When I run polishing training in Relion, it warns:
- Movies for the following micrographs are missing:
[all of them]
My dataset was processed entirely in CS/CS Live and I exported micrographs and particles for polishing in Relion. I followed Method 2 in the pyem wiki.
I made symlinks to my doseweighted, aligned micrographs from CS in MovieExports/Movies/.
I made symlinks to my accepted movies in Movies/.
I create my micrograph star files with:
csparc2star.py --movie --micrograph-path Movies/ P70/J303/P70_S2_accepted_live_exposures.cs MovieExport/corrected_micrographs.star MovieExport/Movies
Following the lead of some helpful posts on this board, I check the micrograph star files and find that they link to micrographs in the wrong location - the last line should be MovieExport/Movies, not Movies:
I can correct the path in the star files with sed:
for file in ./*.star
sed -i 's/_rlnMicrographName Movies/_rlnMicrographName MovieExport\/Movies/g' $file
and similarly can correct the paths for _rlnMicrographName in MovieExports/corrected_micrographs.star, but can’t figure out why I’m getting this output in the first place. Would appreciate if anybody could set me straight.