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

[Guillaume Gaullier]

Hello,

This page of the RELION wiki has some relevant info under sections "Coordinate system" and "Symmetry": https://urldefense.com/v3/__https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Conventions_*26_File_formats__;JQ!!Mih3wA!TJpGpHo4JZAc7MEONemLOB1cU6eFXtMfCOw5p1u9-lxwLtApjHRwFbLMXwb7Cluo_w$ <https://urldefense.com/v3/__https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Conventions_&_File_formats__;!!Mih3wA!TJpGpHo4JZAc7MEONemLOB1cU6eFXtMfCOw5p1u9-lxwLtApjHRwFbLMXwbQck6Xqw$ >
I have not used other programs as much, so I have not yet run into this problem with different conventions. I hope this is still helpful to you.

Cheers,

Guillaume


On 3 Feb 2021, at 23:52, Rodarte, Justas V <jrodarte at fredhutch.org<mailto:jrodarte at fredhutch.org>> wrote:

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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