AreTomo alignment and tomogram reconstruction faulty

[lmcarreira]

Describe your problem

Hi! I have started using Relion 5.0 and noticed that AreTomo alignments performed with Relion are different than the ones I get running AreTomo standalone version. Using a sample thickness of 100nm (In Relion we can only specify sample thickness) I get two different alignment results, the Relion one being the worst as my membrane alignment "breaks" as Z changes. For illustration purposes I am attaching two examples (1 - Standalone AreTomo and 2 - Relion). In 2 I see the membrane discrepancy as I move in Z, which I do not see in 1. Am doing something wrong? 1-Aretomo standalone

2-After AreTomo alignment in Relion 5

Thanks!

[EuanPyle]

So the Align Z in standalone AT is in pixels, whereas in RELION it's given in nm (or maybe A, I'm on my phone so can't check right now!). Maybe the descrepancy is coming from there? Try converting your AT align Z to nm and try that thru RELION

[lmcarreira]

Dear Euan, Thanks for your reply. If you could clarify what is the input in Relion would be great. The documentation (as far as I can see) does not mention this anywhere, but correct me if I am wrong.

Best,

Luís

On Wed, Aug 14, 2024 at 6:19 PM EuanPyle @.***> wrote:

So the Align Z in standalone AT is in pixels, whereas in RELION it's given in nm (or maybe A, I'm on my phone so can't check right now!). Maybe the descrepancy is coming from there? Try converting your AT align Z to nm and try that thru RELION

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