protein-structure-basics

name	protein-structure-basics
description	Use when visualizing protein structures, showing secondary structure, coloring by B-factor, creating surface representations, or generating basic structural figures through PyMOL.
version	0.1.0

Protein Structure Basics

Fundamental workflows for visualizing protein structures.

Send all cmd.* code via: ~/.pymol-agent-bridge/bin/pymol-agent-bridge exec "..." (or heredoc for multi-line). See @pymol-fundamentals for details.

Representations

Cartoon (Most Common)

cmd.hide("everything")
cmd.show("cartoon")

Surface

cmd.show("surface")
cmd.set("transparency", 0.5)  # Semi-transparent

Sticks (Sidechains)

# Show sticks for specific residues
cmd.show("sticks", "resi 50-60")

# Show all sidechains with cartoon backbone
cmd.show("cartoon")
cmd.show("sticks", "sidechain")

Spheres (CPK)

cmd.show("spheres")
cmd.set("sphere_scale", 0.3)  # Smaller spheres

Ribbon

cmd.show("ribbon")

Coloring

By Secondary Structure

cmd.color("marine", "ss h")      # Helices - blue
cmd.color("tv_orange", "ss s")   # Sheets - orange
cmd.color("gray70", "ss l+")     # Loops - gray

By Chain

cmd.util.cbc()  # Color by chain (automatic)
# Or manually:
cmd.color("green", "chain A")
cmd.color("cyan", "chain B")

By B-factor (Flexibility/Disorder)

cmd.spectrum("b", "blue_white_red", "all")
# Blue = low B-factor (rigid)
# Red = high B-factor (flexible)

By Residue Type

# Hydrophobic
cmd.color("yellow", "resn ALA+VAL+LEU+ILE+MET+PHE+TRP+PRO")
# Polar
cmd.color("cyan", "resn SER+THR+ASN+GLN+TYR+CYS")
# Positive
cmd.color("blue", "resn ARG+LYS+HIS")
# Negative
cmd.color("red", "resn ASP+GLU")

Rainbow (N to C terminus)

cmd.spectrum("count", "rainbow", "polymer.protein")

Structure Analysis

Count Residues by Secondary Structure

total = cmd.count_atoms("name CA")
helix = cmd.count_atoms("name CA and ss h")
sheet = cmd.count_atoms("name CA and ss s")
loop = cmd.count_atoms("name CA and ss l+")
print(f"Total: {total}")
print(f"Helix: {helix} ({100*helix/total:.1f}%)")
print(f"Sheet: {sheet} ({100*sheet/total:.1f}%)")
print(f"Loop: {loop} ({100*loop/total:.1f}%)")

List Chains

chains = cmd.get_chains()
for chain in chains:
    count = cmd.count_atoms(f"chain {chain} and name CA")
    print(f"Chain {chain}: {count} residues")

Publication Settings

cmd.bg_color("white")
cmd.set("ray_shadows", 0)
cmd.set("spec_reflect", 0.2)
cmd.set("ambient", 0.5)
cmd.set("antialias", 2)
cmd.set("ray_trace_mode", 1)
cmd.set("cartoon_fancy_helices", 1)
cmd.set("cartoon_smooth_loops", 1)

Complete Workflow

Standard Protein Figure Set

# 1. Load and clean
cmd.delete("all")
cmd.fetch("1ema")  # GFP
cmd.remove("solvent")

# 2. Basic cartoon with secondary structure colors
cmd.hide("everything")
cmd.show("cartoon")
cmd.color("marine", "ss h")
cmd.color("tv_orange", "ss s")
cmd.color("gray70", "ss l+")

# 3. Publication settings
cmd.bg_color("white")
cmd.set("ray_shadows", 0)
cmd.set("spec_reflect", 0.2)
cmd.set("ambient", 0.5)
cmd.set("antialias", 2)
cmd.set("ray_trace_mode", 1)
cmd.set("cartoon_fancy_helices", 1)

# 4. Overview figure
cmd.orient()
cmd.ray(1200, 900)
cmd.png("protein_overview.png")

# 5. B-factor figure
cmd.spectrum("b", "blue_white_red", "all")
cmd.ray(1200, 900)
cmd.png("protein_bfactor.png")

# 6. Side view
cmd.color("marine", "ss h")  # Reset colors
cmd.color("tv_orange", "ss s")
cmd.color("gray70", "ss l+")
cmd.turn("y", 90)
cmd.ray(1200, 900)
cmd.png("protein_side.png")

Tips

• Always use cmd.ray(w, h) then cmd.png(path) without dimensions
• ss h = helix, ss s = sheet/strand, ss l+ = loop/coil
• B-factor visualization helps identify flexible regions and potential disorder
• Multiple views (front, side, top) tell a more complete story
• Consider showing key functional residues as sticks on top of cartoon