/scipion-em-modelangelo

Scipion plugin for ModelAngelo: an automatic atomic model building program for cryo-EM maps. With or without providing a sequence.

Primary LanguagePythonGNU General Public License v3.0GPL-3.0

Modelangelo plugin

This plugin provide a wrapper for Model angelo which allows de novo atomic modelling

Installation

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

  1. Developer's version

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

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

Configuration variables

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

MODEL_ANGELO_ENV_ACTIVATION = conda activate model_angelo

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

If model-angelo 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 model-angelo as a module):

MODEL_ANGELO_ACTIVATION = module load model-angelo/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 modelangelo.tests.tests_model_angelo.TestModelAngel