scipion-em-opusdsd 3.0.1

Plugin to use Opusdsd programs within the Scipion framework

This plugin provides a wrapper for OPUS-DSD software: Deep structural disentanglement for cryo-EM single-particle analysis.

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:

1. Stable version

scipion installp -p scipion-em-opusdsd

2. Developer’s version

   • download repository

   git clone -b devel https://github.com/scipion-em/scipion-em-opusdsd.git

   • install

   scipion installp -p /path/to/scipion-em-opusdsd --devel

OPUS-DSD software will be installed automatically with the plugin but you can also use an existing installation by providing OPUSDSD_ENV_ACTIVATION (see below).

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 below but depending on your conda version and shell you will need something different: CONDA_ACTIVATION_CMD = eval “$(/extra/miniconda3/bin/conda shell.bash hook)”

OPUSDSD_ENV_ACTIVATION (default = conda activate opusdsd-2.3.0): Command to activate the opusdsd environment.

Verifying

To check the installation, simply run the following Scipion test:

scipion test opusdsd.tests.test_protocols_opusdsd.TestOpusDsd

Supported versions

0.3.2b

Protocols

• preprocess

• training VAE

• training ab initio

References

1. OPUS-DSD: deep structural disentanglement for cryo-EM single-particle analysis. Zhenwei Luo, Fengyun Ni, Qinghua Wang, Jianpeng Ma. https://www.nature.com/articles/s41592-023-02031-6