Plot a histogram of local resolution values from a local resolution map of a cryo-EM reconstruction from RELION.
Plot a local resolution histogram from a local resolution map and a mask.
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 (
mask.mrc files from RELION, respectively).
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: Will it work with MRC files produced by my favorite software (not RELION)?
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.
I reused code suggested by @biochem_fan. My contribution was simply to package it into a command-line tool that's documented and easy to install.
$ pip install localres
$ localres --help Usage: localres [OPTIONS] <relion_locres.mrc> <mask.mrc> Plots 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.
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