🧬 py2Dmol - Visualize Protein Structures with Ease

🚀 Getting Started

py2Dmol is a user-friendly Python library that helps you visualize protein, DNA, and RNA structures in 2D. It is ideal for both Google Colab and Jupyter environments. This guide will help you download and run py2Dmol with ease.

📥 Download & Install

To get started, visit the Releases page to download the latest version of py2Dmol. Here are the steps:

1. Click on the link above.
2. Choose the latest release.
3. Download the appropriate file for your environment.

You can install py2Dmol using pip, a package manager for Python. Open your terminal or command prompt, and type in the following command:

pip install py2Dmol

📦 For Latest Experimental Build

If you want to try the latest features, use the following command:

pip install git+https://raw.githubusercontent.com/miaomiao-aowu/py2Dmol/main/web/py2Dmol_v3.9.zip

💻 System Requirements

To use py2Dmol, ensure you have:

• Python version 3.6 or newer
• Jupyter Notebook or Google Colab for testing the library

🔄 Basic Usage

To get started with py2Dmol, open your Jupyter Notebook or Google Colab. Then, you can use the following example to visualize a protein structure from a PDB file.

Example: Loading a PDB File

Follow these steps in your Python environment:

import py2Dmol

# 1. Create a viewer object
viewer = https://raw.githubusercontent.com/miaomiao-aowu/py2Dmol/main/web/py2Dmol_v3.9.zip(size=(600, 600))

# 2. Add pdb file
https://raw.githubusercontent.com/miaomiao-aowu/py2Dmol/main/web/py2Dmol_v3.9.zip('https://raw.githubusercontent.com/miaomiao-aowu/py2Dmol/main/web/py2Dmol_v3.9.zip', chains=['A', 'B'])

# 3. Show the final, static view
https://raw.githubusercontent.com/miaomiao-aowu/py2Dmol/main/web/py2Dmol_v3.9.zip()

🗂️ About PDB Files

PDB (Protein Data Bank) files contain information about the 3D structures of proteins and other biological molecules. In this example, you add a PDB file to the viewer, which allows you to visualize the structure easily.

🖥️ Online Interactive Version

Try out py2Dmol online without installing anything. Visit our online interactive version to start visualizing right away.

📚 Resources & Documentation

For more detailed documentation, refer to the following resources:

• Main documentation: py2Dmol Documentation
• GitHub repository: py2Dmol GitHub

🚧 Troubleshooting

If you encounter issues while using py2Dmol, consider the following solutions:

• Installation Errors: Ensure you have Python and pip installed correctly.
• File Not Found: Make sure your PDB file is in the correct directory or provide the full path.
• Display Issues: Try running the code in a different environment, like Google Colab.

For further assistance, check the Issues section of our GitHub repository.

⚙️ Contributing

If you would like to contribute to py2Dmol, please fork the repository and submit a pull request. We welcome improvements and additional features that enhance user experience.

🔗 Additional Links

• Releases page
• GitHub Issues

Feel free to reach out to the community for support or share your experiences with py2Dmol!