scipion-em-carbonara 0.0.1

Plugin to run CARBonAra within the Scipion framework

CARBonAra Scipion plugin

This plugin allows to run CARBonAra commands within the Scipion framework.

CARBonAra allows protein sequence designing based on structure atomic coordinates. Since this method takes into account the context to perform sequence generation, it is particularly helpful to design proteins embedded in molecular environments that include non-protein entities such as nucleic acids (See https://github.com/LBM-EPFL/CARBonAra/ for details and features).

Download the repository

git clone [e-mail]:scipion-em/scipion-em-carbonara.git

Install this plugin

You will need to use 3.0.0 version of Scipion to run these protocols. Instructions to install this plugin (2 options):

• Stable version

cd scipion-em-carbonara
scipion3 installp -p scipion-em-carbonara

OR through the plugin manager GUI by launching Scipion and following Configuration >> Plugins

• Developer’s version

cd scipion-em-carbonara
scipion3 installp -p path_to_scipion-em-carbonara --devel

• Configuration variables

The installation of CARBonAra within Scipion automatically defines the variable CARBONARA_ENV_ACTIVATION for specifying how to activate the conda environment required to run the final CARBonAra command.

CARBONARA_ENV_ACTIVATION = conda activate carbonara

• Binary files

The carbonara executable for Scipion will be automatically installed in your folder miniconda/envs/carbonara/bin.

Tests

Tested with the first published Carbonara version. To check the installation, simply run the following Scipion test:

scipion tests carbonara.tests.test_protocol_carbonara_sampling_sequence

Protocols

• protocol_sampling_sequence: Automatic method to generate multiple sequences able to fold in a certain structural configuration.

Examples

FAQ

Buildbot status

Status devel version: