[3dem] Missing metadata .star file during relion_movie_reconstruct

[tnakane.protein at osaka-u.ac.jp]

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!DzgL_cR5OU0kgtefEJNa2ENE_qtYP8b-M4tLW0RNRqvpo7qN3engBtPCvjwOId1uZU58PbgRaSsrUSP2sQRME7lFtYHUXNtYlrQ$ 

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>