Tools intro: PyMOL & VS Code

This introductory session walks through the core tools used in the course: PyMOL for protein and molecular visualization, and Visual Studio Code for editing and running code. You’ll get a practical overview of how PyMOL is used to explore structures, highlight key regions, and generate figures. You’ll also learn how PyMOL integrates with Python for scripting and automation to support reproducible analysis. In the second part, the video introduces the concept of an IDE (integrated development environment) and how tools like VS Code help organize code, run commands, and connect to remote compute environments. This is a high-level orientation to the tools and workflow you’ll be using before diving into hands-on exercises. More info about this Bootcamp can be found at https://rosettamlbootcamp2025.github.io/ Lead: Ian Anderson Affiliation: UC Davis Chapters 0:00 Introduction and refresher overview 0:38 What is PyMOL and tool comparisons 2:20 PyMOL as a Python-based tool and scripting capabilities 3:28 Interface basics: views, selections, and navigation 5:27 Rendering modes (sticks, lines, spheres) 6:22 Wizards and measurements (distances, analysis) 7:15 Creating publication-quality figures and aesthetics 10:38 Visual Studio Code and remote workflows 12:53 Workshop setup and next steps