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Plugin to use Locscale programs within the Scipion framework

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Locscale plugin

This plugin provides a wrapper around LocScale program for local sharpening of cryo-EM density maps.

PyPI release License Supported Python versions SonarCloud quality gate Downloads

Installation

You will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:

  1. Stable version

    scipion installp -p scipion-em-locscale
    
  2. Developer's version

    • download repository
    git clone -b devel https://github.com/scipion-em/scipion-em-locscale.git
    
    • install
    scipion installp -p path/to/scipion-em-locscale --devel
    

LocScale software will be installed automatically with the plugin but you can also use an existing installation by providing LOCSCALE_ENV_ACTIVATION (see below).

Important: you need to have conda (miniconda3 or anaconda3) pre-installed to use this program.

Configuration variables

CONDA_ACTIVATION_CMD: If undefined, it will rely on conda command being in the PATH (not recommended), which can lead to execution problems mixing scipion python with conda ones. One example of this could can be seen below but depending on your conda version and shell you will need something different: CONDA_ACTIVATION_CMD = eval "$(/extra/miniconda3/bin/conda shell.bash hook)"

LOCSCALE_ENV_ACTIVATION (default = conda activate locscale-2.1): Command to activate the LocScale environment.

Verifying

To check the installation, simply run the following Scipion test:

scipion test locscale.tests.test_protocol_locscale.TestProtLocscale

Supported versions

2.1

Protocols

  • local sharpening

References

  1. A.J. Jakobi, M. Wilmanns and C. Sachse, Model-based local density sharpening of cryo-EM maps, eLife 6: e27131 (2017).
  2. A.Bharadwaj and A.J. Jakobi, Electron scattering properties and their use in cryo-EM map sharpening, Faraday Discussions D2FD00078D (2022)

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Plugin to use Locscale programs within the Scipion framework

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