sorry if this topic was raised previously but I havent found a clear answer.
I have done preprocessing, 2D classification, Hetergeneous and Homogeneous refinements in Cryosparc.
Now I would like to run a 3D classification without alignment in Relion; but before I do that, I would like to run a re-extract job to center the particles and rescale the particles.
So, in order to do the re-extract job, I need a particles.star (I generated it with csparc2star.py) and a micrograph STAR file.
How do I generate a micrograph STAR? (what’s command line in pyem)
Hi Proteino, I’m not sure you need to generate a star file for the mics. Could you import the mics to relion and then use that import star file?
You could re-extract in cryoSPARC with recentering, then convert.
Or, you could use
star.py --to-micrographs (which you have along with
Or, you could just use your particles file in Relion, the micrographs file is no longer required in the current version.
so for star.py --to-micrographs creates a micrographs.star file with references to the micrographs, so for this case which star file do you input:
is it the one from?
csparc2star.py passthroughparticles.cs particles.cs particles1.star
stack.py --star outputfile.star particles1.star output.mrcs
thank you guys for helping me