Tutorial 0 Introduction and Environment variables

Introduction

In this series of tutorials you will learn how to use LIT-AlphaFold for input generation, monomer structure prediction, multimer structure prediction, as and multistate structure prediction.

As an example you will be guided in generating the structure of the CXCL12 - CXCR4 dimer. The tutorials presents the instructions to generate the inputs using both local genetic databases and the MMseqs2 webserver. Since we expect that input generation using the webserver will be more common than by using the local databases, all the scripts will reference the results obtained using MMseqs2.

Before performing any of the tutorials it is necessary to activate the conda environment used by LIT-AlphaFold that was created during the installation.

conda activate lit-af

NEW: Starting from LIT-AlphaFold 1.1.0 the script inputs and some of the input files have been changed to use hydra to handle configurations, and structured .in.yaml file have replaced the unstructured .in input files.

Configuration file

In the folder conf there are the configuration files used for prediction. Before running any calculation you need to change the config.yaml files in the folders conf/features and conf/predict, changing the value of data_dir to your local directory where AlphaFold databases, and the AlphaFold weights are stored.

Environment variables

Setting environment variables is not necessary to run LIT-ALphaFold per se, but it is important for the proposed tutorials. The location of the folder containing LIT-AlphaFold can be quite long to write down. An environment variable containing the absolute path to the scripts is created. All these instructions are executed by the script export_env_variables.sh

export LITAF=/your/local/path/to/lit-alphafold

echo $LITAF