UID2PNG

This script automates the retrieval of protein structure models from the AlphaFold Database using UniProt IDs and generates high-quality PyMOL visualizations for each structure.

It performs the following tasks:

1. Reads a list of protein UIDs from a TSV/CSV file.
2. Downloads the corresponding AlphaFold models from https://alphafold.ebi.ac.uk/
3. Edits a PyMOL script template for each protein.
4. Runs PyMOL in headless mode to generate:
   • A PyMOL session file (.pse)
   • A snapshot image (.png)

Requirements

• Python 3.7+
• PyMOL installed and available in your shell as $pymol
• Python packages:
  • pandas
  • requests
  • tqdm

You can install the required Python packages using:

pip install pandas requests tqdm

Input

The script requires:

• CSV/TSV file containing protein UIDs.
  • The file must have a column named uid (or customize in the script).
  • The file should be tab-separated (.tsv) or comma-separated (.csv).
• PyMOL script template (.pml file) that the script modifies for each protein.
  • The template must have placeholder commands at specific line numbers (default: line 3 for loading PDB, line 18 for saving PNG, line 19 for saving PSE).

Example input TSV (armadillo_proteins_entries.csv): uid P12345 Q8N1Q1 O96017

Usage

Default (no arguments)

1. Edit the script to set paths for:

   • The working directory (working_dir)
   • Input CSV/TSV file containing protein UIDs (list_path)
   • PyMOL template .pml file (pymol_template_path)
   • Output directory (pymol_dir)

2. Run the script from the command line:

python3 run_af2_pymol.py

With custom arguments

python3 run_af2_pymol.py
--csv path/to/your_protein_uids.csv
--uid_column uid
--output_dir ./output_dir
--pml_template ./template_script.pml
--cleanup_log

Output Files

For each protein UID, the script generates the following files in your specified output directory:

• UID.pdb — AlphaFold structure file
• UID.pml — PyMOL input script
• UID.pse — PyMOL session file
• UID.png — Rendered image of the structure
• UID.log — Log file from the PyMOL run

Note: If the --cleanup_log option is enabled, the .log files will be automatically deleted after execution.