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

[Matthias Wolf]

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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