Metadata-Version: 2.1
Name: localres
Version: 1.6
Summary: Plot the histogram of local resolution values of a cryo-EM reconstruction
Home-page: https://github.com/Guillawme/localres
Author: Guillaume Gaullier
Author-email: contact@gaullier.org
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/Guillawme/localres/issues
Project-URL: Source, https://github.com/Guillawme/localres
Description: # localres
        
        [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3575229.svg)](https://doi.org/10.5281/zenodo.3575229)
        
        Plot the histogram of local resolution values of a cryo-EM reconstruction.
        
        From a cryo-EM reconstruction, one can calculate local resolution and generate a
        color-coded 3D map showing local resolution across the 3D reconstruction (or
        within slices of it). This command-line tool complements this by allowing one to
        quantitatively answer the question "how many map voxels inside the mask have a
        given local resolution?". This tool generates a histogram of local resolution
        values from a local resolution map and a mask (`relion_locres.mrc` and
        `mask.mrc` files from RELION, respectively; `cryosparc_*_map_locres.mrc` and
        `cryosparc_*_volume_mask_refine.mrc` from cryoSPARC, respectively).
        
        ## FAQ
        
        **Q:** Doesn't RELION already do this?
        
        **A:** Yes, RELION-3.1 already prints out this histogram. This tool, however,
        doesn't require an installation of RELION, allowing one to inspect files quickly
        from a different computer. This tool also lets you adjust the number of bins in
        the histogram, and save the histogram as an SVG file (which is useful for
        adjusting styling to make a pretty figure).
        
        **Q:** Doesn't cryoSPARC already do this?
        
        **A:** Yes, cryoSPARC already prints out this histogram. This tool, however,
        doesn't require an installation of cryoSPARC, allowing one to inspect files
        quickly from a different computer. This tool also lets you adjust the number of
        bins in the histogram, and save the histogram as an SVG file (which is useful
        for adjusting styling to make a pretty figure).
        
        **Q:** Will it work with MRC files produced by my favorite software (not RELION
        or cryoSPARC)?
        
        **A:** If these MRC files have the same structure, then yes. But I don't know
        for sure, because this tool has only been tested with files produced by RELION
        and cryoSPARC.
        
        ## Acknowledgments
        
        I would not have been able to put this tool together without the
        [`mrcfile`](https://github.com/ccpem/mrcfile) library.
        
        I reused code suggested by
        [@biochem_fan](https://twitter.com/biochem_fan/status/1161347681110962177). My
        contribution was simply to package it into a command-line tool that's documented
        and easy to install.
        
        ## Installation
        
        ```
        $ pip install localres
        ```
        
        ## Usage
        
        ```
        $ localres --help
        Usage: localres [OPTIONS] <relion_locres.mrc> <mask.mrc>
        
          Plot a histogram of local resolution values from a local resolution map
          and a mask both produced by RELION.
        
          For meaningful results, the mask.mrc file must be the one used for the 3D
          refinement and post-processing jobs that produced the relion_locres.mrc
          file.
        
        Options:
          -t, --title TEXT    Title of the histogram (default: no title).
          -b, --bins INTEGER  Number of bins in the histogram (default: 100).
          -o, --output TEXT   File name to save the histogram (optional: with no file
                              name, simply display the histogram on screen without
                              saving it; recommended file formats: .png, .pdf, .svg or
                              any format supported by matplotlib).
        
          -h, --help          Show this message and exit.
        ```
        
Keywords: cryo-EM map local resolution histogram visualization
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Classifier: Environment :: Console
Classifier: Natural Language :: English
Requires-Python: >=3.9.1
Description-Content-Type: text/markdown
