ProS²Vi - a Python Tool for Visualizing Proteins Secondary Structure

Setup Instructions

Follow these steps to set up ProS²Vi on your system.

Clone the Repository

1. Clone the GitHub Repository: Open your terminal and clone the repository using the following command: bash git clone https://github.com/Alisaraie-Group/ProS2Vi.git

2. Navigate to the Project Directory: Change to the directory containing the cloned repository: bash cd ProS2Vi

Prerequisites

1. Preferred Operating System: ProS²Vi needs to be run on a Linux system. For Windows users, you need to install Windows Subsystem for Linux (WSL) from the Microsoft website.
2. Installation Methods: You can install all the required components manually or automatically using the provided bash script.
3. Installation Methods: You can install all the required components manually or automatically using the provided shell script.

• Manual Installation:

  1. Install Python: Ensure Python is installed on your system. bash sudo apt-get install python3
  2. Install DSSP: bash sudo apt-get install dssp
  3. Install wkhtmltopdf: bash sudo apt-get install wkhtmltopdf
  4. Set Up a Virtual Environment: bash python -m venv venv source venv/bin/activate
  5. Install Python Requirements: bash pip install -r requirements.txt

• Automatic Installation: Run the install_dependencies.sh script that check ands install all dependencies including Python, DSSP, wkhtmltopdf, and then creates a virtual environment and installs the required Python libraries: bash chmod +x install_dependencies.sh ./install_dependencies.sh

Running ProS²Vi

You can use ProS²Vi either through a command-line parser or via a Flask-based GUI. Follow the detailed steps below for each method.

Using the Flask-based GUI

1. Run Main Script: Execute python3 pros2vi_gui.py from the terminal. This will launch a browser window.
2. Add the Protein Structure: In the browser, upload your PDB file or enter the PDB code.
3. Optional Arguments: Enter values in the optional input fields if needed.
4. Submit and Visualize: Press Submit to create the visualization. The visualization will be saved in the main directory.

Using the Command-line Parser

1. Run the Script: Provide the path to the PDF/mmCIF file and optional arguments. Example: bash python3 pros2vi_cli.py pdb_folder/1fat.pdb

2. Specify Additional Arguments: Use positional arguments for additional options. Example:

   • 30 Residues per Line and PDF Output: bash python visual.py pdb_folder/1fat.pdb -r 30 -pdf Here, -r 30 sets 30 residues per line, and -pdf generates a PDF output.

- **200 DPI Resolution and PNG Output**:
  ```bash
  python visual.py pdb_folder/1fat.pdb -o output/test.png -d 200
  ```
  Here, `-o output/test.png` sets the output path and filename to `test.png`, and `-d 200` sets the DPI to 200.

Citing ProS²Vi

If you use ProS²Vi in academic work, please cite the software as

@software{qasim_2024_12554831, author = {Qasim, Muhammad Luckman and Alisaraie, Laleh}, title = {Alisaraie-Group/ProS2Vi: ProS2Vi 1.0.1}, month = jun, year = 2024, publisher = {Zenodo}, version = {v1.0.1}, doi = {10.5281/zenodo.12554831}, url = {https://doi.org/10.5281/zenodo.12554831} }

and the article as

@misc{qasim2024pros2vipythontoolvisualizing, title={ProS2Vi: a Python Tool for Visualizing Proteins Secondary Structure}, author={Luckman Qasim and Laleh Alisaraie}, year={2024}, eprint={2408.03436}, archivePrefix={arXiv}, primaryClass={q-bio.BM}, url={https://arxiv.org/abs/2408.03436}, }