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Scipion plugin for ModelAngelo: an automatic atomic model building program for cryo-EM maps. With or without providing a sequence.
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scipion-em/scipion-em-modelangelo
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============================================================== DISCONTINUED.- modelangelo is part os scipion-em-relion plugin DISCONTINUED.- modelangelo is part os scipion-em-relion plugin DISCONTINUED.- modelangelo is part os scipion-em-relion plugin DISCONTINUED.- modelangelo is part os scipion-em-relion plugin DISCONTINUED.- modelangelo is part os scipion-em-relion plugin DISCONTINUED.- modelangelo is part os scipion-em-relion plugin DISCONTINUED.- modelangelo is part os scipion-em-relion plugin DISCONTINUED.- modelangelo is part os scipion-em-relion plugin DISCONTINUED.- modelangelo is part os scipion-em-relion plugin DISCONTINUED.- modelangelo is part os scipion-em-relion plugin ============================================================== ==================== Modelangelo plugin ==================== This plugin provide a wrapper for `Model angelo <https://github.com/3dem/model-angelo>`_ which allows *de novo* atomic modelling Installation ------------ a) Stable version .. code-block:: scipion3 installp -p scipion-em-modelangelo b) Developer's version * download repository .. code-block:: git clone https://github.com/scipion-em/scipion-em-modelangelo.git * install .. code-block:: 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: .. code-block:: 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): .. code-block:: 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
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Scipion plugin for ModelAngelo: an automatic atomic model building program for cryo-EM maps. With or without providing a sequence.