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name: 3d-molecule-ray-tracer description: "Generate photorealistic rendering scripts for PyMOL and UCSF ChimeraX to create publication-quality molecular visualizations. Supports ray-tracing, depth of field, ambient occlusion, and cinematic lighting for journal covers and high-impact figures. Use for creating visually compelling protein structure images; not for routine structural analysis or measurements." version: 1.0.0 category: Visual tags: ["pymol", "chimerax", "rendering", "visualization", "ray-tracing"] author: AIPOCH license: MIT status: Draft risk_level: High skill_type: Hybrid (Tool/Script + Network/API) owner: AIPOCH reviewer: '' last_updated: '2026-02-15'

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

1. Basic Functionality: Generate script for PDB ID → Valid script created
2. File Input: Generate script from PDB file → Valid script created
3. Preset Override: Custom parameters override preset → Correct settings applied
4. 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

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💡 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.