Particles coordinate value in cryosparc exported into relino star file

Import and Export
1

Hi,

After use csparc2star.py to export metadata into relion star file, I used relion to re-extract all particles and do Class2D. But I found the coordinates in star file don’t spot particles accurately. Should I do something to change the particles location in star file? Thank you!

Jianhao

2

following… _ _ _ _ _ _

3

@DanielAsarnow I have had this problem as well, even with --swapxy… in my case, an additional manual flip in Y after csparc2star.py (using awk, like awk '{ $4=4092-$4; print $0}' whatever.star > whatever_flipY.star) seemed to fix the issue, but this doesn’t seem to always be necessary, so I am a little confused too…

Oli

4

I tried to flip coordinateY, but it doesn’t work for my case.

5

Since this is coming up a fair amount, I added --invertx and --inverty to csparc2star.py. I also updated the help text for these and --swapxy to hopefully avoid some confusion.

1 Like
6

Thanks @DanielAsarnow! Do these options also invert directionality of offsets or just coords? And should they do so if one wants to extract re-centered particles? (same q for --swapxy)

7

No, thankfully the shift conventions are consistent with Heymann et al. 2005 except for change of sign in all 3 major processing suites. The coordinate issue is a combination of conventional disagreements and FORTRAN style iteration in some programs.

1 Like
8

Good to know, thanks!