My csparc2star.py converted files do not have _rlnAngleRot or rlnAngleTilt or rlnRandomSubset

Import and Export
1

Hi everyone

I am new to cryoEM data processing and I was trying to convert particles from my 2D classification in CryoSPARC to a star file.
I exported the output files in CryoSPARC, created softlinks to the particles_exported.cs and particles_exported.csg files in the Relion workspace where I had installed pyem, then executed the code
“csparc2star.py particles_exported.cs from_cs.star”
csparc2star.py ran fine without any error. Yet when I open my “from_cs.star” file it is like the following:
data_optics

loop_

_rlnVoltage #1

_rlnSphericalAberration #2

_rlnAmplitudeContrast #3

_rlnOpticsGroup #4

_rlnImageSize #5

_rlnImagePixelSize #6

_rlnImageDimensionality #7

300.000000 2.700000 0.100000 1 200 1.597500 2

data_particles

loop_

_rlnImageName #1

_rlnMicrographName #2

_rlnCoordinateX #3

_rlnCoordinateY #4

_rlnAnglePsi #5

_rlnOriginXAngst #6

_rlnOriginYAngst #7

_rlnDefocusU #8

_rlnDefocusV #9

_rlnDefocusAngle #10

_rlnPhaseShift #11

_rlnCtfBfactor #12

_rlnOpticsGroup #13

_rlnClassNumber #14

It lacks rlnAngleRot, rlnAngleTilt or, rlnRandomSubset.

I noticed the same issue previously when I was converting another file to star file (that time I used both particles.cs file and passthrough_particles.cs file for making star file). My output file was lacking the angle information that time too.

I really appreciate your time and suggestions

2

Did you performed any 3D refinement job before 2D classification? If not, it is natural that the star file doesn’t contain rlnAngleRot, rlnAngleTilt and rlnRandomSubset fields because they are parameters specific to 3D calculation.

3

Thanks @kttn. I really appreciate your help
I was trying to convert results from 2D classification only.