Plugin to use motioncorr programs within the Scipion framework
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.
If you have imported movies with a gain file in DM4 format, you need to flip the gain reference upside-down in the motioncor2 protocol! (see details)
When importing EER movies, you should specify dose per single EER frame during import step.
If you are processing EER movies and providing *.gain reference file camera defects will be automatically extracted from the gain file header and converted to Motioncor2 format. This step is omitted if you provide a defects file yourself.
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:
scipion installp -p scipion-em-motioncorr
git clone -b devel https://github.com/scipion-em/scipion-em-motioncorr.git
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/motioncor2-1.5.0, 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 this plugin will guess the right default binary from MotionCor2_1.5.0_CudaXY_05-31-2022 (X is for cuda major version, Y for the minor). You can always set a different one by explicitly setting MOTIONCOR2_BIN 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.
For an automatically updated installation of motioncor2 binaries, do not define neither MOTIONCOR2_HOME nor MOTIONCOR2_BIN.
To check the installation, simply run the following Scipion test:
scipion test motioncorr.tests.test_protocols_motioncor2.TestMotioncor2AlignMovies
Motioncor2 is free for academic use only. For commercial use, please contact David Agard or Yifan Cheng for licensing:
1.4.0, 1.4.2, 1.4.4, 1.4.5, 1.4.7, 1.5.0
align tilt-series movies
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).
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