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3d Molecule Ray Tracer

Name: 3d Molecule Ray Tracer
Author: renhaosu2024

作者 renhaosu2024 · GitHub ↗ · v0.1.0 · MIT-0

cross-platform ⚠ suspicious

279

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当前安装

版本数

在 OpenClaw 中安装

/install 3d-molecule-ray-tracer

功能描述

Generate photorealistic rendering scripts for PyMOL and UCSF ChimeraX to create publication-quality molecular visualizations. Supports ray-tracing, depth of...

使用说明 (SKILL.md)

3D Molecule Ray Tracer

Advanced molecular visualization tool that generates professional-grade rendering scripts with cinematic effects for creating publication-quality and cover-worthy molecular images.

Features

Multi-Software Support: Generate scripts for PyMOL and UCSF ChimeraX
Photorealistic Rendering: Ray-tracing, depth of field, ambient occlusion
Cinematic Lighting: Studio, outdoor, and dramatic lighting presets
Publication Presets: Pre-configured settings for journals, covers, and presentations
Customizable Scenes: Fine control over camera, materials, and atmosphere

Usage

Basic Usage

# Generate PyMOL script with default settings
python scripts/main.py --pdb 1mbn

# Generate cover-quality render script
python scripts/main.py --pdb 1mbn --preset cover

# Generate ChimeraX script
python scripts/main.py --software chimerax --pdb 1abc --preset publication

Parameters

Parameter	Type	Default	Required	Description
`--software`	str	pymol	No	Target rendering software (pymol/chimerax)
`--pdb`	str	None	Yes	PDB file path or 4-letter PDB ID
`--preset`	str	standard	No	Rendering preset (standard/cover/publication/cinematic)
`--style`	str	cartoon	No	Molecular representation style
`--resolution`	int	from preset	No	Output resolution in pixels
`--bg-color`	str	white	No	Background color
`--ao-on`	flag	False	No	Enable ambient occlusion
`--shadows`	flag	False	No	Enable shadow casting
`--fog`	float	from preset	No	Fog density (0-1)
`--dof-on`	flag	False	No	Enable depth of field
`--dof-focus`	str	center	No	DOF focus point
`--dof-aperture`	float	from preset	No	Aperture size (higher = more blur)
`--lighting`	str	from preset	No	Lighting preset
`--output`	str	auto	No	Output script filename

Advanced Usage

# Cover-quality render with depth of field
python scripts/main.py \
  --software pymol \
  --pdb 1mbn \
  --preset cover \
  --dof-on \
  --dof-focus "A:64" \
  --dof-aperture 2.0 \
  --style surface \
  --output cover_render.pml

# Cinematic 4K render
python scripts/main.py \
  --software pymol \
  --pdb complex.pdb \
  --preset cinematic \
  --resolution 3840 \
  --ao-on \
  --shadows \
  --lighting cinematic

Rendering Presets

Preset	Resolution	Ray Trace	DOF	AO	Shadows	Use Case
Standard	2400px	✓	✗	✗	✗	Quick high-quality
Cover	3000px	✓	✓	✓	✓	Journal covers
Publication	2400px	✓	✗	✓	✗	Manuscript figures
Cinematic	3840px	✓	✓	✓	✓	Presentations

Supported Software

Software	Best For	Features
PyMOL	Traditional rendering, ease of use	Ray tracing, shadows, AO
ChimeraX	Modern effects, large structures	PBR lighting, ambient occlusion, VR

Technical Difficulty: MEDIUM

⚠️ AI自主验收状态: 需人工检查

This skill requires:

Python 3.8+ environment
PyMOL 2.5+ or ChimeraX 1.5+ installed separately
Understanding of molecular visualization concepts

Dependencies

Required Python Packages

pip install -r requirements.txt

External Software

PyMOL: https://pymol.org/
UCSF ChimeraX: https://www.cgl.ucsf.edu/chimerax/

Risk Assessment

Risk Indicator	Assessment	Level
Code Execution	Python scripts executed locally	Medium
Network Access	Fetches PDB structures from RCSB (optional)	Low
File System Access	Writes rendering scripts	Low
Instruction Tampering	Standard prompt guidelines	Low
Data Exposure	No sensitive data exposure	Low

Security Checklist

No hardcoded credentials or API keys
No unauthorized file system access (../)
Output does not expose sensitive information
Prompt injection protections in place
Input file paths validated
Output directory restricted to workspace
Script execution in sandboxed environment
Error messages sanitized
Dependencies audited

Prerequisites

# Python dependencies
pip install -r requirements.txt

# Install PyMOL or ChimeraX separately

Output Example

✓ Rendering script generated: /path/to/cover_render.pml

Configuration:
  Software: pymol
  Preset: cover
  Style: cartoon
  Resolution: 3000px
  Depth of Field: ON
  Ambient Occlusion: ON
  Shadows: ON
  Lighting: cinematic

