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pymol-setup

Install pymol-agent-bridge and configure a local socket for Claude-PyMOL integration.

3|Updated Jan 28, 2026
Search Tags:#troubleshooting#integration#setup#virtual-environment#pymol#pymol-agent-bridge
One-click install
npx skills add https://github.com/ANaka/claudemol --skill pymol-setup
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pymol-setup
Source: https://github.com/ANaka/claudemol/tree/main/claude-plugin/skills/pymol-setup
Command: npx skills add https://github.com/ANaka/claudemol --skill pymol-setup

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This skill streamlines the initial connection between Claude and PyMOL by installing and configuring the PyMOL integration, and by guiding users through common socket and setup issues.

Core Features & Use Cases

  • Install pymol-agent-bridge and configure a local socket so Claude can control PyMOL
  • Diagnose common socket errors and guide users through safe, permission-aware steps
  • Support setup in common environments (virtualenv/venv, conda, or global) with guided prompts

Quick Start

Install pymol-agent-bridge into your chosen environment and run the initial setup to enable Claude to connect to PyMOL.

Frequently Asked Questions about pymol-setup

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I connect Claude to PyMOL for molecular visualization control?▼

To connect Claude to PyMOL, you need to install the pymol-agent-bridge package and configure a local socket. This setup enables Claude to control PyMOL directly through a stable integration.

How do I troubleshoot PyMOL socket errors during agent integration?▼

PyMOL socket errors during agent integration are diagnosed by verifying your installation and checking environment configurations. The setup workflow guides you through safe, permission-aware steps to resolve these connection issues.

Can I set up the PyMOL agent bridge in a conda or virtualenv environment?▼

Yes, you can set up the PyMOL agent bridge in conda, virtualenv, or global Python environments. The guided setup process detects your active environment and configures the integration accordingly.

What is the best way to diagnose PyMOL setup issues with Claude?▼

The best way to diagnose PyMOL setup issues is to run the automated troubleshooting workflow. It verifies your installation, detects active environments, and applies safe prompts to resolve configuration errors.

Do I need pymol-agent-bridge to control PyMOL from Claude?▼

Yes, pymol-agent-bridge is required to establish a local socket connection between Claude and PyMOL. It automates the configuration needed for Claude to send commands to the PyMOL application.

Why does PyMOL integration fail when using a global Python environment?▼

PyMOL integration may fail in a global Python environment due to permission restrictions or missing dependencies. The setup workflow detects these limitations and guides you through safe, permission-aware installation steps.

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