Symmetry expand and particle subtraction

Local Refinement
1

Hi developers,
From cryosparc v 2.9, it is possible to import the symmetry expanded particles from relion.star files and proceed to the local refinement job. This is a very useful function.
recently I was trying to import the expanded particles and conduct particle subtraction in cryosparc, however, it seems the particle subtraction job didn’t read the orientation of imported particles correctly. For example, when the imported particles are expanded from C2 symmetry (within relion), the output of subtraction job (mask of the subtraction is non-symmetic) always shows that two particles are identical, while the same particles.star can lead to correct output directly from local refinement job.

I am wondering if there is a way to do the subtraction job with imported symmetry-expanded particles correctly?

Thanks.

Xiaonan

2

Hi @hxn,

Just to clarify, is this the workflow you used:

  1. create particles in cryosparc, and create a refined volume
  2. export cryosparc particles via pyem to .star format
  3. apply symmetry expansion in Relion
  4. import expanded .star file back into cryosparc
  5. import a mask into cryosparc
  6. try to apply particle subtraction using original volume from #1 and particles from #4 and mask from #5

This should work, though it is not a workflow we test often. Can you further explain how you know the results are wrong or post a couple of example images?

4

Hi @hxn if you open the two images in two different browser tabs and flip between them, there is actually a difference, though it’s relatively minor. Part of the density is being subtracted. Is there a change that your mask and volume are misaligned, or the mask doesn’t actually include too much density?