Installing VSCode and PyMOL

Welcome! This guide will walk you through installing two important programs step by step. Don’t worry if you have never installed software like this before — just follow each step carefully and you will be fine.

The two programs we are installing are:

• Visual Studio Code (VSCode) — a text editor for writing code
• PyMOL — a program for viewing 3D protein structures

Part 1: Installing Visual Studio Code (VSCode)

Visual Studio Code is a free program made by Microsoft for writing and editing code. Think of it like Microsoft Word, but for programming.

On Windows

1. Open your web browser (e.g. Chrome, Edge) and go to: https://code.visualstudio.com

2. Click the big blue Download for Windows button. A file ending in .exe will be downloaded to your computer.

3. Open your Downloads folder and double-click the .exe file you just downloaded.

4. A setup window will appear. Follow these steps inside the installer:
   • Click “I accept the agreement”, then click Next
   • Keep clicking Next on the following screens (the default settings are fine)
   • On the screen that says “Select Additional Tasks”, tick the box that says “Add to PATH” — this is important
   • Click Install
   • Click Finish when it is done
5. VSCode should now open automatically. If it does not, search for “Visual Studio Code” in the Start Menu.

On Mac

1. Open your web browser and go to: https://code.visualstudio.com

2. Click the Download for Mac button. A file ending in .zip will be downloaded.

3. Open your Downloads folder. Double-click the .zip file — it will turn into an application file called Visual Studio Code.

4. Important: Drag the Visual Studio Code application into your Applications folder. Do not run it directly from the Downloads folder, or it may not work properly.

5. Open your Applications folder and double-click Visual Studio Code to launch it.

6. If a message appears saying “Visual Studio Code cannot be opened because it is from an unidentified developer”, go to System Settings → Privacy & Security, scroll down, and click Open Anyway.

Checking VSCode Works

Once VSCode is open, you should see a welcome screen. That means the installation was successful! You do not need to do anything else with it for now.

Part 2: Installing PyMOL

PyMOL is a program used by scientists to visualise the 3D shapes of proteins and other molecules. You will use it to explore molecular structures in your project.

We will download PyMOL directly from the official website — no Python installation required, as Python is already included in the installer.

On Windows

1. Open your web browser and go to: https://pymol.org

2. Under the Download PyMOL 3.1 section, click Windows — EXE Installer. A file called something like PyMOL-3.1.7.2-Windows-x86_64.exe will be downloaded (about 367MB — it may take a few minutes).

3. Open your Downloads folder and double-click the .exe file.

4. If a warning window appears saying “Windows protected your PC”, click More info and then Run anyway — this is normal for software downloaded from the internet.

5. Follow the installer steps — the default settings are all fine. Click Next through each screen, then Install, then Finish.

6. Search for PyMOL in the Start Menu to launch it. A window with a 3D viewer should open.

On Mac

1. Open your web browser and go to: https://pymol.org

2. Under the Download PyMOL 3.1 section, click macOS — DMG Disk Image. A file called something like PyMOL-3.1.7.2_0-MacOS-x86-64-py310.dmg will be downloaded (about 167MB).

3. Open your Downloads folder and double-click the .dmg file. A window will appear showing the PyMOL icon and an Applications folder shortcut.

4. Drag the PyMOL icon into the Applications folder shown in that window.

5. Open your Applications folder and double-click PyMOL to launch it.

6. If a message appears saying “PyMOL cannot be opened because it is from an unidentified developer”, go to System Settings → Privacy & Security, scroll down, and click Open Anyway.

Checking PyMOL Works

When PyMOL opens, you will see two windows: a viewer window (black, where molecules are displayed) and a control panel. That means the installation was successful!

Troubleshooting

If you get stuck at any step, do not worry — just take a screenshot of what you see and send it to your mentor at chensimichelle@gmail.com.