ProtPeek

A Python desktop widget to load and display a rotating 3D protein structure from PDB codes or UniProt IDs.

Features

• 200x200px always-on-top widget
• Enter PDB code (4 characters) or UniProt ID (6+ characters) and click play to load structure
• Supports both RCSB PDB and AlphaFold structures via UniProt IDs
• 3Dmol.js viewer for interactive protein visualization
• Slow clockwise rotation of the structure
• Multiple visualization styles: cartoon, ball and stick
• Close and edit code buttons after loading
• Info button in the top-right shows app details
• Single-file EXE build supported (PyInstaller)

Requirements

• Python 3.8+
• PyQt5
• PyQtWebEngine
• requests

Setup

1. Install dependencies:

   pip install PyQt5 PyQtWebEngine requests

2. Run the app:

   python main.py

Build Single EXECUTABLE

Windows

1. Run the build script:

   build.bat

   The script will:

   • Create a virtual environment if it doesn't exist
   • Install all dependencies
   • Build the EXE using PyInstaller
   • Output the EXE to the dist folder

2. Manual build (if needed):

   python -m venv .venv
   .venv\Scripts\activate
   pip install -r requirements.txt
   pip install pyinstaller
   pyinstaller --onefile --noconsole --clean --name ProtPeek --add-data "3Dmol.js;." --collect-all PyQt5 --collect-all PyQt5.QtPlugins main.py

Linux

1. Make the build script executable:

   chmod +x build.sh

2. Run the build script:

   ./build.sh

   The script will:

   • Create a virtual environment if it doesn't exist
   • Install all dependencies
   • Build the executable using PyInstaller
   • Output the executable to the dist folder

3. Manual build (if needed):

   python3 -m venv .venv
   source .venv/bin/activate
   pip install -r requirements.txt
   pip install pyinstaller
   pyinstaller --onefile --noconsole --clean --name ProtPeek --add-data "3Dmol.js:." --collect-all PyQt5 --collect-all PyQt5.QtPlugins main.py

   Note: Use : instead of ; for --add-data separator on Linux.

Download Prebuilt Windows Binary [exe] (64-bit)

Download

Usage

• Enter a PDB code (e.g., 1UBQ) for structures from RCSB PDB
• Enter a UniProt ID (e.g., Q92793) for AlphaFold predicted structures
• Select visualization style (cartoon or ball and stick)
• Click play to load and view the structure

Info button

Click the ℹ button in the top-right to display:

"A Python desktop widget to quickly load and display a rotating 3D protein structure from PDB codes or UniProt IDs.
Developed by Saurabh Gayali."

Notes

• 3Dmol.js is required in the same directory as the executable for the viewer to work.
• The widget is always on top and positioned at the bottom-right of your screen.
• The application properly terminates all background processes when closed.
• Build scripts will use icons from the icons folder when available (.ico on Windows, .png on Linux). If missing, builds will proceed without icons.

Acknowledgements

This project uses 3Dmol.js for interactive molecular visualization.

Rego, N., & Koes, D. (2015).
3Dmol.js: molecular visualization with WebGL.
Bioinformatics, 31(8), 1322–1324.
https://doi.org/10.1093/bioinformatics/btu829