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PyMOL: Molecular Visualization via claudemol

PyMOL：通过claudemol实现分子可视化

Summary

概述

This skill enables Claude Code to control PyMOL molecular visualization software through the claudemol socket interface. It supports:

Setup: Cross-platform installation of claudemol and PyMOL
Visualization: Rendering proteins, small molecules, and complexes
Publication figures: Ray-traced high-resolution images
Interactive control: Send PyMOL commands programmatically

本技能允许Claude Code通过claudemol套接字接口控制PyMOL分子可视化软件，支持：

配置：跨平台安装claudemol和PyMOL
可视化：渲染蛋白质、小分子和复合物
学术发表用图像：光线追踪生成高分辨率图像
交互式控制：以编程方式发送PyMOL命令

Applicable Scenarios

适用场景

Task Category	Examples
Setup	Install PyMOL, configure claudemol, verify connection
Structure Loading	Load PDB files, fetch from RCSB, open local structures
Representations	Cartoon, surface, sticks, spheres, ribbons, lines
Coloring	Color by chain, spectrum, B-factor, custom colors
Selections	Select residues, chains, ligands, binding sites
Camera	Orient view, zoom, rotate, save viewpoints
Ray Tracing	High-quality renders, publication figures
Export	Save images (PNG), sessions (PSE), movies

任务类别	示例
配置	安装PyMOL、配置claudemol、验证连接
结构加载	加载PDB文件、从RCSB获取结构、打开本地结构
结构展示方式	卡通模型、表面模型、棍状模型、球状模型、带状模型、线状模型
着色	按链着色、光谱着色、B因子着色、自定义颜色
选区	选择残基、链、配体、结合位点
视角控制	调整视角、缩放、旋转、保存视角
光线追踪	高质量渲染、学术发表用图像
导出	保存图像（PNG）、会话（PSE）、动画

Setup Instructions

配置指南

Quick Setup (All Platforms)

快速配置（全平台）

Run the automated setup script:

bash

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

运行自动化配置脚本：

bash

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

Manual Setup

手动配置

1. Install claudemol

1. 安装claudemol

bash

pip install claudemol

bash

pip install claudemol

2. Install PyMOL

2. 安装PyMOL

macOS (Recommended):

bash

brew install pymol

Windows/Linux (Headless):

bash

pip install pymol-open-source

Windows (Licensed PyMOL): Connect to existing PyMOL installation - see

references/troubleshooting.md

macOS（推荐方式）：

bash

brew install pymol

Windows/Linux（无界面模式）：

bash

pip install pymol-open-source

Windows（授权版PyMOL）： 连接已安装的PyMOL - 详见

references/troubleshooting.md

3. Configure PyMOL

3. 配置PyMOL

bash

claudemol setup

This adds the socket plugin to PyMOL's startup.

bash

claudemol setup

此操作会将套接字插件添加到PyMOL的启动项中。

4. Launch and Verify

4. 启动与验证

Start PyMOL normally

Check that port 9880 is listening:

bash

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

正常启动PyMOL

检查9880端口是否处于监听状态：

bash

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

Socket Communication

套接字通信

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

claudemol通过9880端口的TCP套接字与PyMOL通信。

Basic Pattern

基础模式

python

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()

python

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

多命令示例

python

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

python

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

Quick Reference

快速参考

Loading Structures

加载结构

python

undefined

python

undefined

From local file

从本地文件加载

cmd.load('/path/to/structure.pdb') cmd.load('/path/to/structure.cif')

From RCSB PDB

从RCSB PDB数据库获取

cmd.fetch('1ubq') cmd.fetch('6lu7', type='cif')

undefined

cmd.fetch('1ubq') cmd.fetch('6lu7', type='cif')

undefined

Representations

结构展示方式

python

undefined

python

undefined

Show representations

展示模型

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

Hide representations

隐藏模型

cmd.hide('lines', 'all') cmd.hide('everything', 'solvent')

undefined

cmd.hide('lines', 'all') cmd.hide('everything', 'solvent')

undefined

Coloring

着色

python

undefined

python

undefined

Color by chain (automatic colors)

按链自动着色

cmd.util.cbc()

Spectrum coloring (rainbow N to C)

光谱着色（从N端到C端彩虹色）

cmd.spectrum('count', 'rainbow', 'all')

Specific colors

指定颜色

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

B-factor coloring

基于B因子着色

cmd.spectrum('b', 'blue_white_red', 'all')

undefined

cmd.spectrum('b', 'blue_white_red', 'all')

undefined

Selections

选区

python

undefined

python

undefined

Create named selections

创建命名选区

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

选区运算

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

undefined

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

undefined

View and Camera

视角与相机控制

python

undefined

python

undefined

Orient and zoom

调整方向与缩放

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

Set specific view

设置特定视角

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

cmd.set_view([...]) # 18元素矩阵

Store and recall views

保存与调用视角

cmd.view('view1', 'store') cmd.view('view1', 'recall')

undefined

cmd.view('view1', 'store') cmd.view('view1', 'recall')

undefined

Ray Tracing and Export

光线追踪与导出

python

undefined

python

undefined

Basic ray trace

基础光线追踪

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

Publication quality

学术发表级质量

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)

undefined

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)

undefined

Visualization Workflows

可视化工作流

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

完整工作流请参考

references/visualization.md

：

基础蛋白质可视化
带链着色的卡通模型
带透明度的表面模型
配体结合位点展示
结构域高亮
学术发表级图像生成

Command Reference

命令参考

See

references/commands.md

for complete command documentation:

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

完整命令文档请参考

references/commands.md

：

所有
```
cmd.*
```
函数
选区语法
参数设置
颜色调色板

Troubleshooting

故障排查

See

references/troubleshooting.md

for platform-specific issues:

macOS GLUT errors
Windows headless mode
Connection refused errors
Display problems

平台特定问题请参考

references/troubleshooting.md

：

macOS GLUT错误
Windows无界面模式问题
连接被拒绝错误
显示问题

Common Issues

常见问题

Issue	Resolution
Connection refused	Ensure PyMOL is running with claudemol plugin loaded
Port 9880 in use	Kill other processes or change port
No GUI (Windows pip)	Use headless mode or licensed PyMOL
GLUT missing (macOS)	Install via Homebrew instead of pip
Slow ray tracing	Reduce resolution or simplify scene

问题	解决方法
连接被拒绝	确保PyMOL已运行且加载了claudemol插件
9880端口被占用	终止其他占用该端口的进程或修改端口
无GUI界面（Windows pip安装版）	使用无界面模式或安装授权版PyMOL
macOS缺失GLUT	使用Homebrew安装而非pip
光线追踪速度慢	降低分辨率或简化场景

External Resources

外部资源

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

PyMOL官方文档：https://pymol.org/dokuwiki/
PyMOL维基：https://pymolwiki.org/
claudemol GitHub仓库：https://github.com/colorifix/claudemol
开源版PyMOL：https://github.com/schrodinger/pymol-open-source