When running partinet detect on PartiNet denoised micrographs and writing a STAR file, the Y-axis coordinates in the output are flipped relative to the original micrograph coordinate space. This is can be easily fixed when importing into CryoSPARC using the flip in y toggle but no equivalent exists for RELION. This means particles picked by PartiNet cannot be directly used in downstream tools like RELION without manual correction.
Current workaround: extract particles in cryoSPARC and restack for import into RELION (tedious)
Fix: flip coordinates in y-axis when writing the STAR file only if they were denoised with PartiNet i.e with a flag partinet star --flipy etc
When running
partinet detecton PartiNet denoised micrographs and writing a STAR file, the Y-axis coordinates in the output are flipped relative to the original micrograph coordinate space. This is can be easily fixed when importing into CryoSPARC using theflip in ytoggle but no equivalent exists for RELION. This means particles picked by PartiNet cannot be directly used in downstream tools like RELION without manual correction.Current workaround: extract particles in cryoSPARC and restack for import into RELION (tedious)
Fix: flip coordinates in y-axis when writing the STAR file only if they were denoised with PartiNet i.e with a flag
partinet star --flipyetc