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Plot the class distribution as a function of iteration from a Class2D or Class3D job from RELION

Project description

classconvergence

DOI

Plot the class distribution as a function of iteration from a Class2D or Class3D job from RELION.

This tool was tested with star files produced by RELION-3.1.0. Earlier versions of RELION are not supported.

Acknowledgments

I would not have been able to put this tool together without the starfile library.

Installation

I recommend to install this tool in a dedicated conda environment. You can create one like so (replace ENV_NAME with the name you want to give to this environment):

$ conda deactivate
$ conda create --name ENV_NAME python=3.9
$ conda activate ENV_NAME

Once the conda environment is active, you can install the tool with the following command:

$ pip install classconvergence

Usage

$ classconvergence --help
Usage: classconvergence [OPTIONS] <job_directory>

  Plot the class distribution as a function of iteration from a Class2D or
  Class3D job from RELION.

Options:
  -c, --count        Plot particle counts per class (default, same effect as
                     not passing any option).

  -p, --percent      Plot percentages of particles per class (default:
                     counts).

  -o, --output TEXT  File name to save the plot (optional: with no file name,
                     simply display the plot on screen without saving it;
                     recommended file formats: .png, .pdf, .svg or any format
                     supported by matplotlib).

  -h, --help         Show this message and exit.

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