- name
- 3d-molecule-ray-tracer
- description
- Generate photorealistic rendering scripts for PyMOL and UCSF ChimeraX
- 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 publicationParameters
| 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 cinematicRendering 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.txtExternal 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
- [x] No hardcoded credentials or API keys
- [x] No unauthorized file system access (../)
- [x] Output does not expose sensitive information
- [x] Prompt injection protections in place
- [x] Input file paths validated
- [x] Output directory restricted to workspace
- [x] Script execution in sandboxed environment
- [x] Error messages sanitized
- [x] Dependencies audited
Prerequisites
# Python dependencies
pip install -r requirements.txt
# Install PyMOL or ChimeraX separatelyOutput 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.pmlEvaluation 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.