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SBC-Utrecht / pytom-match-pick

GPU-accelerated template matching for cryo-ET
https://sbc-utrecht.github.io/pytom-match-pick/
GNU General Public License v2.0
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RELION-5 input compatibility #190

Open rdrighetto opened 2 months ago

rdrighetto commented 2 months ago

Hi! I just saw the 0.7 release which looks awesome!

I see that output is now compatible with RELION-5, which is great! I was wondering if there are any plans to make input compatible with RELION-5 as well? i.e. one could give a tomograms.star file and pytom-match-pick could figure out tilt angles, defocus per tilt, dose etc from there by itself?

I can make a PR if I ever get there but I won't promise since I am already delayed in delivering the Scipion plugin 😬 Thought it didn't hurt to ask just in case anyone is already planning something similar 😃

McHaillet commented 2 months ago

Thanks for making an issue about this! It was already on my mind :)

No time to work on it atm, but if I do find time I'll definitely add it.

It attached a tilt-series STAR file here for reference from the RELION-5 beta (weirdly it still says # version 30001 in the header..). I guess a user would still need to provide amplitude contrast, spherical abberation, and voltage as input.

Potentially the CtfMaxResolution could also be exploited although that seems like a bigger project.

tomo200528_100.txt

sroet commented 2 months ago

I guess a user would still need to provide amplitude contrast, spherical abberation, and voltage as input.

That would not be needed if the ReconstructTomograms/jobXXX/tomograms.star file is used instead of the one from the tilt-series.

Attached is the tomograms.star from the same job as the txt above

tomograms.star.txt