[3dem] Missing metadata .star file during relion_movie_reconstruct

[Ioannis Skalidis]

Hello Takanori,

Thanks a lot, apparently that was the mistake, everything seems to be in
order now!

Ioannis.


Στις Πέμ 16 Ιουλ 2026 στις 12:40 μ.μ., ο/η tnakane.protein at osaka-u.ac.jp <
tnakane.protein at osaka-u.ac.jp> έγραψε:

> Hi,
>
> > --corr_mic /home/dose_damage/CtfFind/job007 \
>
> This should be `corrected_micrographs.star` from a MotionCorr job, not
> CtfFind.
>
> Please look at
> https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind2008&L=CCPEM&P=R371345__;!!Mih3wA!DCUL5YnBP-cbndqpFjpWgHRqaTwK6z8z4q_yU7qvdqkig98J6CLgZjoD9pJnEKxob57ApgaJ0tYNxhwt5H0a1XTe$ 
>
> Best regards,
>
> Takanori Nakane
>
> ________________________________________
> From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Ioannis Skalidis
> via 3dem <3dem at ncmir.ucsd.edu>
> Sent: 16 July 2026 19:04
> To: 3dem at ncmir.ucsd.edu
> Subject: [3dem] Missing metadata .star file during relion_movie_reconstruct
>
> Dear 3DEM,
>
> I am currently processing two SPA datasets of the same protein and
> planning to do a detailed dose-dependent radiation damage comparison so I
> can optimize imaging conditions.
>
> To do this, I use RELION 5.1.0 and specifically relion_movie_reconstruct,
> after I got everything done, all the way to the final Refine3D after
> CTFRefine/Bayesian Polishing of the particles. This is the command I'm
> running:
>
> relion_movie_reconstruct --i
> /home/dose_damage/Refine3D/job063/run_data.star \
> --o recon_attempt_1.mrc \
> --movie_angpix 0.513 \
> --coord_angpix 0.513 \
> --sym C1 \
> --corr_mic /home/dose_damage/CtfFind/job007 \
> --traj_path /home/dose_damage/Polish/job059 \
> --frame 1 \
> --ctf true \
> --ewald true \
> --window 400 \
> --scale 400 \
> --mask_diameter 200 \
> --j 2
>
> Initially, I get an error about the CtfFind version, but it is bypassed:
>
> WARNING: /home/dose_damage/CtfFind/job007 seems to be from a previous
> version of Relion. Attempting conversion...
>          You should make sure metadata in the optics group table after
> conversion is correct.
>
> Then I get the following, at which the process crashes:
>
> ERROR:
> Cannot get metadata STAR file for
> MotionCorr/job004/data/20260505_145243_dosecheck_Frames/FoilHole_4581204_Data_4580666_4580668_20260505_152108_fractions.mrc
>
> When I check the directory, the .star file for each micrograph is there.
> Is it looking for something different? Have I made a mistake in the inputs
> I provide to the command? Any advice would be appreciated since it's the
> first time I use the specific RELION module.
>
> Cheers,
> Ioannis.
>
>
> Dr. Ioannis Skalidis | Structural Biochemist | Bsky: @johnskal.bsky.social<
> https://urldefense.com/v3/__https://bsky.app/profile/johnskal.bsky.social__;!!Mih3wA!GExj8fcVn7fQxEmkVhwIkXXpdWYQ7ieh6MQRyJtiamVDsS3S1ih-JSVKPrDi-G3r48nphYPPwJasog7oX0ANP5Jh$>
> | Mobile: +30 698 807 7306 | johnskalidis at gmail.com<mailto:
> johnskalidis at gmail.com>
>
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