Pymol

Setup Instructions

Quick Setup (All Platforms)

Run the automated setup script:

python /path/to/skills/pymol/scripts/setup_pymol.py

Manual Setup

1. Install claudemol

pip install claudemol

2. Install PyMOL

macOS (Recommended):

brew install pymol

Windows/Linux (Headless):

pip install pymol-open-source

Windows (Licensed PyMOL): Connect to existing PyMOL installation - see references/troubleshooting.md

3. Configure PyMOL

claudemol setup

This adds the socket plugin to PyMOL's startup.

4. Launch and Verify

1. Start PyMOL normally
2. Check that port 9880 is listening:

   lsof -i :9880  # macOS/Linux
   netstat -an | findstr 9880  # Windows
   

Socket Communication

claudemol communicates with PyMOL via a TCP socket on port 9880.

Basic Pattern

import socket
import json

def send_pymol_command(code: str, host: str = 'localhost', port: int = 9880) -> dict:
    """Send a command to PyMOL via claudemol socket."""
    sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
    sock.settimeout(30)
    try:
        sock.connect((host, port))
        message = json.dumps({"code": code})
        sock.sendall(message.encode('utf-8'))
        response = sock.recv(65536)
        return json.loads(response.decode('utf-8'))
    finally:
        sock.close()

Multi-Command Example

commands = """
cmd.load('1ubq.pdb')
cmd.show('cartoon')
cmd.color('cyan', 'all')
cmd.orient()
"""
result = send_pymol_command(commands)

Quick Reference

Loading Structures

# From local file
cmd.load('/path/to/structure.pdb')
cmd.load('/path/to/structure.cif')

# From RCSB PDB
cmd.fetch('1ubq')
cmd.fetch('6lu7', type='cif')

Representations

# Show representations
cmd.show('cartoon', 'all')
cmd.show('surface', 'chain A')
cmd.show('sticks', 'resn LIG')
cmd.show('spheres', 'name CA')

# Hide representations
cmd.hide('lines', 'all')
cmd.hide('everything', 'solvent')

Coloring

# Color by chain (automatic colors)
cmd.util.cbc()

# Spectrum coloring (rainbow N to C)
cmd.spectrum('count', 'rainbow', 'all')

# Specific colors
cmd.color('red', 'chain A')
cmd.color('blue', 'resn LIG')
cmd.color('green', 'resi 50-100')

# B-factor coloring
cmd.spectrum('b', 'blue_white_red', 'all')

Selections

# Create named selections
cmd.select('binding_site', 'byres resn LIG around 5')
cmd.select('active_site', 'resi 145+41+166 and chain A')
cmd.select('interface', 'chain A within 4 of chain B')

# Selection algebra
cmd.select('no_water', 'all and not solvent')

View and Camera

# Orient and zoom
cmd.orient()
cmd.zoom('all')
cmd.zoom('chain A', buffer=5)
cmd.center('resn LIG')

# Set specific view
cmd.set_view([...])  # 18-element matrix

# Store and recall views
cmd.view('view1', 'store')
cmd.view('view1', 'recall')

Ray Tracing and Export

# Basic ray trace
cmd.ray(1920, 1080)
cmd.png('/path/to/output.png')

# Publication quality
cmd.set('ray_trace_mode', 1)
cmd.set('ray_shadows', 'on')
cmd.set('antialias', 2)
cmd.ray(2400, 2400)
cmd.png('/path/to/figure.png', dpi=300)

Visualization Workflows

See references/visualization.md for complete workflows:

• Basic protein visualization
• Cartoon with chain coloring
• Surface with transparency
• Ligand binding site
• Domain highlighting
• Publication-quality figures

Command Reference

See references/commands.md for complete command documentation:

• All cmd.* functions
• Selection syntax
• Setting parameters
• Color palettes

Troubleshooting

See references/troubleshooting.md for platform-specific issues:

• macOS GLUT errors
• Windows headless mode
• Connection refused errors
• Display problems

Common Issues

External Resources

• PyMOL Documentation: https://pymol.org/dokuwiki/
• PyMOL Wiki: https://pymolwiki.org/
• claudemol GitHub: https://github.com/colorifix/claudemol
• Open-Source PyMOL: https://github.com/schrodinger/pymol-open-source