| 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
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:
- Structure loading commands
- Background and lighting settings
- Global representation settings
- Specific residue highlighting
- View optimization commands
- Optional: ray tracing for high-quality images
