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

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, AlphaFold data, and the singularity image can vary between users and can be quite long to write down. Three environment variables containing the absolute path to scripts, the data, and the singularity image are created. All these instructions are executed by the script export_env_variables.sh

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

echo $LITAF
echo $AFDATA