Fail to import particles.star

[abnerabner]

Hi,

Thank you for the assistance your work has provided in visualizing the CryoET results.

I am currently importing the particles.star generated in the Extract job of RELION5 into ChimeraX 1.11 and have encountered the following error:

TypeError: Cannot interpret '' as a data type

File "C:\software\ChimeraX 1.11.1\bin\Lib\site-packages\numpy\core\numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^

See log for complete Python traceback.

The .star file is like:

# version 50001

data_particles

loop_ 
_rlnTomoName #1 
_rlnParticleID #2 
_rlnCenteredCoordinateXAngst #3 
_rlnCenteredCoordinateYAngst #4 
_rlnCenteredCoordinateZAngst #5 
_rlnOriginXAngst #6 
_rlnOriginYAngst #7 
_rlnOriginZAngst #8 
_rlnAngleRot #9 
_rlnAngleTilt #10 
_rlnAnglePsi #11 
_rlnClassNumber #12 
_rlnTomoTiltSeriesPixelSize #13 
_rlnOpticsGroup #14 
_rlnTomoParticleName #15 
_rlnTomoVisibleFrames #16 
_rlnImageName #17 
_rlnGroupNumber #18 
_rlnNormCorrection #19 
_rlnLogLikeliContribution #20 
_rlnMaxValueProbDistribution #21 
_rlnNrOfSignificantSamples #22 
_rlnRandomSubset #23 
20251127_car3_L3_ts_002       1573  -3314.42373     -4.32789   762.306278    96.372379    55.212379    -50.62763    -22.43322    99.321748    -45.89277            7    11.760000           40 20251127_car3_L3_ts_002/1573 [1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1] Extract/job404/Subtomograms/20251127_car3_L3_ts_002/1573_stack2d.mrcs            1     1.000000 1.384036e+06     0.456668            1            2 
20251127_car3_L3_ts_002       1463  3350.196280  -3254.13373   472.822278     2.292378    -15.34762    -85.90763    30.448271   102.084165    52.747243            7    11.760000           40 20251127_car3_L3_ts_002/1463 [1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1] Extract/job404/Subtomograms/20251127_car3_L3_ts_002/1463_stack2d.mrcs            1     1.000000 1.376701e+06     0.319156            2            1 
20251127_car3_L3_ts_002        951   214.902280  4404.546280   -821.03673    -74.14763    31.692379    64.032380    -70.23159    93.679784   113.283046            7    11.760000           40 20251127_car3_L3_ts_002/951 [1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1] Extract/job404/Subtomograms/20251127_car3_L3_ts_002/951_stack2d.mrcs            1     1.000000 1.376705e+06     0.544832            1            1 

Do you have any suggestions? Thank you very much!!!

[abnerabner]

It seems that pandas3 is the cause of this problem. Without modifying the source code, there is a temporary solution: delete all the string columns in particles.star, and then ensure that the number of columns in the header is correct, and then the file can be successfully imported.

[derpaule]

Just an additional comment that may be helpful:
starparser can efficiently remove those columns, e.g.

starparser --i run_data_216.star --remove_column "_rlnTomoName/_rlnImageName/_rlnTomoParticleName/_rlnTomoVisibleFrames"

HTH,
Tim