Hello everyone, @Omid and @olibclarke,
I always use cryolo for picking and directly import to csparc using the following very simple script.
It can be adapted to a different routine, but to make sure that it will work each time, I use the csparc’s /path_to/motioncorrected/*_patch_aligned_doseweighted.mrc as input for cryolo (which is important for the x,y axis to be the same and to match the name for each micrograph) and I import only the coordinates, while connecting the exposures to the imported particles. Make sure that all exposures used as input for cryolo are dragged to be connected with the particles (it will fail if there are particles for micrographs that are not included in the exposure set, eg because some exposures have been rejected to a previous curate exposures step).
After that you can use the imported particles and any selected subset of the exposures as input for an extraction job. For example, for a csparc live session, export exposures to csparc and then use the “all_exposures” set to connect with the particles at the import particles step but only the “accepted_exposures” for the extract from mics step (to avoid manually selecting mics twice).
Hope that helps.
Best,
Left
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cd cryolo_output/STAR
echo ' ' > ../picks.star
echo 'data_' >> ../picks.star
echo ' ' >> ../picks.star
echo 'loop_' >> ../picks.star
echo '_rlnMicrographName #1' >> ../picks.star
echo '_rlnCoordinateX #2' >> ../picks.star
echo '_rlnCoordinateY #3' >> ../picks.star
foreach file (*.star)
awk -v f="$file" '{if (NF>3) printf "%s\t%s\t%s\n", f, $1, $2}' $file >> ../picks.star
end
sed -i 's|.star|.mrc|g' ../picks.star
gedit ../picks.star #if you want to inspect the output
cd ../../
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