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https://github.com/azazellochg/relion

Scripts for Relion 1.2+
https://github.com/azazellochg/relion

bash matlab

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Scripts for Relion 1.2+

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README 

        
Relion

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###Scripts for Relion 1.2+



#####JumperAnalysis



This MATLAB package provides a quantitative analysis to determine the iteration of convergence and the number of distinguishable classes, based on the statistics of the single particles in an iterative classification scheme, as used by Relion 3D classification.



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#####exclude_bad_classes_relion



You may use the following script to remove bad 2D (or 3D) classes from your dataset. It will clean up your star file, removing particles from bad classes.



The input parameters are:



* PLT file containing the bad class numbers (one number per line)

* Data STAR file containing the last CL2D/CL3D iteration you want to clean up

* Name of the output star file



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#####make_star_for_ptcl_sort



This script will extract coordinates of all particles from gempicker output and convert them to box format, then remove bad particles (not extracted in relion) and create a data star file for particle sorting according to picking references.



*Protocol:*



0. Do CTF correction and preliminary 2D classification in Relion to generate 2D references for autopicking

1. Run gempicker using 2D class average references from relion (do not renumber them!), rescale box files, remove particles too close to the border (use change_box script)

2. Extract particles in relion, creating data star file

3. Run this script, it will add reference-related columns to input star file

4. Run particle sorting in relion, remove particles with too low/high Z-score



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#####plot_classes



You may use the following script to plot particle distribution inside 2D classes from your dataset. The script also prints min,max and average number of particles over all classes. It will use the data star file after successfull 2D classification.



The input parameter is:



* Data STAR file containing the last CL2D iteration



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#####remove_bad_img.sh



Sometimes for negative stain "remove dust" options in relion are not working properly, creating strange pattern of dots. Here the script will use IMAGIC to remove images with extremely low/high pixel densities. Particles order should be the same in imagic stack and corresponding star file!



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#####remove_pref_views.sh



The script removes over-represented views within Relion STAR files. First, the user should plot [angular distributions](https://github.com/leschzinerlab/Relion/blob/master/plot_indivEuler_histogram_fromStarFile.py) to find the preferential views. The script requires angular range and number of particles to be removed. Optionally, before removing particles can be sorted by MaxProb or likelihood value (to remove particles withing specified angular range with the worst MaxProb or likelihood).



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#####renumber_classes



This small script will renumber class numbers in input star file. This can be useful when one wants to do particle sorting in Relion with only selected (i.e., good ones) 2D classes and not all of them, as suggested by default. The suggested procedure is the following:

* extract (+regroup if necessary) particles according to selected 2D classes in Relion display

* extract class images of the previous selection

* run the script on both files

* run _Particle sorting_ in Relion using these two input files



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#####star_fix_origins.sh



This script will parse an input particle star file and will create corrected coordinate star files for the particle re-extraction in Relion as well as micrograph star file. This can be useful e.g. after 3D refinement to decrease interpolation. It is recommended to start the script in Relion project folder so it can locate the micrographs correctly!