protein-struct-viz

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:

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