STRC Research

PyMOL

2 min read

PyMOL

Professional molecular visualization software. More powerful than Mol* for publication-quality figures, scripting, and advanced rendering.

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

Connections

Graph View

Backlinks