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pymol

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Visualize, analyze, and render protein and molecular structures using PyMOL. Use when the user wants to create images of protein structures, perform structural alignments or superposition, measure distances or contacts, highlight binding sites or active site residues, color by B-factor/pLDDT, or analyze protein-ligand interactions. Do not use for docking, molecular dynamics, or sequence-only analysis.

skills/pymol/SKILL.md

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Nov 9, 2026

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Oct 23, 2026
License
Apache-2.0

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# 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
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