Cryomethods plugin

Cryomethods is a cryo-electron microscopy image processing plugin of Scipion framwork focussed mainly on processing macromolecular complexes showing extensive heterogeneity. Cryomethods will be integrated in the Scipion plugin manager but in the meantime you can install from the following steps:

1) Install CUDA:

#for example:

$sudo apt install nvidia-cuda-toolkit=10.1.243-3

2) Install miniconda:

#link to install (https://docs.conda.io/en/latest/miniconda.html)

$eval "$(/home/jvargas/.local/miniconda3/bin/conda shell.bash)"

$conda activate

3) Install scipion3 (for a detailed description check https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install.html):

$sudo apt-get install gcc-8 g++-8 libopenmpi-dev make libopenmpi-dev python3-tk libfftw3-dev libhdf5-dev libtiff-dev libjpeg-dev libsqlite3-dev openjdk-8-jdk

$export PATH=$PATH:/usr/local/cuda/bin

$conda activate

$export CXX_CUDA=g++-8

$pip install --user scipion-installer

$python -m scipioninstaller /path/where/you/want/scipion -j 4

4) Install Relion3

#if you do not have installed cmake , install it $sudo apt-get install cmake

$scipion3 plugins

#Relion requires gcc & g++ version 8. It is very likely that you are running version 9 or newer. You have to do the following:

#Use update-alternatives to change gcc to version 8 (https://linuxconfig.org/how-to-switch-between-multiple-gcc-and-g-compiler-versions-on-ubuntu-20-04-lts-focal-fossa)

$sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-8 8

$sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-8 8

$sudo update-alternatives --config gcc #(select version 8 for Relion compilation only, then change again to the previous version)

5) Install cryomethods:

Install the native build tools and FFTW headers once. alignLib is written in C; no Fortran compiler is required.

$sudo apt-get install build-essential libfftw3-dev

SWIG is installed automatically in the Scipion Python environment by the plugin installer.

Install the plugin through Scipion. The installer now compiles alignLib, checks every compiler command, and configures its runtime library path. No second repository, folder rename, manual compilation, or symbolic links are needed.

$scipion3 installp -p scipion-em-cryomethods --devel $scipion3 config --update

Optional validation:

$scipion3 python -c "from cryomethods import Plugin; Plugin.setEnviron(); import frm; print('alignLib OK')"

6) Use case: 3D autoclassification

We have included a use case to show how to run the 3D autoclassification method of CryoMethods plugin with real data. To run this example run in the command line the following line:

$scipion3 tests cryomethods.tests.test_protocols_cryomethods.Test3DAutoClasifier

This line, download the test data and run the 3D autoclassification method automatically. To open the new created project run the following line:

$scipion3 last

7) Use case: 2D autoclassification

To run this example run in the command line the following line:

$scipion3 tests cryomethods.tests.test_protocols_cryomethods.Test2DAutoClasifier

This line, download the test data and run the 3D autoclassification method automatically. To open the new created project run the following line:

$scipion3 last