# PyMOL-MCP-Vis

> Use this tool when you need to visually analyze and verify molecular structures, as it enables control of PyMOL for molecular visualization and structural biology analysis, accepting commands as input and producing visual screenshots as output for verification. It solves problems in molecular structure analysis, protein-ligand interaction visualization, and structural biology research. This tool is ideal for use cases where visual confirmation of molecular structures is required, such as in biochemistry and pharmacology research.

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

## Description

Enables Claude to control PyMOL for molecular visualization and structural biology analysis. It uniquely features screenshot capture capabilities that provide a visual feedback loop, allowing the AI to see and verify the results of its commands.

## Trust

- **Trust score (0–1):** 0.69
- **Verification tier:** scanned
- **Last scanned:** 2026-09-02

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** other
- **Updated:** 2026-09-02

## Source

- **Source listing:** [Glama](https://glama.ai/mcp/servers/quifji584i)
- **Repository:** <https://github.com/ryannmperez/pymol-mcp-vis>

## 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": "ryannmperez-pymol-mcp-vis"
    }
  }
}
```

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