@tarek it doesn’t affect reconstructions, or imported coordinates. You say switching X and Y “fixes” the coordinates, but I’ve gone over this before and found that the coordinates aren’t right regardless of the convention, when they are actually displayed in
relion_display_gui. I left it the way it is because it was closer than the other way during these tests. (I also tried a few possible alternate conventions). I also think the convention in cryoSPARC may have changed at some point, and might not agree between movies (3D) and micrographs (2D). There’s also another field,
micrograph_blob/shape, but right now I’m just looking at the
For example with a command like:
relion_display --coords J31/imported/stack_0495_2x_SumCorr.star --i J31/imported/stack_0495_2x_SumCorr_T.mrc --angpix 1.2156 --lowpass 20 --particle_radius 100 --pick --scale 0.2 &
are the particles really in the right place and centered?
If @apunjani gives us the conventions, or we’re very sure we have it figured out, I can update
csparc2star.py one last time. The official export feature should be released soon, so if it’s not a trivial edit I may decide to skip it.