Pymol

Source: science_skills/pymol/

Overview

• The output/ directory contains PNG images and a .pse session file.
• Any measurements or metrics (distances, RMSD, atom counts) are printed to stdout by the PyMOL script. Report these values to the user.
• Present PNG images to the user and describe the visualization.
• Tell the user they can open the .pse file in their local PyMOL to further explore, rotate, or modify the visualization.
• If the user wants modifications, load the saved .pse in a new script and re-run.
• Large sessions with surfaces can exceed the --max_output_mb limit (default 500 MB). Increase it with --max_output_mb=1000 if needed.

Core Rules

• Output paths must be absolute or relative to the user's project root.

References

• science_skills/pymol/references/PYMOL_REFERENCE.md
• science_skills/pymol/references/RECIPES.md

Prerequisites

• Requires uv on PATH
• Use wrapper scripts for rate limits