To render:
  pymol cover_render.pml
  # Or within PyMOL:
  @ cover_render.pml

Evaluation Criteria

Success Metrics

Successfully generates valid PyMOL/ChimeraX scripts
Scripts execute without errors in target software
Output images meet quality standards
Handles edge cases gracefully

Test Cases

Basic Functionality: Generate script for PDB ID → Valid script created
File Input: Generate script from PDB file → Valid script created
Preset Override: Custom parameters override preset → Correct settings applied
Both Software: Generate for PyMOL and ChimeraX → Both scripts valid

Lifecycle Status

Current Stage: Draft
Next Review Date: 2026-03-15
Known Issues: None
Planned Improvements:
- Blender integration
- AI-assisted composition suggestions
- Real-time preview mode

References

See references/ for:

PyMOL-specific rendering techniques
ChimeraX lighting documentation
Colorblind-friendly palettes
Journal submission guidelines

Limitations

Static Images Only: Generates scripts for still images, not animations
Software Dependency: Requires separately installed PyMOL or ChimeraX
Rendering Time: High-quality renders can take 10-30 minutes per image
Learning Curve: Advanced effects require understanding of photography concepts
File Sizes: High-res images can be 10-50 MB each
No Automatic Layout: Creates single images; figure assembly requires separate tools

💡 Tip: For creating multiple related figures, save your complete scene setup (lighting, camera, colors) as a PyMOL session file (.pse) or ChimeraX session (.cxs), then modify only the specific elements needed for each figure. This ensures consistency across figure panels.

安全使用建议

This skill appears coherent with its stated purpose, but take these precautions before use: (1) inspect the generated .pml/.cxc scripts before running them — they will be executed by PyMOL/ChimeraX and can contain arbitrary commands; (2) if you provide a 4-letter PDB ID the generated script will call PyMOL's fetch (network access) — be aware of network activity; (3) run rendering commands in a sandbox or on a non-sensitive workstation if you are unsure; (4) ensure PyMOL/ChimeraX and Python dependencies are installed from trusted sources; (5) if you need higher assurance, share the full scripts/main.py for a line-by-line review (the provided file was truncated in the listing).

功能分析

Type: OpenClaw Skill Name: 3d-molecule-ray-tracer Version: 0.1.0 The skill bundle is a utility for generating molecular visualization scripts for PyMOL and ChimeraX. It is classified as suspicious because it possesses risky capabilities, specifically the generation of executable scripts and the ability to write files to user-specified paths without adequate input validation in 'scripts/main.py'. While these functions are aligned with the stated purpose in 'SKILL.md' and no evidence of intentional malice (such as data exfiltration or backdoors) was found, the lack of sanitization on the '--pdb' and '--output' arguments represents a vulnerability that could be exploited to overwrite arbitrary files or inject commands into the target visualization software.

能力评估

✓ Purpose & Capability

Name and description (generate rendering scripts for PyMOL/ChimeraX) align with the included Python script and SKILL.md. There are no surprising required env vars, binaries, or unrelated dependencies declared.

ℹ Instruction Scope

SKILL.md and the Python code generate PyMOL/ChimeraX scripts and accept either local PDB file paths or 4-character PDB IDs. The generated PyMOL script uses the PyMOL 'fetch' command for PDB IDs (which triggers network access when the script is run). Instructions do not request unrelated files, credentials, or broad system data, but you should inspect generated scripts before executing them because they will run inside PyMOL/ChimeraX and can execute arbitrary commands in those applications.

✓ Install Mechanism

No install specification — this is instruction/script-only plus a local Python file. That is the lowest-risk pattern for an extension of this type.

✓ Credentials

The skill requests no environment variables or credentials. The only external interaction is optional PDB fetching via PyMOL/ChimeraX (expected for the purpose).

✓ Persistence & Privilege

always is false; the skill does not request persistent platform privileges or modify other skills. It runs locally and generates scripts that the user may execute with PyMOL/ChimeraX.

如何使用

确保已安装 OpenClaw（本地或 Docker 部署）
在对话框中输入安装命令：/install 3d-molecule-ray-tracer
安装完成后，直接呼叫该 Skill 的名称或使用 /3d-molecule-ray-tracer 触发
根据 Skill 的参数说明提供必要输入，即可获得结构化输出

版本历史

v0.1.0

- Initial release of 3d-molecule-ray-tracer skill. - Generates photorealistic rendering scripts for PyMOL and UCSF ChimeraX, supporting ray-tracing, depth of field, ambient occlusion, and cinematic lighting. - Includes presets for publication, cover, and cinematic-quality images. - Offers fine control over camera, materials, lighting, and scene parameters. - Requires separate installation of PyMOL or ChimeraX and Python 3.8+. - Intended for creating high-impact, publication-quality molecular visualizations.

元数据

Slug 3d-molecule-ray-tracer

版本 0.1.0

许可证 MIT-0

累计安装 0

当前安装数 0

历史版本数 1

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