pymol-visualize

name	pymol-visualize
description	Visualize, analyze, and render protein/molecular structures with PyMOL: images, structural alignment/superposition, distance/contact measurement, binding-site highlighting, and coloring by B-factor/pLDDT. Not for docking, MD, or sequence-only analysis. Local tool.
license	Apache-2.0

Pymol Visualize (Codex-native)

Codex-native adaptation of Google DeepMind's pymol skill (science-skills, Apache-2.0). Uses the public API directly through Codex's own tools.

Gates (ask before proceeding)

• Terms notice: on first use in a workspace, tell the user to review the source's terms of use and record the notice in provenance.
• Network / install: read-only public access; be polite about rate limits. Write large responses to a file and parse them; if you write helper code, run it via uv run, never bare python3. Ask before installs or large downloads.

Endpoints

• PyMOL (open-source) run locally

Workflow

1. Confirm a structure file is available (fetch via $cx-pdb-search or $cx-alphafold-structure-analysis).
2. Drive PyMOL with a script (load, select, color, orient, ray, png); ask before installing PyMOL and run it via uv run.

• Provenance & review: record queries, endpoints, and cited identifiers with $science-provenance; check claims with $science-review before presenting.

Boundaries

• This renders/analyzes existing coordinates; it does not dock or simulate.
• State the source and confidence of the structure (experimental vs predicted; pLDDT lives in the B-factor column).