Follow your classification and refinement in Relion in the real time!
Simple python script which enables to follow the progress of 2D/3D classification and refinement in Relion.
---Requirements---
- Python 3+ with:
- matplotlib
- gemmi
- mrcfile
- numpy
- pandas
---How to run---
Install own python enviroment:
python3 -m venv new-env
Activate enviroment:
source new-env/bin/activate
Install packages:
pip install numpy matplotlib pandas gemmi mrcfile
Run script from command line:
python follow_rln_classification.py --i /path/to/classification/folder/ --w wait_time_in_seconds
Help can be accesed by:
python follow_rln_classification.py --h
usage: follow_rln_classification.py [-h] [--i I] [--w W]
Real-time preview Relion classification output from Class2D, Class3D and
Refine3D jobs, including volume projections, class distributions and estimated
resolution plots
optional arguments:
-h, --help show this help message and exit
--i I Classification folder path
--w W Wait time in seconds between refreshes. Adjust accordingly to
the expected time of the iteration. If the time is up and there
no new classification results plots will freeze
Double click the .py file and chose the directory where the classification or refinement has already been started. Opened window will update as soon as the iteration is finished.
---Update---
200420: Now single script avaiable for all classification runs, including plotting of class distribution and class estimated resolution. All previous scripts are obsolete.
191010: class2D: now preview also works for the runs which were continued (run_ctXX_itXX...).
2D classification preview:
3D classification preview:
Class distribution and estimated resolution plots:
