Hi @hansenbry,
Thanks for your question and for sending the outputs of those commands. The error you are seeing may be related to the box size of the reconstruction as users have reported seeing this error when the box size is larger than 440. What we suggest is that the particles are cropped in real space and /or Fourier space so that the box is a maximum of 440 before they are input to Flex Data prep, and that the downstream jobs are re-run.
- Downsample Particles, specifying Fourier crop to box size less than or equal to 440. Consider a Crop / pad to box size of less than 512, if the current 512 pixel box has a “generous margin” around the particles.
- Confirm with a Homogeneous Reconstruction Only and the downsampled particles job that real- and Fourier-space crop parameters from the previous step were appropriate.
- Input the downsampled particles to 3D Flex Data Prep.
- Use a Volume Tools job to create a soft-padded mask of the consensus volume output by 3D Flex Data Prep.
- Use the outputs of the preceding steps for 3D Flex Mesh Prep, Training and Reconstruction.
As you mentioned that you already tried downsampling the particles to a box of 256, at what stage were your particles downsampled? If your workflow differed from that shown above could you try this out and see if it resolves the issue for you?