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Cryoten plugin

This plugin provide a wrapper for Cryoten which efficiently enhances Cryo-EM Density Maps using transformers

Installation

  1. Stable version
scipion3 installp -p scipion-em-cryoten

  1. Developer's version

    • download repository
    git clone https://github.com/scipion-em/scipion-em-cryoten.git
    • install
    scipion3 installp -p path_to_scipion-em-cryoten --devel

Cryoten will be installed automatically with the plugin using a Conda environment.

Configuration variables

There are some variables related to the cryoten installation. If you have installed cryoten within Scipion, you may define CRYOTEN_ENV_ACTIVATION for specifying how to activate the environment. This variable with be used together with the general conda activation to generate the final cryoten command. For example:

CRYOTEN_ENV_ACTIVATION = conda activate cryoten_env

If this variable is not defined, a default value will be provided that will work if the latest version is installed.

If cryoten is installed already outside Scipion, one could define MODEL_ANGELO_ACTIVATION. This variable will provide an activation (or load) command that can be anything and the Scipion conda activate will not be prepended. For example (loading cryoten as a module):

MODEL_ANGELO_ACTIVATION = module load cryoten/main

If you need to use CUDA different from the one used during Scipion installation (defined by CUDA_LIB), you can add MODEL_ANGELO_CUDA_LIB variable to the config file.

Protocols

  • Model builder

Tests

  • scipion3 tests cryoten.tests.tests_cryoten.TestCryoten