Chapter 2: Molecular Visualization with PyMOL & ChimeraX

Chapter 2: Molecular Visualization with PyMOL & ChimeraX

Visualizing 3D structures is vital for analyzing catalytic active sites, protein-ligand interactions, mutations, and conformational changes. PyMOL and UCSF ChimeraX are the standard visualization and rendering engines used across structural biology.

1. Production PyMOL Scripting (pml)

# save as render_complex.pml and run via: pymol -c render_complex.pml
reinitialize

# Fetch crystal structure of SARS-CoV-2 main protease bound to nirmatrelvir (PDB: 7VH8)
fetch 7vh8, type=mmtf, async=0

# Clean display
hide everything
bg_color white
set ray_shadows, 0
set antialias, 2

# Show protein cartoon
show cartoon, chain A
color grey85, chain A

# Highlight catalytic dyad residues: Cys145 and His41
select catalytic_dyad, (chain A and resi 41+145)
show sticks, catalytic_dyad
color firebrick, catalytic_dyad

# Show small molecule inhibitor (organic)
select inhibitor, org
show sticks, inhibitor
set stick_radius, 0.25, inhibitor
color marine, inhibitor and elem C

# Find hydrogen bonds between inhibitor and protein active site
distance hbonds, inhibitor, (chain A and not elem C), 3.2, mode=2
color dash, yellow

# Set camera and ray-trace high-resolution figure
orient inhibitor
zoom inhibitor, 6
ray 2400, 1800
png binding_pocket_hires.png, dpi=300

2. UCSF ChimeraX for Cryo-EM & Large Complexes

UCSF ChimeraX provides next-generation GPU rendering, interactive ambient occlusion lighting, and native tools to fit atomic models into cryo-EM electron density volumes.

# ChimeraX command line
open 6zsl
open 11145 from emdb
volume #2 style surface level 0.035 color #80b3ff transparency 0.5
fitmap #1 inMap #2