Ignoring non-existent motion-corrected images in gCTF

[bforsbe]

Originally reported by: Mazbit (Bitbucket: Mazbit, GitHub: Unknown)

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Hi guys,

I come across a tiny issue. My test data deliberately contains awful movies of broken ice, for which MOTIONCORR fails without producing a corrected image --> good!

Nevertheless, corrected_micrographs.star includes the non-existing images and produces an error with gCTF. Perhaps corrected_micrographs.star could be generated based on actual MOTIONCORR outputs.

Thanks
Mazdak

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• Bitbucket: https://bitbucket.org/tcblab/relion2-beta/issue/45

[bforsbe]

Original comment by Bjoern Forsberg (Bitbucket: bforsbe, GitHub: bforsbe):

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Hi Mazdak,

So this is something which does not happen when you run MOTIONCORR without the use of RELION?

[bforsbe]

Original comment by Mazbit (Bitbucket: Mazbit, GitHub: Unknown):

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Hi Bjoern,

if the inputs are really bad, MOTIONCORR won't spit out a corrected image with or without wrapper. It's a cheap way for reducing a dataset right at the beginning. But Gctf won't run and report an error if some of its inputs (ie corrected micrographs) are missing. Therefore, it could be better to create the micrographs_corrected.star file by reading in MOTIONCORR outputs.

cheers
Mazdak

[bforsbe]

Original comment by Bjoern Forsberg (Bitbucket: bforsbe, GitHub: bforsbe):

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Ah, that clears it up. Your suggestion makes sense.

[biochem-fan]

The current wrapper should handle this.