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#

ParameterTypeDescriptionpdb_filestringPath to PDB file or PDB ID (e.g., "1abc")residueslistList of residue specifications (chain:resnum:resname)stylestringVisualization style: "sticks", "spheres", "surface", "cartoon"color_schemestringColor scheme: "rainbow", "chain", "element", custom hexoutput_namestringOutput 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 IndicatorAssessmentLevelCode ExecutionPython scripts with toolsHighNetwork AccessExternal API callsHighFile System AccessRead/write dataMediumInstruction TamperingStandard prompt guidelinesLowData ExposureData handled securelyMedium

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