Pymol

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 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.