PyMOL

What It Does

• Publication-quality 3D protein structure rendering
• Ray-tracing for photorealistic images
• Python scripting for automated analysis
• Electrostatic surface calculation
• Distance/angle measurements
• Movie/animation creation

How to Use

### Installation

        # Open-source version
        conda install -c conda-forge pymol-open-source
        
        # Or pip (requires system dependencies)
        pip install pymol-open-source
        

### Basic Commands

        # Load structure
        load AF-Q7RTU9-F1-model_v4.pdb, strc
        
        # Color by pLDDT (B-factor column in AF predictions)
        spectrum b, blue_white_red, strc, minimum=50, maximum=100
        
        # Select and show residue 1659
        select e1659, resi 1659
        show sticks, e1659
        color red, e1659
        
        # Electrostatic surface
        from pymol import cmd
        cmd.set("surface_color", "electrostatic")
        
        # Save image
        ray 2400, 1800
        png strc_e1659a.png, dpi=300
        

Verified Status

PARTIAL — pymol-open-source 3.2.0a0 installed via pip but fails to import (missing libGLEW, libnetcdf — the pip wheel was built for a different conda environment). Needs conda install in a clean environment or use PyMOL desktop app. For now, Mol* viewer covers all visualization needs.

STRC Research Usage

• Not yet used but would be valuable for:

- Publication-quality structure figures

- Electrostatic surface analysis of E1659A

- Automated batch rendering of mini-STRC variants

STRC Research Usage

• Not yet used but would be valuable for:

- Publication-quality structure figures

- Electrostatic surface analysis of E1659A

- Automated batch rendering of mini-STRC variants