# pymol-mcp

> pymol-mcp — wjgoarxiv-pymol-mcp. Use this tool when you need to analyze and visualize molecular structures, trajectories, and interactions, particularly for clathrate-hydrate cage analysis and molecular dynamics simulations. It solves problems related to understanding H-bond networks, order parameters, and cage perception, providing outputs such as visualizations and occupancy metrics. It takes molecular structures and trajectories as inputs, making it suitable for use in biochemistry, materials science, and chemical engineering contexts.

Canonical page: https://skillsregistry.net/skills/wjgoarxiv-pymol-mcp  
JSON: https://api.skillsregistry.net/v1/skills/wjgoarxiv-pymol-mcp

## Description

Headless PyMOL for molecular visualization, GROMACS/LAMMPS MD trajectories, and clathrate-hydrate cage analysis: H-bond networks, F3/F4 order parameters, and TRACE cage perception + occupancy.

## Trust

- **Trust score (0–1):** 0.68
- **Verification tier:** scanned
- **Last scanned:** 2026-09-03

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** other
- **Updated:** 2026-09-03

## Source

- **Source listing:** [Glama](https://glama.ai/mcp/servers/f3mf7asepj)
- **Repository:** <https://github.com/wjgoarxiv/pymol-mcp>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "wjgoarxiv-pymol-mcp"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/wjgoarxiv-pymol-mcp` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/wjgoarxiv-pymol-mcp/pull`

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SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt