Error parsing Relion star file

[mgflast]

Hi,

Fyi, this bit:

ArtiaX/src/io/RELION/RELIONParticleData.py

Lines 267 to 270 in 4af3bc2

	if names_present:
	n = row["rlnTomoName"].split("_")
	num = int(n[-1])
	p["rlnTomoName"] = num

Causes trouble with Relion5 run_data.star files from Refine3D jobs in the Warp/Relion/M pipeline when the rlnTomoName does not match the format expected by ArtiaX:

data_particles
loop_ 
_rlnTomoName #1 
_rlnTomoParticleId #2 
_rlnCoordinateX #3 
_rlnCoordinateY #4 
_rlnCoordinateZ #5 
_rlnAngleRot #6 
_rlnAngleTilt #7 
_rlnAnglePsi #8 
_rlnTomoParticleName #9 
_rlnOpticsGroup #10 
_rlnImageName #11 
_rlnOriginXAngst #12 
_rlnOriginYAngst #13 
_rlnOriginZAngst #14 
_rlnTomoVisibleFrames #15 
_rlnGroupNumber #16 
_rlnClassNumber #17 
_rlnNormCorrection #18 
_rlnRandomSubset #19 
_rlnLogLikeliContribution #20 
_rlnMaxValueProbDistribution #21 
_rlnNrOfSignificantSamples #22 
250531_l10p1_6.tomostar            1  1874.308000   205.841000   389.089000   -140.54286    75.867094    -32.74906 250531_l10p1_6/1            1 ../../warp_tiltseries/particleseries/250531_l10p1_6/250531_l10p1_6_3.00A_000001.mrcs    -10.06860     -1.06860     -7.82835 [1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1]            1            1     1.000000            1 2.143634e+06     0.018656           73 
250531_l10p1_6.tomostar            2  1863.532000   218.536000   388.401000   -152.46425    78.981686   -132.67546 250531_l10p1_6/2            1 ../../warp_tiltseries/particleseries/250531_l10p1_6/250531_l10p1_6_3.00A_000002.mrcs    -31.82835    -20.32185     -3.57510 [1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1]            1            1     1.000000            1 2.142892e+06     0.020107           87 
250531_l10p1_6.tomostar            3  1852.731000   231.212000   387.734000    46.243825    84.012415   -137.90682 250531_l10p1_6/3            1 ../../warp_tiltseries/particleseries/250531_l10p1_6/250531_l10p1_6_3.00A_000003.mrcs    -15.57510     -5.32185     5.424899 [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     1.000000            2 2.220612e+06     0.007983          221 

Error:

ValueError: invalid literal for int() with base 10: '6.tomostar'

File "C:\Users\Mart Last\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-packages\chimerax\artiax\io\RELION\RELIONParticleData.py", line 269, in read_file
num = int(n[-1])
^^^^^^^^^^

A try/catch clause would help :)