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.
Generate PyMOL scripts for highlighting specific protein residues in molecular structures.
This skill creates PyMOL command scripts to visualize protein structures with specific residues highlighted using various representation styles (sticks, spheres, surface, etc.).
The skill generates .pml script files that can be executed directly in PyMOL to:
| 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 |
chain:resnum:resname or resnum (for single chain)A:145:ASP, B:23:LYS, 156A:* (all residues in chain A)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.
Generated .pml script includes:
See references/ directory for:
Medium - requires understanding of PyMOL scripting syntax and protein structure concepts.
| 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 |
No additional Python packages required.