Symmetry averaging in local refinement

Features and Functionality
1

Hi cryosparc developers,

It could be helpful to allow symmetry averaging of the EM density during local refinement. Currently, to achieve similar effect, I perform symmetry expansion before local refinement. But it would be nice if I don’t have to take this work-around.

Thanks a lot for your attention!

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2

Hi cryosparc developers,

I join Chenzhao that it will be great to be able to run Local Refinement with symmetry. In my case it is impossible to run symmetry expansion before local refinement because my subunits are too small (high symmetry).

Did you plan to do it soon ?

Thanks

3

Hi @chenzhao and @Kevin_BBK,

Thank you both for your request. We have been working on a re-work of local refinement, and incorporating point group symmetry is one part of the planned additions. These new features won’t make it into our immediately upcoming release, but it is currently being actively worked on.

For my research, does your desired workflow look something like this:

  • Homogeneous/NU-refinement with symmetry enforced
  • Local refinement with symmetry enforced, using (unsubtracted) particles & volume from the previous refinement

In addition, do you use a local refinement mask that covers just the asymmetric unit, portions from multiple asymmetric units, or either (depending on the dataset)?

Thanks, and best regards,
Michael

4

For my case, I work on a complex having 2 domains presenting different points of symmetry. The whole complex is refined in C1, the domain A shows C6 symmetry and the domain B C5 symmetry. Then, I do a local refinement (map and particle inputs from the previous refinement) using a mask for each domain but without symmetry because this functionality does not exist yet.
Doesn’t work if I use a classical refinement with a mask (using symmetry or not). So I can’t do symmetry expansion follow by a local refinement, and I can’t anyway do this workflow because the subunits are small.

Hoping that help you,

Kevin

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5

Hi @mmclean,

I am sorry for my delayed replying and thank you for working on incorporating this functionality. My case is very standard, which is simply to run local refinement from a global refinement job with symmetry imposed. In terms of mask, I routinely do both cases that you have mentioned above (mask covering only one asymmetric unit and mask covering portions of multiple asymmetric units).

Again thanks a lot for considering our suggestions.

Best,
Chen

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