PPIIMoL
PPIIMoL
PPIIMoL is a Python module for PyMOL that automates the detection of polyproline II (PPII) helices in proteins. It streamlines structural analysis by:
- Identifying characteristic torsional angles (phi and psi) of PPII helices.
- Detecting potential non-canonical hydrogen bonds (Cα-H···O=C) relevant to structural stability.
- Exporting results for further analysis.
- Providing direct, customizable visualization in PyMOL.
This tool was developed as part of a Bachelor's Thesis in Computer Engineering in collaboration with the CSIC neuroscience laboratory.
Features
- 🔍 Automatic detection of PPII segments via phi/psi angle analysis.
- 🧬 Identification of Cα-H···O=C interactions relevant to structural stability.
- 📊 CSV export of detected segments and interactions.
- 🎨 Direct visualization in PyMOL with customizable color codes.
- 🖱️ Simple Tkinter-based GUI — no commands required; all actions are accessible via buttons.
Requirements
Installation
Quick method:
- Download `PPIIMoL.py` directly from the GitHub repository.
- In PyMOL, run:
run /path/to/PPIIMoL.py
Full repository (optional):
- Clone the repository to also get example files and documentation:
git clone https://github.com/silviaenma/PPIIMoL.git
- In PyMOL, run:
run PPIIMoL/PPIIMoL.py
(Optional) Install permanently as a plugin:
- In PyMOL: Plugin → Plugin Manager → Install New Plugin.
- Select `PPIIMoL.py` or the full `PPIIMoL` folder.
- Restart PyMOL.
Usage
Once loaded, PPIIMoL opens a Tkinter-based graphical interface. From this window, you can:
- Load a PDB file.
- Detect PPII helices.
- Export results as CSV.
- Change visualization colors directly.
Results are automatically exported to a folder named with the current date, containing CSV files with detected segments and interactions. Detected PPII helices are highlighted in PyMOL according to the selected color scheme.
Repository
The project is hosted on GitHub: PPIIMoL on GitHub
License
This project is licensed under the GNU GPLv3.