Pymol

Google DeepMindOfficialPublished by Google DeepMind

Skill
Tool integration
Science and research
Apache-2.0
No issues found

From the author

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.

— the description by Google DeepMind

AutoGineer summary

Written by AutoGineer from the skill’s own files, not by the author

PyMOL is a tool for the visualization, analysis, and rendering of protein and molecular structures. It operates in a headless environment using OSMesa for software rendering, allowing users to generate images of structures, measure distances, perform structural alignments, and analyze protein-ligand interactions. The skill requires existing structure files and provides output in PNG format along with session files for further local exploration.

What it does

Renders protein and molecular structure images
Performs structural alignments and superpositions
Measures distances and contacts between residues
Highlights binding sites and active site residues
Colors structures by B-factor or pLDDT values
Analyzes protein-ligand interactions

When to use it

When you need to visualize a protein structure file
When you want to compare two structures via alignment
When you need to identify or highlight specific residues or binding sites
When you want to generate images of molecular structures for analysis
When you need to save a session for further inspection in local PyMOL

Advantages

Enables headless rendering without requiring a GPU or display
Supports standard structural analysis tasks like distance measurement and alignment
Provides session files for continued work in local environments
Automates visualization workflows through Python scripting

Usage examples

“Create an image of my protein structure colored by secondary structure.”: The agent generates a PNG image showing the protein with helices, sheets, and loops colored distinctly and saves a .pse session file.
“Show me the active site residues for this protein.”: The agent identifies the specified residues, renders them as sticks, and provides an image highlighting the active site.
“Align these two protein structures and tell me the RMSD.”: The agent performs the structural alignment and reports the calculated RMSD value to the user.
“Color my AlphaFold model by pLDDT confidence.”: The agent applies canonical AlphaFold coloring thresholds to the structure and renders the result.

Install

Download the skill as a ZIP:
https://mp-staging.autogineer.com/agent-skills/google-deepmind/pymol/download
Unzip it into the cross-client skills folder of your project:
```
mkdir -p .agents/skills && unzip pymol.zip -d .agents/skills
```

Documentation by Google DeepMind

PyMOL

Prerequisites

uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
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:

The user wants to run AlphaFold predictions.
The user wants docking or molecular dynamics simulations.
The user only has a sequence and no structure file — fetch the structure first. Check if any other installed skills can retrieve structures from the PDB or AlphaFold Database before proceeding.

Setup (Agent Instructions)

Ensure that uv is installed on the host system. The PyMOL scripts use PEP 0723 headers to declare their dependencies, and uv run will automatically handle installing them (including pymol-open-source-whl) when the script is executed.

Core Rules

Output paths must be absolute or relative to the user's project root. Always run PyMOL scripts from the user's project directory.
Software rendering only. Use cmd.png() for output. Never use cmd.draw() or cmd.ray() with hardware acceleration — OSMesa does not support it. Set environment variable PYOPENGL_PLATFORM=osmesa for headless rendering.
Always save a .pse session file alongside any PNG output. This lets the user open the session in their local PyMOL for further inspection.
Always call cmd.quit() at the end of every PyMOL script. Omitting it causes the process to stop responding.
Init boilerplate is mandatory. Every PyMOL script must begin with the initialization sequence. from pymol import cmd must come after finish_launching(), not before.
See references/PYMOL_REFERENCE.md for selection syntax, common commands, and gotchas.
Pre-Flight File Check: Before writing the PyMOL script or running it, you MUST verify that the requested structure file actually exists on the host machine.
Verify Structure Load: After loading a structure with cmd.load(), always verify it succeeded by checking cmd.count_atoms("all"). If the result is 0, print an error to stdout and call cmd.quit() immediately.
Auto-detect Alpha-Carbon Trace: For a cartoon representation your PyMOL scripts should automatically detect if the structure is an alpha-carbon trace (cmd.count_atoms("name CA") == cmd.count_atoms("all")), then you MUST follow the Alpha carbon trace cartoon recipe.
Notification: If this skill is used, ensure this is mentioned in the output.

Quick Start

Ensure structure files are downloaded to a directory in the user's project.
Write a PyMOL Python script (e.g., render.py) with the required init boilerplate and PEP 0723 header.
Run it via uv run: bash uv run render.py

Minimal example script (`render.py`)

# /// 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()

Common Recipes

See references/RECIPES.md for complete, copy-paste ready recipes. Available recipes:

Cartoon with secondary structure coloring — basic helix/sheet/loop coloring
Alpha carbon trace cartoon — force cartoon representation for CA-only structures
B-factor (pLDDT) coloring — continuous spectrum coloring by B-factor
AlphaFold pLDDT coloring — canonical threshold-based confidence colors
Highlight specific residues — show active site or key residues as sticks
Surface rendering — transparent surface over cartoon
Electrostatic surface rendering — vacuum electrostatics (qualitative)
Multi-chain complex colors — automatic per-chain coloring
B-factor putty analysis — tube width proportional to flexibility
Cavity and pocket visualization — surface cavity detection with ligand focus
Multi-structure batch rendering — render a directory of structures
Measure distance between residues — CA–CA distance with labels
Zoom into binding pocket — simple pocket focus
Protein-ligand interaction — ligand isolation, styled rendering, polar contacts
Two-structure superposition with RMSD — align/cealign with auto-fallback
In silico mutagenesis — mutate residues with the mutagenesis wizard
Load and modify an existing session — re-open a .pse file

Interpreting Output

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.

Files

ATTRIBUTION.mdAdded by AutoGineer892 B
LICENSELicence file added by AutoGineer11.1 KiB
SKILL.md6.5 KiB
references/PYMOL_REFERENCE.md5.3 KiB
references/RECIPES.md11.1 KiB
references/citation.bib143 B

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Requirements and compatibility

Works with: Claude Code, Claude apps, OpenAI Codex, GitHub Copilot, Cursor, Gemini CLI, Kiro, OpenCode, Goose, Amp, Roo Code, JetBrains Junie, Factory Droid, Devin (ex-Windsurf), Mistral Vibe, OpenHands, Letta

“Works with” means the tool reads the open Agent Skills format; a skill written for one tool may use features others lack.

Needs: Needs Python

Security

No issues found by our static scan· No issues found

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Attribution and licence

Published by

Google DeepMind

Publisher

Google DeepMind (Official)

Source

google-deepmind/science-skills · skills/pymol · commit 4de6786

Licence

Apache License 2.0 (redistribution allowed)

LICENSE (added by AutoGineer from LICENSE)
ATTRIBUTION.md (written by AutoGineer)

Synced

2026-11-08

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