Protein Alpha Helix Structure

import matplotlib.pyplot as plt
import numpy as np

np.random.seed(123)

# Simulate protein backbone with side chains
n_residues = 50
t = np.linspace(0, 4*np.pi, n_residues)

# Alpha helix backbone
x_backbone = np.cos(t) * 2
y_backbone = np.sin(t) * 2
z_backbone = t / np.pi

# Add side chain atoms
n_atoms = 200
x_atoms = []
y_atoms = []
z_atoms = []
colors = []

for i in range(n_residues):
    n_side = np.random.randint(2, 6)
    for j in range(n_side):
        offset = np.random.uniform(0.5, 1.5)
        angle = np.random.uniform(0, 2*np.pi)
        x_atoms.append(x_backbone[i] + offset * np.cos(angle))
        y_atoms.append(y_backbone[i] + offset * np.sin(angle))
        z_atoms.append(z_backbone[i] + np.random.uniform(-0.3, 0.3))
        colors.append(i)

fig = plt.figure(figsize=(10, 8), facecolor='#ffffff')
ax = fig.add_subplot(111, projection='3d', facecolor='#ffffff')

# Backbone
ax.plot(x_backbone, y_backbone, z_backbone, color='#1e40af', linewidth=2, alpha=0.8)

# Atoms
scatter = ax.scatter(x_atoms, y_atoms, z_atoms, c=colors, cmap='viridis', 
                     s=40, alpha=0.7, edgecolors='white', linewidths=0.5)

ax.set_xlabel('X (Å)', color='#1f2937', fontsize=10)
ax.set_ylabel('Y (Å)', color='#1f2937', fontsize=10)
ax.set_zlabel('Z (Å)', color='#1f2937', fontsize=10)
ax.set_title('Protein Alpha Helix Structure', color='#1f2937', fontsize=14, fontweight='bold', pad=20)

ax.tick_params(colors='#6b7280', labelsize=8)
ax.xaxis.pane.fill = False
ax.yaxis.pane.fill = False
ax.zaxis.pane.fill = False
ax.xaxis.pane.set_edgecolor('#e5e7eb')
ax.yaxis.pane.set_edgecolor('#e5e7eb')
ax.zaxis.pane.set_edgecolor('#e5e7eb')

ax.view_init(elev=25, azim=45)
plt.tight_layout()
plt.show()