction. I recall someone posted that this could be due to how particle files are written in batch when not calling all of those particles to be used.

Here’s details of what I am doing. My goal is to save time and processing space by not doing another extraction to generate an unbinned particle stack. Currently, if I want to switch from binned consensus particles to unbinned subset particles, every unbinned particle stack needs to be re-extracted, which is costly in terms of time and storage, even though there’s already a good unbinned particle stack.

Extract binned particles. In parallel extract unbinned particles. Refine binned (all in cryoSPARC up to this point), 3D classify binned in relion, subset select, point subset to unbinned extract, import and refine in cryosparc. It always gives the ValueError and cannot get around it by downsample. Is there any way to get these particles to refine? The unbinned extract particles are just fine for other jobs, its just problematic taking a subset of them. I do not think it’s a problem of corrupt particles, since the original particles still refine. I am on v3.1.0+210216 and don’t want to update unless there is a known fix.