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Interactive Visualization

synth-pdb includes a powerful built-in 3D viewer powered by 3Dmol.js. This allows you to instantly visualize your generated structures, energy minimization results, and NMR restraints directly in your web browser.

The --visualize Flag

Simply add --visualize to any generation command to launch the viewer.

synth-pdb --sequence "LKELEKELEKELEKELEKELEKEL" --conformation alpha --visualize

This will: 1. Generate the PDB file. 2. Create a temporary HTML page. 3. Open it in your default web browser.

Viewer Controls

The viewer is fully interactive:

  • Rotate: Left-click and drag.
  • Zoom: Scroll wheel (or pinch zoom).
  • Pan: Right-click (or Ctrl+Left-click) and drag.

Feature Toggles

  • 👻 Ghost Mode: Makes the protein transparent (0.4 opacity). Useful for seeing internal details like NOE restraints inside a Space-Filling (Sphere) model.
  • 🔴 Restraints: Toggles the visibility of NOE cylinders on/off to declutter the view.

Features

Visualization Styles

Use the dropdown menu to change the representation: * Cartoon: (Default) Shows the secondary structure (helices as ribbons, sheets as arrows). Best for seeing the overall fold. * Stick: Shows all bonds as sticks. Best for seeing chemical details and side-chain packing. * Sphere: Space-filling model (Van der Waals radii). Best for seeing packing density and surface. * Line: Wireframe. Lightweight, good for seeing through the structure.

Color Schemes

  • Spectrum: (Default) Rainbow gradient from Blue (N-terminus) to Red (C-terminus).
  • Chain: Colors by chain ID (all 'A' for synth-pdb).
  • Element: Standard CPK coloring (Carbon=Green/Grey, Oxygen=Red, Nitrogen=Blue, Sulfur=Yellow).
  • SS: Secondary Structure (Helices=Magenta, Sheets=Yellow, Loops=White).

NMR Restraints (NOEs)

If you generate NEF restraints using --gen-nef, they will validly appear as translucent red cylinders connecting the protons.

# Generate structure, Minimize, Create NEF restraints, and Visualize
synth-pdb --length 20 --minimize --gen-nef --visualize
  • Cylinders: Represent the NOE distance restraint.
  • Visualization: Allows you to verify that the restraints match the geometry (i.e., the connected atoms are indeed close).

Visual Learning Examples

Here are curated examples designed to demonstrate specific structural biology concepts visually.

1. The Alpha Helix (Leucine Zipper)

Observe the tight packing and the protruding side chains. 

synth-pdb --sequence "LKELEKELEKELEKELEKELEKEL" --conformation alpha --visualize

2. The Beta Hairpin

See two antiparallel beta strands connected by a turn. Note the hydrogen bonds (implied) between the strands. 

synth-pdb --sequence "VVVVVGGVVVVV" --structure "1-5:beta,6-8:random,9-12:beta" --visualize

3. Polyproline II Helix (Collagen-like)

Compare this left-handed, extended helix to the standard right-handed alpha helix. 

synth-pdb --sequence "GPGPPGPPGPPGPP" --conformation ppii --visualize

4. Minimization in Action

Generate a structure with clashes, then minimize it. Compare the "before" and "after" (by running two commands) to see how physics relaxes the geometry. 

# Before (Clashed)
synth-pdb --length 30 --conformation random --visualize

# After (Relaxed)
synth-pdb --length 30 --conformation random --minimize --visualize