Pymol
Visualize, analyze, and render protein and molecular structures using PyMOL.
Install
npx skills add google-deepmind/science-skills --skill pymol -g -a claude-code -y- Repository
- google-deepmind/science-skills3.4k
- Category
- Engineering
- Updated
- 12d ago
- License
- Apache-2.0
- Context cost
- Mediumabout 1,532 tokens
- Runs scripts
- No, instructions only
What it does
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.
PyMOL
Prerequisites
uv: Read theuvskill and follow its Setup instructions to ensureuvis 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.
