MCP Tools DirectoryAbout this integration
Local MCP integration for molecular visualization, trajectory inspection and hydrate-cage analysis using headless PyMOL. It requires a prepared Python/conda environment but no account authorization for local rendering.
- Transport
- stdio
- Authentication
- none
- Initial setup
- none
- Runtime
- unattended
- Evidence
- documented
- Package
- pymol-mcp
- Last compatibility test
- Not independently tested
Connect your agent
pymol-mcpLocal installation is required: use a Python/conda environment that can import pymol2. No account authorization is documented for local rendering. Arbitrary-code tools are opt-in and excluded from the default review. Documentation reviewed; not installed, executed or independently tested.
Capabilities: Molecular visualization, Trajectory inspection, Headless image rendering
Connected profiles
Additional details
pymol-mcp
Source ↗ · Checked 2026-09-170.1.0
Source ↗ · Checked 2026-09-17Publisher documents an embedded headless PyMOL worker for CI without a GUI or click-based runtime.
Source ↗ · Checked 2026-09-17The documented local stdio configuration has no API key or account login. Python 3.11+ and a conda environment containing pymol2 must be prepared first.
Source ↗ · Checked 2026-09-17Launch the prepared conda Python interpreter with -m pymol_mcp; the publisher explicitly says not to use isolated uvx environments.
Source ↗ · Checked 2026-09-17Publisher documentation reviewed; package and integration endpoint not executed or independently security-audited.
Source ↗ · Checked 2026-09-17