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! (bug details)
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:
- Stable version
scipion installp -p scipion-em-motioncorr
- download repository
git clone 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/motioncor2-1.4.2, 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
to 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.
To check the installation, simply run the following Scipion test:
scipion test motioncorr.tests.test_protocols_motioncor2.TestMotioncor2AlignMovies
1.2.6, 1.3.0, 1.3.1, 1.3.2, 1.4.0, 1.4.2
- movie alignment
- 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).