star.file format error using pyem

[mqcarba]

Hi I have an issue in the .star file format after creating using pyem. I'm not able to run 2D class in Relion 4.0. I got this answer from Takanori in the Relion forum:

biochem-fan commented 1 hour ago
The column name rlnOpticsGroup1 does not make sense.
Please ask to pyem developers. This is not RELION's problem but theirs.

My star file is:

data_optics

loop_
_rlnVoltage 3dem/relion#1
_rlnImagePixelSize 3dem/relion#2
_rlnSphericalAberration 3dem/relion#3
_rlnAmplitudeContrast 3dem/relion#4
_rlnOpticsGroup 3dem/relion#5
_rlnImageSize 3dem/relion#6
_rlnImageDimensionality 3dem/relion#7
_rlnOpticsGroup1 3dem/relion#8
200.000000 1.100000 2.700000 0.100000 6 256 2 6

data_particles

loop_
_rlnImageName 3dem/relion#1
_rlnMicrographName 3dem/relion#2
_rlnCoordinateX 3dem/relion#3
_rlnCoordinateY 3dem/relion#4
_rlnDefocusU 3dem/relion#5
_rlnDefocusV 3dem/relion#6
_rlnDefocusAngle 3dem/relion#7
_rlnPhaseShift 3dem/relion#8
_rlnCtfBfactor 3dem/relion#9
_rlnOpticsGroup1 3dem/relion#10
000001@J220/extract/000032024661002688670_FoilHole_17705165_Data_17702841_17702843_20221217_092342_Fractions_patch_aligned_doseweighted_particles.mrcs J89/motioncorrected/000032024661002688670_FoilHole_17705165_Data_17702841_17702843_20221217_092342_Fractions_patch_aligned_doseweighted.mrc 3568 696 29705.314453 29126.382812 21.248625 0.000000 0.000000 6

[asarnow]

There's no condition in which a column label like _rlnOpticsGroup1 will be emitted - same for those extra strings after the field names. Have you modified the output file aside from the instructions in the wiki?

[mqcarba]

Attached is the .starfile I got

[asarnow]

That's not the file you showed Takanori. Anyway, just follow the instructions in the wiki here to correct the paths to the particle stacks, and it will work.

[mqcarba]

ok I was able to fix it. I loaded a 2D classification job. The only message I got is this. Should I worry about it? Thank you again!