Quick update on converting particle coordinates.
--swapxy was always needed for correct coordinate output, it is now the default. If you pass the argument, you will be reminded that it is no longer needed. This change will make converting less tiresome and also less prone to user error. In the very unlikely event you need to unswap the axes, you can use
Further, there was a logic error in
--inverty that could make the argument have no effect. This has been addressed. I have also determined that
--inverty is necessary only when applying coordinates obtained after Patch Motion to micrographs produced by Relion or Motioncor2 (or, I assume, WARP), because Patch Motion physically flips the images relative to what is shown in SerialEM / Digital Micrograph. The same effect can be obtained using Invert Y from the Extract Particles options. (For example, if you forgot --inverty and are extracting the Motioncor2 images in cryoSPARC again).
I apologize if this changes how you have to call csparc2star.py - but then I would also ask, why are you rotating your micrographs 90˚ after motion correction?
More details are given in a github issue and as comments in the conversion code.