Converting to star file

[peter.cherepanov]

I tried several ways, with and without passthrough file, using cs files from a Refinement or Select 2D jobs. The only method that worked was to convert cs to star without any options:
csparc2star.py cryosparc_P116_J670_001_particles.cs cryosparc_P116_J670_001_particles.star

then curing mcs file names in the resulting star file with sed:
sed 's/J664\/imported\/[0-9]*_FoilHole/Extract\/job025\/Micrographs\/FoilHole/g'

then re-calling the lines using grep and copying the header from the original relion extract star file:

Feature request - preserve MicrographName column from star file

A temporary work around is to use the _rlnImageName column to grep all the particles in a cryosparc-generated subset from the original input particle star file. e.g. awk '{print $9}' csparc.star > particles.list to make a list of particle names; touch csparc_relion.star to make a fresh star file; Then while read line; do fgrep "$line" all_particles.star; done < particles.list >> csparc_relion.star to grep the particles from the input star and output to another file. (And then add starfile hea…

I don’t know what changed. I think we are using the latest version of csparc. Dashboard says “Current version: v3.2.0+210713”. Pyem is fairly recent (updated on 20210614).

Peter