PyMOL

Prerequisites

1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
2. User Notification: If .licenses/pymol_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the license at https://www.pymol.org/, then (2) create the file recording the notification text and timestamp.

Overview

All PyMOL commands run on the host via uv with OSMesa software rendering — no GPU, display, or X server is needed. Structure files must be downloaded to the host before running PyMOL.

Do NOT use when: