Plugin to use cryoDRGN within the Scipion framework
Project description
This plugin provide a wrapper around cryoDRGN software: Deep Reconstructing Generative Networks for cryo-EM heterogeneous reconstruction.
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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:
Stable version
scipion installp -p scipion-em-cryodrgnDeveloper’s version
download repository
git clone https://github.com/scipion-em/scipion-em-cryodrgn.gitinstall
scipion installp -p path_to_scipion-em-cryodrgn --devel
cryoDRGN binaries will be installed automatically with the plugin at software/em/cryoDRGN-0.2.1, but you can also link an existing installation.
Important: you need to have conda (miniconda3 or anaconda3) pre-installed to use this program.
Configuration variables
CONDA_ACTIVATION_CMD: If undefined, it will rely on conda command being in the PATH (not recommended), which can lead to execution problems mixing scipion python with conda ones. One example of this could can be seen bellow but depending on your conda version and shell you will need something different: CONDA_ACTIVATION_CMD = eval “$(/extra/miniconda3/bin/conda shell.bash hook)”
CRYODRGN_HOME (default = software/em/cryoDRGN-0.2.1): Path where the cryoDRGN is installed.
CRYODRGN_ACTIVATION_CMD (default = conda activate cryodrgn-0.2.1): Command to activate the cryoDRGN environment.
Verifying
To check the installation, simply run the following Scipion test:
scipion test cryodrgn.tests.test_protocols_cryodrgn.TestCryoDrgn
Supported versions
0.2.1
Protocols
preprocess
training
References
CryoDRGN: Reconstruction of heterogeneous structures from cryo-electron micrographs using neural networks. Ellen D. Zhong, Tristan Bepler, Bonnie Berger, Joseph H. Davis. 2020, https://www.biorxiv.org/content/10.1101/2020.03.27.003871v1
Reconstructing continuous distributions of 3D protein structure from cryo-EM images. Ellen D. Zhong, Tristan Bepler, Joseph H. Davis, Bonnie Berger. ICLR 2020, https://arxiv.org/abs/1909.05215
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Source Distribution
Hashes for scipion-em-cryodrgn-3.0.0b1.tar.gz
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| BLAKE2b-256 | 84ceebd83bb46155cc4710913aa0cdaaae0ef7edb0ffaf15b60c9aa9579116b3 |
