Python Batch Mutation Wizard (PyBmw)

PyBmw is an advanced plugin for PyMOL designed to streamline in-silico protein mutagenesis. It provides a powerful graphical user interface (GUI) to perform single and large-scale batch mutations efficiently, enhancing the standard capabilities of PyMOL's mutagenesis wizard.

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📋 Table of Contents

• 🚀 Installation
  • Method 1: URL Installation (Recommended)
  • Method 2: Manual Installation
• 📖 Documentation
  • ✨ Core Features
  • ⚙️ Basic Workflow
• ✍️ Authors
• 📄 License

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🚀 Installation

PyBmw can be installed using one of the following methods.

Method 1: URL Installation (Recommended)

This method allows for direct installation into PyMOL from the GitHub repository.

1. Copy the Raw File URL:

   https://raw.githubusercontent.com/protmind/Python-Batch-Mutation-Wizard-PyBmw-/main/pybmw.py
   

2. Install via PyMOL Plugin Manager:

   • Launch PyMOL and navigate to Plugin -> Plugin Manager.
   • Select the Install New Plugin tab, then the From URL... sub-tab.
   • Paste the copied URL into the "URL" field and click Fetch.
   • The plugin will be installed and available in the Plugin menu.

Method 2: Manual Installation

This method involves downloading the script and installing it from a local file.

1. Download the Plugin Script: Download the pybmw.py script from this repository via the Code -> Download ZIP option.

2. Install via PyMOL Plugin Manager:
   • Launch PyMOL and navigate to Plugin -> Plugin Manager.
   • Select the Install New Plugin tab.
   • Click Choose file... and locate the pybmw.py script on your local machine.

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📖 Documentation

✨ Core Features

PyBmw offers several modes of operation to accommodate diverse mutagenesis workflows.

🎯 High-Throughput Mutagenesis

• Batch Mode: Apply a single amino acid mutation to a large selection of residues simultaneously. Ideal for creating alanine scanning libraries.
• Import from CSV: For extensive mutagenesis projects, define mutations in an external CSV file. This feature automates the selection and staging of hundreds of mutations.
  • CSV File Format: A simple two-column file with Residue Identifier (Chain ResidueID) and Target Amino Acid (three-letter code). No header row is needed.
  • Example (mutations.csv):

    A 123,TRP
    A 45,ALA
    B 98,PHE
    C 210,GLY
    

🔬 Precision and Control

• Individual Mode: Assign a unique target mutation to each residue in a selection via an organized table.
• Step-by-Step Mode: Sequentially execute a list of mutations, allowing for individual rotamer selection and visual inspection at each step.

🔧 Additional Functionality

• Smart Refinement: Utilizes PyMOL's sculpting feature to refine sidechain rotamer conformations.
• Visual Feedback: Staged residues are highlighted in yellow. Mutated residues turn cyan and are labeled for easy identification.
• Data Export: Save your work as a clean PDB file, a complete PyMOL session file (.pse), or both.

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⚙️ Basic Workflow

The following steps outline a typical mutagenesis session using PyBmw.

1. Load Structure: Open a PDB file in PyMOL.
2. Select Residues: Select one or more residues for mutation in the PyMOL viewer.
3. Launch PyBmw: Navigate to Plugin -> Python Batch Mutation Wizard (PyBmw).
4. Stage Residues: Click Add to Selection in the plugin window to load the selected residues into the mutation table.
5. Configure and Execute Mutations:
   • Choose the desired mode (Batch, Individual, Step-by-Step, or Import from CSV).
   • Define the target mutations.
   • Click Mutate All or step through with Apply This Mutation.

6. **Export Your Work**: Click **Export Files...** to save the modified coordinates and/or session.

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✍️ Authors

• Jayaraman Muthukumaran
• ND Yash
• Abhinav Singh

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📄 License

This project is distributed under the MIT License. See the LICENSE file for more information.