Import successfull but resulting star file contains only single movie for all tiit angles

[jamstujam]

Hello,

We recently installed Relion 5.0-beta-3.0 on our AlmaLinux 9.4 system and I am trying to use a tilt series through the workflow. However, I've run into an issue with the import. According to relion, the import is successful:

[20:49:46] Started import_tilt_series job. serialem.py:76
Creating output directory at Import/job020/tilt_series serialem.py:80
Found 1 mdoc files and 33 image files. serialem.py:86
Wrote tilt-series data STAR file serialem.py:127
Import/job020/tilt_series.star
writing per tilt-series STAR files... serialem.py:130
Working... ???????????????????????????????????????? 100% 0:00:00
Wrote STAR files for 1 tilt-series. serialem.py:150

However, when I look at the resulting star file for the tilt series, it lists the first tilt image (as listed in the mdoc) for all the tilt angles (column 1; see below). So, it seems to find the image files and mdoc file, but the output is not correct. I have double checked the files (symbolic link to original data using bith cp -s and ln -s), and the mdoc lists the correct movie for each tilt angle, so I'm at a bit of a loss on what to change.

I did try motion correction, however, it only corrects the one tilt movie noted in the star file.

Any advice is appreciated.

Best,
Jamie

Created by the starfile Python package (version 0.4.12) at 20:49:46 on 17/07/2024

data_cells2

loop_
_rlnMicrographMovieName #1
_rlnTomoTiltMovieFrameCount #2
_rlnTomoNominalStageTiltAngle #3
_rlnTomoNominalTiltAxisAngle #4
_rlnMicrographPreExposure #5
_rlnTomoNominalDefocus #6
frames2/12_Jul10_18.31.48.tif 11 0.000165 -88.600000 0.000000 -5.000000
frames2/12_Jul10_18.31.48.tif 11 2.999830 -88.600000 3.300000 -5.000000
frames2/12_Jul10_18.31.48.tif 11 6.000470 -88.600000 6.600000 -5.000000
frames2/12_Jul10_18.31.48.tif 11 9.000130 -88.600000 9.900000 -5.000000
frames2/12_Jul10_18.31.48.tif 11 11.999300 -88.600000 13.200000 -5.000000
frames2/12_Jul10_18.31.48.tif 11 15.000400 -88.600000 16.500000 -5.000000
frames2/12_Jul10_18.31.48.tif 11 -2.999500 -88.600000 19.800000 -5.000000
frames2/12_Jul10_18.31.48.tif 11 -5.999650 -88.600000 23.100000 -5.000000
frames2/12_Jul10_18.31.48.tif 11 -8.999800 -88.600000 26.400000 -5.000000
frames2/12_Jul10_18.31.48.tif 11 -12.000000 -88.600000 29.700000 -5.000000
frames2/12_Jul10_18.31.48.tif 11 -15.000100 -88.600000 33.000000 -5.000000
frames2/12_Jul10_18.31.48.tif 11 18.000600 -88.600000 36.300000 -5.000000
frames2/12_Jul10_18.31.48.tif 11 21.000200 -88.600000 39.600000 -5.000000
frames2/12_Jul10_18.31.48.tif 11 23.999900 -88.600000 42.900000 -5.000000
frames2/12_Jul10_18.31.48.tif 11 26.999600 -88.600000 46.200000 -5.000000
frames2/12_Jul10_18.31.48.tif 12 29.999200 -88.600000 49.500000 -5.000000
frames2/12_Jul10_18.31.48.tif 11 -17.999800 -88.600000 52.800000 -5.000000
frames2/12_Jul10_18.31.48.tif 11 -20.999400 -88.600000 56.100000 -5.000000
frames2/12_Jul10_18.31.48.tif 11 -23.999600 -88.600000 59.400000 -5.000000
frames2/12_Jul10_18.31.48.tif 11 -27.000700 -88.600000 62.700000 -5.000000
frames2/12_Jul10_18.31.48.tif 12 -29.999400 -88.600000 66.000000 -5.000000
frames2/12_Jul10_18.31.48.tif 12 32.998900 -88.600000 69.300000 -5.000000
frames2/12_Jul10_18.31.48.tif 12 35.998100 -88.600000 72.600000 -5.000000
frames2/12_Jul10_18.31.48.tif 12 38.999200 -88.600000 75.900000 -5.000000
frames2/12_Jul10_18.31.48.tif 12 41.997400 -88.600000 79.200000 -5.000000
frames2/12_Jul10_18.31.48.tif 12 44.996100 -88.600000 82.500000 -5.000000
frames2/12_Jul10_18.31.48.tif 12 -32.999500 -88.600000 85.800000 -5.000000
frames2/12_Jul10_18.31.48.tif 12 -35.999700 -88.600000 89.100000 -5.000000
frames2/12_Jul10_18.31.48.tif 12 -38.999800 -88.600000 92.400000 -5.000000
frames2/12_Jul10_18.31.48.tif 12 -42.000000 -88.600000 95.700000 -5.000000
frames2/12_Jul10_18.31.48.tif 12 -45.000200 -88.600000 99.000000 -5.000000
frames2/12_Jul10_18.31.48.tif 13 47.997200 -88.600000 102.300000 -5.000000
frames2/12_Jul10_18.31.48.tif 13 -47.999800 -88.600000 105.600000 -5.000000

[EuanPyle]

hi can you paste the mdoc please?

[jamstujam]

Yes, of course. Apologies I was on vacation. I've attached the mdoc for the tilt series that I tried to import.

importmdoc.txt

[EuanPyle]

Not certain, but the problem may be to do with the dots in the file names. Maybe try replacing the dots in the file name (and the corresponding mdoc) with underscores and see what happens. Should be simple enough to write a script to do that but email me tomorrow if you need some help with that