PyMolGridVisualiser

PyMolGridVisualiser is a Python tool designed to generate PDF visualisations of PDB files in a grid layout. Utilizing PyMOL, this tool makes it easier to visualise multiple protein structures at once.

Table of Contents

• Installation
• Usage
• FAQ

How It Works

• Searches the provided directory and its all subdirectories to find all .pdb files.
• Selects num_files worth of pdbs at random and generates an image for it via pymol API.
• Puts the images to a PDF document.

Quick Start

To quickly get started with PyMolGridVisualiser:

1. Clone this repository:

   git clone https://github.com/profdocpizza/PyMolGridVisualiser.git
   

2. Navigate to the PyMolGridVisualiser directory:

   cd PyMolGridVisualiser
   

3. Install the required packages using Anaconda:
   (If this step is taking too long, check Alternative Installation in Installation Guide)

   conda env create -f environment.yml
   

4. Activate the environment:

   conda activate pymolgrid
   

5. Get PyMol license file from https://pymol.org/edu/ and copy it to PyMolGridVisualiser directory. File ends with .lic.

6. Unzip example pdb files:

   unzip examples/pdbs/all_pdbs.zip -d examples/pdbs/
   

7. Run the tool on sample PDB files:

   python src/protein_visualiser.py --input_folder examples/ --output_filename example_pdbs
   

8. The PDF output file will be saved in /outputs directory by default.

9. Run the tool on your PDB files with custom settings:

   python src/protein_visualiser.py --input_folder "PATH/TO/YOUR/PDBS/DIRECTORY/" --filename_pattern "STRING_TO_LOOK_FOR" --num_files 1000 --grid 8 5 --output_pdf_name "YOUR_DESIRED_PDF_NAME" --output_directory "PATH/TO/OUTPUT/DIRECTORY"

For detailed usage instructions, visit the Usage Guide.