Symmetry expand and particle subtraction



Hi developers,
From cryosparc v 2.9, it is possible to import the symmetry expanded particles from 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 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?




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?


Hi @apunjani
Yes, this is the workflow I used.
I see the result strange because the particle turns from black to white…

These days I tried to expand symmetry directly inside the newest version of cryosparc and then did subtraction, but cannot see any difference between the ‘original particle’ and ‘subtracted particle’ images inside the job.