Symmetry (plot) reporting during NU-Refine does not reflect imposed symmetry?

Hi CryoSPARC team (not sure who best to @; @hsnyder, @mmclean ?) and users,

I’ve been playing with a C10 complex the last few days on a recently updated CS 4.3 install. I’ve been experimenting with imposing different symmetries (C10, C5, C2, C1) and noticed something a little odd: the Viewing Direction Distribution doesn’t reflect imposed symmetry.

C1 plot:

C2 plot:

C5 plot:

C10 plot:

Resolution does reflect imposed symmetry, however: C10 gives 2.8 Å, C5 gives 3 Å, C2 gives 3.3 Å, C1 gives 3.5 Å. All other settings in the NU-Refine are identical.

I went back to some older projects (processed with CS 4.2.1 and earlier) and octahedral, icosahdral and D2 symmetry viewing distributions reflect the sort of pattern I would expect from the imposed symmetry.

Not an urgent issue, by any means, but thought it would be worth seeing if others report similar?

Edit: not checked homogeneous or heterogeneous refinement.

This is expected I think - from what I understand in cryosparc, symmetry is not actually enforced on the particle orientations, only on the reference volume… there was a discussion somewhere on the forum, will see if I can locate it.

However if the orientation plot doesn’t match the expected symm, it is a good idea to have a look and see if there might be some pseudosymmetry,



Here is a good explanation: What is actually occuring when symmetry is imposed? - #2 by DanielAsarnow

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Thanks, @olibclarke :smiley:

I was already looking for pseudosymmetry (although there shouldn’t be any) hence the different symmetry impositions (also did symmetry expansion, local, classification, variability, etc…) but having four different symmetries give me really, really similar viewing plots just made me want to ask as I don’t remember seeing it quite so pronounced!

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