Generating a micrograph STAR file with particles from CryoSPARC

Import and Export
1

Hi everyone,
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)

thank you

2

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?

3

You could re-extract in cryoSPARC with recentering, then convert.

Or, you could use star.py --to-micrographs (which you have along with csparc2star.py).

Or, you could just use your particles file in Relion, the micrographs file is no longer required in the current version.

4

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

or from
stack.py --star outputfile.star particles1.star output.mrcs

thank you guys for helping me