D Molecule Ray Tracer

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.

Output Requirements

Every final response should make these items explicit when they are relevant:

• Objective or requested deliverable
• Inputs used and assumptions introduced
• Workflow or decision path
• Core result, recommendation, or artifact
• Constraints, risks, caveats, or validation needs
• Unresolved items and next-step checks

Error Handling

• If required inputs are missing, state exactly which fields are missing and request only the minimum additional information.
• If the task goes outside the documented scope, stop instead of guessing or silently widening the assignment.
• If scripts/main.py fails, report the failure point, summarize what still can be completed safely, and provide a manual fallback.
• Do not fabricate files, citations, data, search results, or execution outcomes.

Input Validation

This skill accepts requests that match the documented purpose of 3d-molecule-ray-tracer and include enough context to complete the workflow safely.

Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:

3d-molecule-ray-tracer only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.

Response Template

Use the following fixed structure for non-trivial requests:

1. Objective
2. Inputs Received
3. Assumptions
4. Workflow
5. Deliverable
6. Risks and Limits
7. Next Checks

If the request is simple, you may compress the structure, but still keep assumptions and limits explicit when they affect correctness.