Filament picking, helical reconstruction and GSFSC

Helical Processing
1

Dear CS,

I have a question: When using filament picking & extraction, do the extracted particles are split according to the filaments they come from? i.e.To avoid having duplicate particles, Are the two particle datasets used to calculate the GSFSC always contain data from different filaments?

Thanks

H.

2

Dear @hsosa,

Yes, this is the case when using particles picked in CryoSPARC and when using the Helical Refinement job, but not the case for other refinement jobs.

  • When particles are picked via Filament tracer and refined in helical refinement, all particles in one filament will be assigned to the same half-set
  • When picked and extracted in blob or template picker and refined in helical refinement, all particles in one micrograph will be assigned to the same half-set

The helical processing tutorial makes a brief mention of this. It’s important to note that Homogeneous and Non-Uniform refinement job types do not split particles according to this way, they split particles randomly, which does cause problems if particles are picked close to each other. Local refinement will by default preserve input splits, so the Helical Refinement → Local Refinement workflow still works as expected.

Let me know if you have other questions,
Michael