[3dem] Symmetry Matrix Differences Between Cryo-EM Software

[Mike Strauss]

Hi Justas, 

just to add to what Matthias said: the different conventions have different historical backgrounds.  My default in Relion - I1, puts the 2-fold axes centered on the faces of the cube, and the 5-fold closest to the z-axis on the x=0 plane (assuming the origin is in the center). I like it because many of the virus structures in my field adopt this convention.  I2 puts this 5-fold on the y-0 plane.  I think these two were used because symmetrisation was easier for memory-limited calculations in the early days - just reorder the pixels and add, no interpolation necessary for the 2-folds.

Another convention uses the 5-fold axis pointing along the z-axis, which follows the convention of the highest symmetry along this axis (like D7 symmetry).

To be clear - they all produce the same structure - just rotated versions of one another - and they are all “correct” conventions, albeit not necessarily common.  If you’re getting crazy structures, it may be because the convention of your reference doesn’t match the convention of your output.

Regards,
mike

--------
Prof. Mike Strauss
Anatomy and Cell Biology / FEMR
McGill University
(514) 398-8084
mike.strauss at mcgill.ca

> On 4. Feb 2021, at 01:17, Matthias Wolf <matthias.wolf at oist.jp> wrote:
> 
> Hi Justas,
>  
> As far as I know, there is no absolute convention – the two possible icososahedral symmetries are called “I” and “I2”.
> One of them describes an icosahedron where you can “walk” between 5-fold axes thru 3- and 2- fold (5-3-2-5), the other thru 2- then 3-fold (5-2-3-5). Which is referred to as “I” and which as “I2” is, in principle, irrelevant. The two icosahedra are different structures, they are not mirrors of one hand.
>  
> So just use one of the two option that works in cryosparc. I guess it would be I2…
>  
> Best,
>    Matthias 
>  
> From: 3dem On Behalf Of Rodarte, Justas V
> Sent: Thursday, February 4, 2021 7:53 AM
> To: 3dem at ncmir.ucsd.edu
> Subject: [3dem] Symmetry Matrix Differences Between Cryo-EM Software
>  
> Hi all,
>  
> I’m a relative newcomer to the field of Cryo-EM, so my apologies if this question is easy/misplaced/previously answered. I’m working on a VLP with I symmetry that displays 80 spikes. Some programs (Relion, cisTEM) apply symmetry correctly when moving onto 3D ab-initio, while others (Cryosparc), don’t. I was able to trace this to the fact that these programs use different matrices to apply symmetry, an example is included below. Does anyone know why this is though? To me it appears to be an oversight that two popular programs apply the same symmetry differently?
>  
> Thank you all for any help or advice you can provide!
>  
> Best,
> Justas Rodarte
>  
>  
> I1 Sym Matrix Relion
> rot_axis 2, 1 0 0
> rot_axis 5, 0.85065080702670 0 -0.5257311142635
> rot_axis 3, 0.9341723640 0.3568220765 0
>  
> I1 Sym Matrix Cryosparc
> rot_axis 2, 0 1 0
> rot_axis 5, -0.85065080702670 0 0.5257311142635
> rot_axis 3, -0.9341723640 0.3568220765
>  
>  
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