errors when run relion_prepare_subtomograms.py

[yuanhaowang1213]

I was following the procedure exactly on the 2016 nature protocol paper, and got error on the procedure 9. Here is the output:

WARNING: skipping, since cannot get CTF values for ./Tomograms/tomogram1/ctffind/tomogram1_image59.44_0.mrc

I fixed this by change to ctffind3. The python file read it support ctffind4, but which version?
But got other issues,

1. Traceback (most recent call last):
   File "relion_prepare_subtomograms.py", line 448, in
   micnames, avgdefoci, defocusv = read_relion_star(outputstarname_read)
   File "relion_prepare_subtomograms.py", line 137, in read_relion_star
   micnames.append(fields[imgnamecolumn])
   UnboundLocalError: local variable 'imgnamecolumn' referenced before assignment

I checked the file ./Tomograms/tomogram1/ctffind/results/micrographs_ctf.star
It only gave
"# RELION; version 3.0.8# RELION; version 3.0.8

data_

loop_
_rlnMicrographName #1
_rlnCtfImage #2
_rlnDefocusU #3
_rlnDefocusV #4
_rlnCtfAstigmatism #5
_rlnDefocusAngle #6
_rlnVoltage #7
_rlnSphericalAberration #8
_rlnAmplitudeContrast #9
_rlnMagnification #10
_rlnDetectorPixelSize #11
_rlnCtfFigureOfMerit #12
./Tomograms/test1/ctffind/test1_image59.44_0.mrc /home/wangy0k/Desktop/recomcomp/warped3_frommylab/nowarp/reliontest/./Tomograms/test1/ctffind/results/./Tomograms/test1/ctffind/test1_image59.44_0.ctf:mrc 32975.910156 38577.839844 5601.929688 77.410004 300.000000 2.700000 0.070000 10000.000000 1.000000 0.104640
...

2. What should be set for SkipCTFCorrection and Relion2 in the relion_prepare_subtomograms.py?

The default setting is Relion2 = True, SkipCTFCorrection = False, but there will be no ctffind.star generated.

Environment:

• OS: Ubuntu 18.04 LTS
• MPI runtime: OpenMPI 4.5
• RELION version RELION-3.0.8
• Memory: 256
• GPU: RTX Titan

Dataset: EMPIAR 10045

[biochem-fan]

Unfortunately this protocol no longer works in the latest version of RELION. RELION 4.0, which we hope to start public beta testing in a few months, will have a much better tomography pipeline.

Meanwhile, if you really need to reproduce the paper's work, please use the old version of RELION.