Pre-work 2: PyMOL and VS Code Setup

Overview

This assignment ensures you have PyMOL and VS Code installed and configured for the bootcamp. You will:

  1. Install PyMOL (a molecular visualization tool)
  2. Install VS Code (a powerful code editor/IDE)
  3. Verify your installations by completing hands-on tasks

Prerequisites

  • HW1 completed

Part 1: PyMOL Installation

PyMOL is a molecular visualization tool that is super useful for visualizing, manipulating, and analyzing molecular structures, especially proteins. We will use PyMOL to explore protein structures during bootcamp. We recognize that it’s likely you are already quite familiar with PyMOL but if you have been using an alternative visualization software, this is a great opportunity to explore PyMOL. Please be ready to use this in the Bootcamp.

Installation Options

Option 1: Official PyMOL (Requires Educational License) 1. Visit the PyMOL website: https://pymol.org/ 2. Obtain a free educational license: https://pymol.org/edu/ 3. Download and install PyMOL

Option 2: Open-Source PyMOL via Homebrew (Mac users) If you have Homebrew installed:

brew install pymol

Verify installation by launching PyMOL (GUI) from your applications or by running:

pymol

Optional PyMOL Learning Resources

Though a comprehensive understanding of the various features in PyMOL is not within the scope of this course, it may be a useful tool for your future work and presentations.

Customizing PyMOL (Optional)

If you would like to alter your visual defaults, you may do so by editing your .pymolrc, which is a script that gets read every time PyMOL opens. To do so, go to File > Edit pymolrc. Here are the defaults that Rosetta member Joey Lubin uses, which can be pasted into the window that opens.

Part 2: VS Code Installation

VS Code is a powerful IDE that is largely customizable and can incorporate many different extensions and features. If you do not have VS Code or an alternative IDE, please install it before the bootcamp.

Installation Options

Option 1: Download from Website Visit the VS Code website: https://code.visualstudio.com/

Option 2: Install via Homebrew (Mac users) If you have Homebrew installed:

brew install --cask visual-studio-code

Verify installation by launching VS Code or running:

code --version

Part 3: Verification Tasks

Now let’s verify that everything is working correctly!

Task 1: PyMOL Verification

  1. Fetch a protein structure:
    • Open PyMOL
    • In the PyMOL command line, type: fetch 1ubq
    • This fetches ubiquitin (PDB ID: 1UBQ), a small regulatory protein
  2. Style your visualization:
    • Try different representations (cartoon, sticks, surface, etc.)
    • Color the structure in a way you find visually appealing
    • Feel free to experiment!
  3. Save your work:
    • Save the PyMOL session: File > Save Session As...
    • Name it 1ubq_session.pse and save it in this assignment directory
    • Export an image: File > Export Image As > PNG...
    • Name it 1ubq_visualization.png and save it in this assignment directory

Task 2: VS Code Verification

  1. Open VS Code

  2. Create a Python script:

    • Open this assignment folder in VS Code: File > Open Folder...
    • Create a new file called verify_setup.py
    • Copy and paste the verification script (provided in this repository)
    • Run the script to verify your setup

  3. Run the verification script:

    • Open the integrated terminal in VS Code: Terminal > New Terminal
    • Activate your conda environment from HW1: conda activate bootcamp2025_HW1
    • Run: python verify_setup.py
    • The script will check your installations and create a verification_result.txt file

Part 4: Verify Your Work

Since this is a self-guided activity, verify that you have the following files in your working directory:

  1. 1ubq_session.pse - Your saved PyMOL session. Open it to make sure it loads your view.
  2. 1ubq_visualization.png - Your rendered image of Ubiquitin.
  3. verification_result.txt - Output from the verification script showing success.

Self-Check: - Can you navigate comfortably in PyMOL (rotate, zoom, clip)? - Can you run a Python script directly inside VS Code? - Did you successfully install the Python and Jupyter extensions?

If yes, you are ready for the next module!

Troubleshooting

WarningCommon Issues

PyMOL Issues

PyMOL won’t launch: - Make sure you’ve completed the installation fully - Mac users: Try the Homebrew installation method - Make sure you’re launching the GUI application, not just the Python package

Can’t fetch PDB structures: - Check your internet connection - Try: fetch 1ubq, type=pdb1 if the default doesn’t work

VS Code Issues

code command not found: - On Mac: Open VS Code, press Cmd+Shift+P, type “shell command”, and select “Install ‘code’ command in PATH” - On Windows: VS Code should be in your PATH automatically after installation

Python extension not working: - Make sure Python is installed (you should have this from HW1) - Restart VS Code after installing extensions

Questions and Getting Help

If you have questions or encounter issues while working through this module, please open an issue on the GitHub repository (GitHub account required).