Analyse results: Difference between revisions
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= Output files = | = Output files = | ||
For every iteration, RELION will output the following files: | For every iteration, RELION will output the following files: | ||
* <code>rootname_it???_class???.mrc</code> (or <code>rootname_it???_class???.mrcs</code> for 2D refinements) | |||
* <code>rootname_it???_optimiser.star</code> | |||
* <code>rootname_it???_model.star</code> | |||
* <code>rootname_it???_data.star</code> | |||
* <code>rootname_it???__sampling.star</code> | |||
Note that for the 3D auto-refine procedure a gold-standard FSC procedure is employed, where two models are refined independently. This will lead to the following | Note that for the 3D auto-refine procedure a gold-standard FSC procedure is employed, where two models are refined independently. This will lead to the following model and class files: | ||
* <code>rootname_it???_half1_class???.mrc</code> and <code>rootname_it???_half2_class???.mrc</code> | |||
* <code>rootname_it???_half1_model.star</code> and <code>rootname_it???_half2_model.star</code> | |||
The output files contain the following information, respectively: | |||
# The images of the refined 2D/3D structures. | # The images of the refined 2D/3D structures. |
Revision as of 12:19, 19 July 2012
Output files
For every iteration, RELION will output the following files:
rootname_it???_class???.mrc
(orrootname_it???_class???.mrcs
for 2D refinements)rootname_it???_optimiser.star
rootname_it???_model.star
rootname_it???_data.star
rootname_it???__sampling.star
Note that for the 3D auto-refine procedure a gold-standard FSC procedure is employed, where two models are refined independently. This will lead to the following model and class files:
rootname_it???_half1_class???.mrc
androotname_it???_half2_class???.mrc
rootname_it???_half1_model.star
androotname_it???_half2_model.star
The output 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 .
- Information about the angular and translational sampling
What to look out for
The most common indicators to look out for are given below. 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 *model.star
The fall-off of SSNR^MAP with resolution for each model is stored in the tables called data_model_class_N
(with N being the number of the corresponding class) in the _model.star
files. It is often insightful to have a look at these tables in the files themselves. Alternatively, one may use the STAR file utilities to make a plot (requires gnuplot to be installed), using:
relion_star_plottable rootname_it025_model.star data_model_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"
Monitor class distribution
Likewise, the distribution of all images over the various classes is stored in the table called data_model_classes
in the _model.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_it025_model.star data_model_classes rlnClassDistribution
Angular distribution
The angular distribution for each model is stored in the table data_model_pdf_orient_class_N
in the _model.star
files, with N being the class number. The actual angles (rot and tilt) for these values are stored in the rootname_sampling.star
file. combination of these two files could be used to make fancy plots, but no utility for this has been implemented yet.
Per-image indicators
The _data.star
files store per-image indicators. Apart from the obvious orientational and class assignments, look out for the following variables:
_rlnMaxValueProbDistribution
: values close to one indicate that the probability distributions over all orientations and classes have converged to near-delta functions. Values close to zero indicate great uncertainty in the assignments (i.e. near-even distributions). Typically, these values increase during multiple iterations (with constant sampling rates)_rlnLogLikeliContribution
: higher values mean better agreement between experimental data and model. This variable is the equivalent of the cross-correlation coefficient or phase residual in other programs. One could make histograms of all values in order to disard particularly bad images.
Linear plots of these values for each image may be made using:
relion_star_plottable rootname_it025_data.star data_images _rlnLogLikeliContribution