Analyse results

Output files

For every iteration, RELION will output the following files:

1. rootname_it000???_class000???.mrc (or rootname_it000???_class000???.mrcs for 2D refinements)
2. rootname_it000???_optimiser.star
3. rootname_it000???_mlmodel.star
4. rootname_it000???_data.star

These files contain the following information, respectively:

1. The images of the refined 2D/3D structures.
2. General information about the optimisation process.
3. Information about the refined model parameters apart from the images (e.g. the noise spectra, the spherical average of the signal-to-noise ratios in the reconstructed structures, the distribution of the images over the classes, the angular distributions, etc.
4. For each of the individual experimental images: information about their CTF, optimal orientation, translation and class assignment, normalisation correction, height of the (normalised) probability distribution, etc .

What to look for

For a complete list of all metadata labels, on the command-line type: relion_refine --print_metadata_labels

Monitor resolution

The highest resolution for which at least one of the models has SSNR^MAP>1 is stored as _rlnCurrentResolution in the _optimiser.star files. Therefore, progress in terms of resolution may be monitored using:

grep rlnCurrentResolution *optimiser.star

The fall-off of SSNR^MAP with resolution for each model is stored in the tables called data_mlmodel_class_N (with N being the number of the corresponding class) in the _mlmodel.star files. It is often insightful to have a look at these tables in the files themselves. Alternatively, one may use the relion_star_plottable script to make a plot (requires gnuplot to be installed), using:

relion_star_plottable rootname_it000025_mlmodel.star data_mlmodel_class_1 rlnSsnrMap rlnResolution

Although it may be better to rerun gnuplot and plot the produced plot with a limited Y-range:

gnuplot
gnuplot> set yrange [0:20]
gnuplot> load "gnuplot.plt"

TODO: mention resolution, class distribution, noise spectra, angular distribution,

Also mention utilities relion_star_plottable and relion_star_printtable

Monitor class distribution

Likewise, the distribution of all images over the various classes is stored in the table called data_mlmodel_classes in the _mlmodel.star files. Again, looking in the file itself may be easiest, or alternatively a plot may be made using the relion_star_plottable script:

relion_star_plottable rootname_it000025_mlmodel.star data_mlmodel_classes rlnClassDistribution