Improper symmetries

Troubleshooting
1

Dear all,

I have a particle that displays improper symmetry which is S4. cryoSPARC doesn’t recognize it, so the highest symmetry I can run refinement is C2. Is there any option to overcome this issue? Are there some symmetry files that can be included to make the 3Dref step possible? Or maybe there is a different way to describe that kind of symmetry so it would be recognizable by cs?

thanks in advance
best
ab

2

Hi @ArturB,

We’re not actually familiar with the S4 symmetry description – are you able to link to a reference that explains the S4 improper symmetry?

Best,
Michael

3

Sure,

please find the description of S2 and S4 point groups under the links:
S2 - http://gernot-katzers-spice-pages.com/character_tables/S2.html
S4 - http://gernot-katzers-spice-pages.com/character_tables/S4.html

The nice example of a molecule with S4 symmetry is: 1,2,3,4-tetrafluorospiropentane

hope that can help.
best
ab

1 Like
4

Improper rotation is also called rotation-reflection or rotoreflection (along with some other names). Biological macromolecules generally can’t have reflection symmetries, because they are strictly chiral.

Can you provide some more information about your complex? You may have a non-point group symmetry, which can still be treated using local expansion methods from a few different software packages. CryoSPARC can still be used for refinement after importing transformed particles. This approach will also work if you have a true S4 symmetry (of a non-biological sample).

@mmclean Just FYI RELION actually has S symmetries. I guess someone over there is a completionist…

1 Like
5

Hi @DanielAsarnow ,

my complex is built out of 20 subunits (each of them has 11-fold rotational symmetry). This is strange itself, because regular polyhedra are forbidden to be build from hendecagons (by mathematics). I assume my complex is S4 symmetrical on “macro” scale and due to the chirality of AA it is not possible to have the S4 symetry on “micro” scale (in the case of C4 rotatation combined with perpendicular plane reflection). But if we consider C4 rotation combined with inversion at I, it should work (chirality af the AA should not be a problem anymore, right?

any suggestions will be much helpful.
I will relion in the mean time

best
ab

6

Can you provide a diagram to convey what you mean?

There can’t actually be a reflection (or inversion) symmetry, but there could be another rotation symmetry, or simply the asymmetric units are not placed according to a point group (though they are identical).

7

Dear all,

Thank you for the information on improper rotations for this interesting complex! I’ve added S symmetries to our feature tracker as a potential addition down the road.

Best,
Michael