relion star format error

[diffracteD]

Hi,
I just converted a set of particles from cryosparc to relion .star format.
Although it looks ok to my eye, relion is givving this error no matter what I try:

Error in line: opticsGroup1 1 0.42000 300.000000 2.980376 0.100000 3 400 0.910095 2
in: /usr/src/relion-3.1/src/metadata_table.cpp, line 945
ERROR: 
A line in the STAR file contains more columns than the number of labels.
=== Backtrace  ===
.......

Now the .star file look like this:

data_optics

loop_
_rlnOpticsGroupName #1
_rlnOpticsGroup #2 
_rlnMicrographOriginalPixelSize #3
_rlnVoltage #4 
_rlnSphericalAberration #5 
_rlnAmplitudeContrast #6 
_rlnOpticsGroup #7 
_rlnImageSize #8 
_rlnImagePixelSize #9 
_rlnImageDimensionality #10 
opticsGroup1 1 0.42000 300.000000 2.980376 0.100000 3 400 0.910095 2

data_particles

loop_
_rlnImageName #1 
_rlnMicrographName #2 
_rlnCoordinateX #3 
_rlnCoordinateY #4 
_rlnAngleRot #5 
_rlnAngleTilt #6 
_rlnAnglePsi #7 
_rlnOriginXAngst #8 
_rlnOriginYAngst #9 
_rlnDefocusU #10 
_rlnDefocusV #11 
_rlnDefocusAngle #12 
_rlnPhaseShift #13 
_rlnCtfBfactor #14 
_rlnOpticsGroup #15 
_rlnRandomSubset #16 
_rlnClassNumber #17 
000001@/media/datastore-04/zhou/ha1c_rb3_ra2d_relion/particles/000002216567978961468_zhou_chen_20211221_ZC5-4_90-97_0010_X+0Y+0-1_patch_aligned_doseweighted_particles.mrcs /media/datastore-04/zhou/ha1c_rb3_ra2d_relion/micrograph/000002216567978961468_zhou_chen_20211221_ZC5-4_90-97_0010_X+0Y+0-1_patch_aligned_doseweighted.mrc 10804 1933 0.503297 56.916355 -93.108749 0.284405 0.056881 8753.747070 8708.697266 84.756592 -1.859249 0.000000 3 1 1
....

I don't understand why it raising this error. I have 10 items on the opticsgroup line.
Please advise.
Thank you.

[biochem-fan]

Are you sure your new line code is LF, not CR+LF? Try dos2unix.
Does this happen in RELION 4.0 as well?

How did you convert the file? In general, you should report this issue to the author of the conversion script, not us.

[biochem-fan]

OK, I found the issue.

_rlnOpticsGroup #2
_rlnOpticsGroup #7

You have two duplicated columns.

[diffracteD]

I did the conversion using csparc2star.py. But I wrote the initial lines of optics group manually.

[biochem-fan]

/media/datastore-04/zhou/ha1c_rb3_ra2d_relion/particles/

You have another problem. You are not following our guidelines for the path. This will cause issues later.

[mqcarba]

Hi I have a similar issue in the .star file format after creating it with pyem. Thus, I'm not able to run 2D class in Relion 4.0. Could someone please give me some input? Thanks!

data_optics

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

data_particles

loop_
_rlnImageName #1
_rlnMicrographName #2
_rlnCoordinateX #3
_rlnCoordinateY #4
_rlnDefocusU #5
_rlnDefocusV #6
_rlnDefocusAngle #7
_rlnPhaseShift #8
_rlnCtfBfactor #9
_rlnOpticsGroup1 #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

[biochem-fan]

The column name rlnOpticsGroup1 does not make sense.

Please ask to pyem developers. This is not RELION's problem but theirs.

[diffracteD]

Hi, is this issue is happening when you’re trying to move from cryosparc to relion ? This is not clear, by conversation what do you mean. If yes, then are you using the recent version of csparc2star.py ? If yes, could you please provide the command you’re using ?

On Sat, Apr 22, 2023 at 11:20 AM mqcarba ***@***.***> wrote: Hi I have a similar issue in the .star file format after creating it with pyem. Thus, I'm not able to run 2D class in Relion 4.0. Could someone please give me some input? Thanks! data_optics loop_ _rlnVoltage #1 <#1> _rlnImagePixelSize #2 <#2> _rlnSphericalAberration #3 <#3> _rlnAmplitudeContrast #4 <#4> _rlnOpticsGroup #5 <#5> _rlnImageSize #6 <#6> _rlnImageDimensionality #7 <#7> _rlnOpticsGroup1 #8 <#8> 200.000000 1.100000 2.700000 0.100000 6 256 2 6 data_particles loop_ _rlnImageName #1 <#1> _rlnMicrographName #2 <#2> _rlnCoordinateX #3 <#3> _rlnCoordinateY #4 <#4> _rlnDefocusU #5 <#5> _rlnDefocusV #6 <#6> _rlnDefocusAngle #7 <#7> _rlnPhaseShift #8 <#8> _rlnCtfBfactor #9 <#9> _rlnOpticsGroup1 #10 <#10> ***@***.***/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 — Reply to this email directly, view it on GitHub <#849 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACVEQAHTN2V7ZIS4UFD56HTXCQON3ANCNFSM5NQNRYBQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- *Abhisek Mondal, Ph.D.* *Cardiovascular Research InstituteUniversity of California San Francisco555 Mission Bay Blvd. South. Rm 482Dan Minor's LabSan Francisco, CA 94158USPS address:UCSFAbhisek Mondal, Ph.D.Cardiovascular Research Institute, Box 3122555 Mission Bay Blvd., Floor 4San Francisco, CA 94143*

[mqcarba]

Hi I followed pyem github: