Generate PAE/PLDDT/MSA plots

As discussed before, AlphaFold does not automatically generate all visual outputs that are required for the interpretation of its predictions, but it stores information in python-specific .pkl files. Therefore, we supply a python script to do so, after prediction has finished.

In this exercise, you will generate the images from either your own AlphaFold outputs, or from the outputs for the SARSCoV1-VHH.72 protein complex. You can download them here. Upload this file to your $VSC_DATA/alphafold/runs/ directory.

Next, download the python script here.

To run the visualization, take the following steps:

  • First, we need to load the appropriate modules. Run the following two lines:
module load Python/3.8.6-GCCcore-10.2.0
module load matplotlib/3.3.3-foss-2020b

Important: for AlphaFold version 2.3.1 and later: this script has extra dependencies. This page will be updated, but for now you can load the following modules instead:

module load AlphaFold/2.3.1-foss-2022a
module load matplotlib/3.5.2-foss-2022a
  • Then, we run the python script, specifying the file locations of where the input .pkl files are located, and where the outputs should be stored (use a single dot . to specify the current directory). An example:

python --input_dir <input_directory> --output_dir <output_directory> --name <prefix>

For example:

python --input_dir runs/RBD/RBD --output_dir . --name RBD

After this, two .jpg files should have been created in the output directory.

These steps and extra information can also be found at