Switching Warp versions and individual image removal

[Peng Liu]

Dear all,

We recently installed the Linux version of Warp on our tomography workstation. Previously, I had been using the Windows version of Warp for quite some time, which I understand is now considered outdated for cryo-ET data processing. According to the TeamTomo tutorial, the Windows version of Warp is compatible with Dynamo, IMOD, RELION3, and M.

I was wondering if anyone still uses the Windows Warp with the GUI. Many of my earlier datasets were preprocessed using it, and I am concerned about potential compatibility issues with newer tools such as PyTom match-pick and RELION5.

Reprocessing all the datasets with the new WarpTools would take considerable time, but I am happy to do so if it is necessary. I would really appreciate hearing about your experiences or any advice on this.

Additionally, I would like to ask about the recommended way to exclude certain images from a tilt series other than using the --min_intensity flag. Some images may have drift issues during acquisition, which may not be reflected simply by intensity values.

Thank you very much in advance for your help.

Best regards,
Peng

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Dr. Peng Liu

Max-Planck-Institut für biophysikalische Chemie
Am Faßberg 11, 37077 Göttingen
Germany

 : +49(0)17635209768
Email: peng...@mpibpc.mpg.de

[Alister Burt]

Hi Peng,

I recommend reprocessing to avoid potential issues but understand this is a bit of a minefield, Rasmus Jensen wrote some tips for moving over:

https://warpem.github.io/reference/warptools/processing_warp_v1_data/

Tilt removal will remain annoying until we release our new GUI - I haven't used it but Hamid Rahmani put together a tool for deactivating tilts based on IMOD metadata

https://github.com/hamid13r/warp_remove_skipped_views

Cheers,

Alister

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