class averages

MRCS

18051

(None, None)

32 BIT FLOAT

(None, None)

Each subdirectory with 12 random characters contains a single 2D classification run, with an image file run_class.mrcs that contains the actual 2D class averages, the files run_model.star, run_data.star, run_sampling.star and run_optimiser.star with the corresponding metadata from RELION's 2D classification run (see RELION documentation for details), a file job_score.txt that contains the manually assigned job score for that 2D classification run, a backup_selection.star file that contains the different categories of assigned classes, which are converted to individual class scores in the class_ranker program (see function ClassRanker::getClassScoreFromJobScore inside src/class_ranker.cpp), and a file features_normalized.star that contains the features calculated by the region_class_ranker program.

One can visualise the images for each class, e.g. in directory cahg4Zo4Goos, with the following command:

relion_display --sort rlnClassDistribution --reverse --class --i cahg4Zo4Goos/run_optimiser.star --fn_imgs cahg4Zo4Goos/backup_selection.star

Classes shown in red (1 in backup_selection.star) are the best according to the manually assigned class labels in backup_selection.star; magenta (5) are second-best; green (2) third-best; and blue (3) or cyan (4) fourth-best. Yellow classes (6) or non-coloured classes (0) are the worst (score=0).

The normalised_features.star file was calculated in RELION-4.0, running the following command in csh from the main directory:

foreach opt (*/run_optimiser.star)
set dir=`echo ${opt} | awk -F"/" '{print $1}'`
echo $dir
relion_class_ranker --train --do_granularity_features --extract_subimages --subimage_boxsize 64 --nr_subimages 25 --opt ${dir}/run_optimiser.star --select ${dir}/backup_selection.star --fn_score ${dir}/job_score.txt --o ${dir} --write_normalized_features
end

Download #files