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PyMOL · mkurman | DecimalAI

scienceby mkurman

PyMOL

mkurman/pymol

Source mkurman/zorai ↗License MIT

Visualize, analyze, and render protein and molecular structures using PyMOL.

SkillScore65Maintained

Automatic

Research pack

Last verified 8/21/2026

What it changes

Passed 12 of 18 test cases with the skill, and 9 of 18 without it.

Without skill50%

With skill65%

Checks it passed that the model alone missed

The script sets pymol.pymol_argv to include -cq.
The script aligns the structures using cmd.align.
The script sets os.environ PYOPENGL_PLATFORM to osmesa.

and 5 more in the full report

7 fixed10 passed either way6 still failing3 broke

Pass-rate lift: +15 pp
Tokens: +88%
Agent turns: 0%
Response time: +21%

Model gemini-3.6-flashMeasured 8/21/2026v117 of 26 cases passed with skill · 18 comparable

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/mkurman-pymol/SKILL.md https://app.decimal.ai/s/mkurman-pymol/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add mkurman-pymol, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/mkurman-pymol/ and pins it in .decimal/skills.lock

decimalai skills add mkurman-pymol

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/mkurman-pymol/SKILL.md https://app.decimal.ai/s/mkurman-pymol/SKILL.md

Raw file: /s/mkurman-pymol/SKILL.md ↗ · machine-readable summary at /s/mkurman-pymol.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 7 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 7

Prompt

Provide a complete executable script to load `ligand_binding.pdb` and render a cartoon image `binding.png` using `uv run` command.

What was checked, without and with the skill
Checked	Without skill	With skill
The script includes a PEP 0723 metadata block specifying dependency pymol-open-source-whl.	Missed	Passed

case-12 · gemini-3.6-flash · 8/21/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md135 lines3 files

PyMOL

Prerequisites

uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
User Notification: If LICENSE_NOTIFICATION.txt does not already exist in this skill 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

Track record

Benchmark

12 / 18

test cases passed, vs 9 / 18 without

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/3/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

mkurman / zorai

skills/scientific-skills-gdm/pymol/SKILL.md

View on GitHub ↗

License MITImported 8/3/2026Version v1Bundled 2 files

More skills from the same source and nearby in the registry, with their headline benchmark lift.

Ready to supercharge your AI agents?

See it in action

What's inside

PyMOL

Prerequisites

Overview

Setup (Agent Instructions)

Core Rules

Track record

Benchmark

Adoption

SkillSafety

Source

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