Analyse results
Output files
For every iteration, RELION will output the following files:
rootname_it000???_class000???.mrc
(orrootname_it000???_class000???.mrcs
for 2D refinements)rootname_it000???_optimiser.star
rootname_it000???_mlmodel.star
rootname_it000???_data.star
These files contain the following information, respectively:
- The images of the refined 2D/3D structures.
- General information about the optimisation process.
- 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.
- 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
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