Sorting helical heterogeneity

Helical Processing
1
  1. I want to sort out heterogeneity based on the Pitch of the helix. I can generate maps for classifications from the asymmetric map, requested above. Following that How to I carry out the classification using the maps in cryosparc ?

Thanks
Andy

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I used heterogeneous refinement using the created maps with different pitch/rise parameters in the helical refinement job.

For me this worked well,
Good luck,
Jitske

1 Like
3

Hi @Andy,

In general, (asymmetric) 3D classification or heterogeneous refinement (depending on whether you want to fix the poses or not, respectively) are the ways this would be done. Currently, neither job can enforce potentially different helical symmetry per class, but as @ifreezestuff mentioned, the algorithm can be encouraged to separate particles by symmetry type by initializing the classification with maps of different symmetries that were obtained via previous helical refinements. Thus, 3D classification/heterogeneous refinement would be helpful in partitioning your dataset into classes with potentially distinct helical symmetry. For high resolution refinement, you could then run separate helical refinements on each output class.

Best,
Michael

1 Like
4

Hi @mmclean
I need to sort particles with different symmetries, say C16, C17, C18, etc.
If heterogeneous refinement or ab-initial reconstruction can be implemented with different symmetries imposed, it will be great.
Thanks,
Xiangan

5

Hi @xliu,

Thanks for the request. To clarify, do you suspect that you have C16/17/18 symmetry in addition to helical symmetry in your sample?

Best,
Michael

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HI xliu,

You have a similar issue that I faced with one of my projects and yes it will be helpful to know the steps as how to do it in Cryosparc.

So far the process I adapted is to generate a moderate resolution maps of ~10A of the complex (in cryosparc) and then impose different symmetries using BSOFT to get a set of maps- carried out classification of the particles using orientation search in BSOFT and then separately imported the particles in cryopsarc for individual reconstructions.

I, however, will like to carry out all the steps in cryosparc only but was unable yo do so.

Hope this helps.

Andy

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Hi Michael,
There is no helical symmetry in my particles. Sorry about the confusion.
My data set contains different symmetries (C16, C17 and C18 ) mixed together. It is not rare in single particle cryoEM that a complex is assembled together with different symmetries.
Currently, cryoSparc’s heterogeneous refinement can only process density variation with the assumption of all particles having the same symmetry. My problem is to resolve symmetry variation, but the densities in an asymmetric unit in the complexes with different symmetries are coarsely same.
It will be great if you can allow symmetry variation in the “symmetry option” of heterogeneous refinement.
Thank you,
Xiangan

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Hi Andy,
Thanks for your information that BSOFT has such a function to sort out particles with different symmetries.
Xiangan