Missing information in optics.star file Warp to Relion 4.0.1

Felix Lange

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Jun 13, 2023, 4:50:19 AM6/13/23

to Warp

Hi guys,

I am following the tt tutorial for the Warp-Dynamo-Relion pipeline with my own data. I extracted subtomograms in Warp at 5Apx according to the settings given in the tutorial. Now in Relion, the _optics.star is missing entries for the optics causing an error in Relion. The entry now looks like this:

data_optics

loop_
_rlnOpticsGroup #1
_rlnOpticsGroupName #2
_rlnImagePixelSize #3
_rlnImageSize #4
_rlnImageDimensionality #5
1 opticsGroup1 5.000000 60 3

How cann I pass along the missing information? Thanks and all the best,

Felix

Philipp Erdmann

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Jun 13, 2023, 5:34:22 AM6/13/23

to Felix Lange, Warp

Hi Felix,

You’ll need

_rlnVoltage #6

_rlnSphericalAberration #7

_rlnAmplitudeContrast #9

And the corresponding columns with the data (300, 2.7, 0.07)

Best,

Philipp.

Sent from my iPhone

On Jun 13, 2023, at 10:50 AM, Felix Lange <felix.l...@gmail.com> wrote:

Hi guys,

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Felix Lange

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Jun 13, 2023, 8:41:38 AM6/13/23

to Warp

Hi Philipp,

Thank you for your reply! Is there a chance to pass this information via relion_convert_star, or any other command?
Thank you again and all the best,

Felix

Felix Lange

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Jun 13, 2023, 9:00:40 AM6/13/23

to Warp

Hi Philipp,

I fixed it. Thank you for your input!
Cheers,

Felix

3P1L

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Jun 13, 2023, 10:59:56 AM6/13/23

to Warp

relion_convert_star --help

-> --Cs
-> --Q0

Why you cannot automatically add voltage beats me 🤷‍♂️

😅

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