Pymol

What it does

When your agent uses it

• The user wants to create images of protein structures
• Perform structural alignments
• Measure distances
• Highlight binding sites

Example prompts

• “/pymol”

Requirements

• Python 3

Workflow steps

2 steps, taken from the first numbered list in SKILL.md.

1. 1uv: Read the uv skill and follow its Setup instructions to ensure
2. 2User Notification: If .licenses/pymol_LICENSE.txt does not already exist

What it can do on your machine

Read from SKILL.md and the folder at commit 6883275. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Shell commands in SKILL.md call:

  • uv
  • bash

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  Links to these hosts (documentation or services it may open):

  • pymol.org

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Pymol loads about 1.6k tokens when it runs, and up to ~5.9k if it reads all its reference files. Until then it costs about 103 tokens; SKILL.md has 694 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~103

When it runs · the whole SKILL.md, loaded when a task matches

~1.6k

With references · SKILL.md plus every file in references/, read only if the agent opens them

~5.9k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from google-deepmind/science-skills at commit 6883275, republished under its Apache-2.0 licence (© google-deepmind). 694 words, ~1,646 tokens.

name

pymol

description

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.

# /// script
# requires-python = ">=3.10, <3.13"
# dependencies = [
#     "pymol-open-source-whl",
# ]
# ///

import os
import sys

# Set environment variable for headless rendering
os.environ["PYOPENGL_PLATFORM"] = "osmesa"

import pymol # pytype: disable=import-error
pymol.pymol_argv = ["pymol", "-cq"]
pymol.finish_launching()

from pymol import cmd # pytype: disable=import-error

cmd.load("AF-P00520-F1-model_v4.cif", "structure")
cmd.show("cartoon")
cmd.color("green", "ss h")
cmd.color("yellow", "ss s")
cmd.color("gray", "ss l+''")
cmd.orient()
cmd.set("ray_opaque_background", 1)
cmd.png("output/render.png", width=1200, height=900, dpi=150)
cmd.save("output/session.pse")
cmd.quit()

© google-deepmind, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 3 other files (references) in skills/pymol of google-deepmind/science-skills.

• SKILL.md
• references/PYMOL_REFERENCE.md
• references/RECIPES.md
• references/citation.bib

Open the folder on GitHubat commit 6883275

Used in 2 other repositories

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in google-deepmind/science-skills, which our catalogue first saw on October 7, 2026.

• NeuroAIHub/BrainPilotpackages/skills/skills/09_Cellular_Molecular_Neuroscience/pymol
• franklee16/academic-research-skillsscience-skills/pymol