I run Local Motion Correction with extraction box size of 512pix as job parameter and used the output particles for 3D Helical reconstruction. The first iteration of the recontruction made me realise that the particles had different pixel size from the particles I used originally. The original ones were 1/2 f-cropped in patch motion correction (data acquired in super res mode gain y-flipped) and extracted with a box size of 512pix. In opposite, the particle output from Local Motion Correction were not 1/2 f-cropped anymore.
Logically, I thought to re-run Local Motion Correction doubling the box size to 1024pix and, afterwards, downsample 1/2. However, the 1052pix box size Local Motion Correction job gets killed after processing 2-3 micrographs with the following error.
Is there any way you could help to fix this issue?
If the problem you describe here pertains to the same dataset as the one under Asymmetric Helical refinement (sym or convergence problem), where the resolution is apparently not Nyquist-limited, you may consider down-sampling the movies. Movie down-sampling is not currently implemented in CryoSPARC and would therefore have to be performed with an external program.
Again assuming that cufftAllocFailed occurred during processing of the dataset described in your other topic, you may be able to treat the filament asymmetric unit as a single particle, and reduce the extraction box size accordingly, aiming to extract (and pad) the asymmetric unit, but not necessarily entire filaments.