Skill: aipoch-ai/protein-struct-viz (version 1.0.0)

--- name: protein-struct-viz description: Generate PyMOL scripts to highlight specific protein residues in PDB structures. Use this skill when the user needs to visualize specific amino acid residues, create publication-quality protein images, or highlight functional sites in protein structures. version: 1.0.0 category: Bioinfo tags: [] author: AIPOCH license: MIT status: Draft risk_level: High skill_type: Hybrid (Tool/Script + Network/API) owner: AIPOCH reviewer: '' last_updated: '2026-02-06' --- # protein-struct-viz Generate PyMOL scripts for highlighting specific protein residues in molecular structures. ## Overview This skill creates PyMOL command scripts to visualize protein structures with specific residues highlighted using various representation styles (sticks, spheres, surface, etc.). ## Usage The skill generates `.pml` script files that can be executed directly in PyMOL to: - Load PDB structures - Apply custom color schemes - Highlight specific residues with different representation styles - Create publication-ready visualization settings ### Input Parameters | Parameter | Type | Description | |-----------|------|-------------| | `pdb_file` | string | Path to PDB file or PDB ID (e.g., "1abc") | | `residues` | list | List of residue specifications (chain:resnum:resname) | | `style` | string | Visualization style: "sticks", "spheres", "surface", "cartoon" | | `color_scheme` | string | Color scheme: "rainbow", "chain", "element", custom hex | | `output_name` | string | Output filename for the generated script | ### Residue Specification Format - Format: `chain:resnum:resname` or `resnum` (for single chain) - Examples: `A:145:ASP`, `B:23:LYS`, `156` - Wildcards: `A:*` (all residues in chain A) ## Example ```bash python scripts/main.py --pdb 1mbn --residues "A:64:HIS,A:93:VAL,A:97:LEU" --style sticks --color_scheme rainbow --output myoglobin_active_site.pml ``` This will generate a PyMOL script highlighting the specified residues in myoglobin's active site. ## Output Generated `.pml` script includes: 1. Structure loading commands 2. Background and lighting settings 3. Global representation settings 4. Specific residue highlighting 5. View optimization commands 6. Optional: ray tracing for high-quality images ## References See `references/` directory for: - PyMOL command reference - Color palette templates - Example scripts for common visualization tasks ## Technical Difficulty Medium - requires understanding of PyMOL scripting syntax and protein structure concepts. ## Dependencies - PyMOL (installed separately) - Python 3.7+ - No Python package dependencies (generates plain text scripts) ## Risk Assessment | Risk Indicator | Assessment | Level | |----------------|------------|-------| | Code Execution | Python scripts with tools | High | | Network Access | External API calls | High | | File System Access | Read/write data | Medium | | Instruction Tampering | Standard prompt guidelines | Low | | Data Exposure | Data handled securely | Medium | ## Security Checklist - [ ] No hardcoded credentials or API keys - [ ] No unauthorized file system access (../) - [ ] Output does not expose sensitive information - [ ] Prompt injection protections in place - [ ] API requests use HTTPS only - [ ] Input validated against allowed patterns - [ ] API timeout and retry mechanisms implemented - [ ] Output directory restricted to workspace - [ ] Script execution in sandboxed environment - [ ] Error messages sanitized (no internal paths exposed) - [ ] Dependencies audited - [ ] No exposure of internal service architecture ## Prerequisites No additional Python packages required. ## Evaluation Criteria ### Success Metrics - [ ] Successfully executes main functionality - [ ] Output meets quality standards - [ ] Handles edge cases gracefully - [ ] Performance is acceptable ### Test Cases 1. **Basic Functionality**: Standard input → Expected output 2. **Edge Case**: Invalid input → Graceful error handling 3. **Performance**: Large dataset → Acceptable processing time ## Lifecycle Status - **Current Stage**: Draft - **Next Review Date**: 2026-03-06 - **Known Issues**: None - **Planned Improvements**: - Performance optimization - Additional feature support


Security scan verdicts — ClawScan: clean | static analysis: clean | VirusTotal: clean | SkillSpector: suspicious (MEDIUM)