pymol

1# PyMOL
2 
3## Prerequisites
4 
51.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
6    `uv` is installed and on PATH.
72.  **User Notification**: If .licenses/pymol_LICENSE.txt does not already exist
8    in the workspace root directory then (1) prominently notify the user to
9    check the license at https://www.pymol.org/, then (2) create the file
10    recording the notification text and timestamp.
11 
12## Overview
13 
14All PyMOL commands run on the host via `uv` with OSMesa software rendering — no
15GPU, display, or X server is needed. Structure files must be downloaded to the
16host before running PyMOL.
17 
18**Do NOT use when:**
19 
20-   The user wants to run AlphaFold predictions.
21-   The user wants docking or molecular dynamics simulations.
22-   The user only has a sequence and no structure file — fetch the structure
23    first. Check if any other installed skills can retrieve structures from the
24    PDB or AlphaFold Database before proceeding.
25 
26## Setup (Agent Instructions)
27 
28Ensure that `uv` is installed on the host system. The PyMOL scripts use PEP 0723
29headers to declare their dependencies, and `uv run` will automatically handle
30installing them (including `pymol-open-source-whl`) when the script is executed.
31 
32## Core Rules
33 
34-   **Output paths must be absolute or relative to the user's project root.**
35    Always run PyMOL scripts from the user's project directory.
36-   **Software rendering only.** Use `cmd.png()` for output. Never use
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