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Quickstart Guide

Steps

  • (Required) It is assumed that all imported movies or micrographs in the Relion project are in one folder and not in a complex EPU hierarchy.
  • Start any supported version of Relion in a new terminal, the micassess submission script uses its own environment without interference.
  • Go to External section at the bottom
  • As external executable enter relion_ext_micassess.sh
  • As input micrographs use a Motioncorr job result file like corrected_micrographs.star, both float32 and float16 micrographs are supported
  • At the Running tab disable cluster submission. Otherwise Relion will use the Relion template instead of the used micassess script.
  • Press Run and watch the logfiles until its finished.

Relion Import Relion Import

When the script is done look at the Relion log window for something like below. The section before ### is the output of micassess, the lines afterwards come from postprocessing from my script. The list of good micrographs contains the great ones.

Found 433 images belonging to 1 classes.
Found 433 images belonging to 1 classes.
Total:	 433 micrographs
0Great :	 83 micrographs
1Decent :	 308 micrographs
2Contamination_Aggregate_Crack_Breaking_Drifting :	 34 micrographs
3Empty_no_ice :	 8 micrographs
4Crystalline_ice :	 0 micrographs
5Empty_ice_no_particles_but_vitreous_ice :	 0 micrographs
19.17% of the micrographs are great and were written in the *_great.star file.
90.30% of the micrographs are good and were written in the *_good.star file.
Details can be found in the output directory.
#####################################
MicAssess: see the result preview images in: External/job015/MicAssess
MicAssess: consider to delete the movies in: External/job015/movies_to_remove.txt to save disk space
MicAssess: consider to use: External/job015/micrographs_micassessed.star for the next analysis step

So you can use as input for CTF jobs a pattern like:

External/job015/micrographs_micassessed.star

This file is a modified version of the output file from the motioncorrection job. So it contains all necessary values from Relion, it just misses the micrographs and corresponding values considered as not good.

Preview the result via thumbnail images

Just go to the directory and start the filemanager. With doubleclicks on a image you get the image viewer:

cd External/job015/MicAssess
thunar .

Cleanup movies to save disk space

The script generates a list of TIFF movies not used, when you continue with the micrographs_micassessed.star file you could consider to remove them later from the storage or move them to an archive space.

cd External/job015
for i in $(cat movies_to_remove.txt); do find /where_your_movie_topfolder_is/ -name $i; done

If you are think you have the correct movies and not links to a different location you can REALLY DELETE them like:

for i in $(cat movies_to_remove.txt); do find /where_your_movie_topfolder_is/ -name $i -delete; done

Or you can move them to an ARCHIVE SPACE like:

mkdir /dcache/wherever_my_movies
for i in $(cat movies_to_remove.txt); do find /where_your_movie_topfolder_is/ -name $i -exec mv -v {} /dcache/wherever_my_movies \; ; done