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

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

Supported Software

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

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

💡 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.