guanaco

Python library for doing 3D CTF correction

Installation

In order to build this package, the following dependencies are required:

To install from the github repository do the following

export CUDACXX=${PATH_TO_CUDA}/bin/nvcc
python -m pip install git+https://github.com/rosalindfranklininstitute/guanaco.git@master

To install from source, clone this repository. The repository has a submodule for pybind11 so after cloning the repository run

git submodule update --init --recursive

Then do the following:

export CUDACXX=${PATH_TO_CUDA}/bin/nvcc
python -m pip install .

If you would like to run the tests then, clone this repository and then do the following:

export CUDACXX=${PATH_TO_CUDA}/bin/nvcc
python -m pip install .[test]

To install for development, clone this repository and then do the following:

export CUDACXX=${PATH_TO_CUDA}/bin/nvcc
python -m pip install -e .

To run the tests, follow the installation instructions for developers and then do the following:

pytest

To do a tomographic reconstruction with no CTF correction do something do the following

guanaco -i images.mrc -o rec.mrc -d gpu

To correct all images with the same single defocus something do the following

guanaco -i images.mrc -o rec.mrc -d gpu --df=20000 --Cs=2.7

To correct all images with the same defocus range something do the following

guanaco -i images.mrc -o rec.mrc -d gpu --df=20000 --Cs=2.7 --ndf=10

Please use the GitHub issue tracker to submit bugs or request features.

Distributed under the terms of the GPLv3 license, guanaco is free and open source software.