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Plugin to use motioncorr programs within the Scipion framework

Project description

This plugin allows to use motioncor2 program within the Scipion framework.

Motioncor2 is a GPU-accelerated program for correction of electron beam-induced sample motion. It is developed by Shawn Zheng.

prod: prod devel: devel support: support

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-motioncorr
  1. Developer’s version

    • download repository
    git clone https://github.com/scipion-em/scipion-em-motioncorr.git
    
    • install
    scipion installp -p path_to_scipion-em-motioncorr --devel
    

Motioncor2 binaries will be installed automatically with the plugin, but you can also link an existing installation. Default installation path assumed is software/em/motioncor2-1.3.1, if you want to change it, set MOTIONCOR2_HOME in scipion.conf file to the folder where the Motioncor2 is installed. Depending on your CUDA version you might want to change the default binary from MotionCor2_v1.3.1-Cuda92 to a different one by explicitly setting MOTIONCOR2 variable. If you need to use CUDA different from the one used during Scipion installation (defined by CUDA_LIB), you can add MOTIONCOR2_CUDA_LIB variable to the config file. Various binaries can be downloaded from the official UCSF website.

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

scipion test motioncorr.tests.test_protocols_motioncor2.TestMotioncor2AlignMovies

Supported versions

1.2.3, 1.2.6, 1.3.0, 1.3.1

Protocols

  • movie alignment

References

  1. Shawn Q Zheng, Eugene Palovcak, Jean-Paul Armache, Kliment A Verba, Yifan Cheng & David A Agard. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nature Methods volume 14, pages 331–332 (2017).

Project details


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Files for scipion-em-motioncorr, version 3.0.9
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