Visualization Examples

This document demonstrates the different visualization options available in synth-pdb.

1. Browser-Based 3D Viewer

The easiest way to visualize a generated structure is to use the --visualize flag:

python -m synth_pdb.main --length 30 --conformation alpha --visualize

This will automatically open your default web browser and display the structure in a 3D viewer powered by 3Dmol.js.

Features of the 3D Viewer: - Interactive: Rotate, zoom, and pan using your mouse. - Style Overrides: Switch between Cartoon, Stick, Sphere, and Line representations. - Coloring: Choose from Spectrum, Chain, or Secondary Structure color schemes. - NMR Restraints: If generated with NOE restraints (--gen-nef), the viewer can display them as red lines between the atoms. - Hydrogen Bonds: Shows backbone hydrogen bonds as dashed lines. - SSBOND Visualization: Displays disulfide bonds as thick yellow cylinders. - PTM Support: Highlights post-translational modifications (like phosphorylation) with orange markers.

2. PyMOL Scripting

For professional-quality rendering and detailed analysis, synth-pdb can generate PyMOL scripts (.pml files).

python -m synth_pdb.main \
  --input-pdb structure.pdb \
  --input-nef data.nef \
  --mode pymol \
  --output-pml view_restraints.pml

Then open the script in PyMOL:

pymol view_restraints.pml

The script will automatically: - Load your PDB structure and NEF data. - Style the protein as a cartoon and sticks. - Visualize NOE restraints as distance cylinders (colored by violation if applicable). - Set up standard views for analysis.

3. High-Fidelity Solvent Visualization

If you run energy minimization with explicit solvent, you can choose to keep the water molecules in the final PDB:

python -m synth_pdb.main \
  --sequence "MEELQK" \
  --minimize \
  --solvent explicit \
  --keep-solvent \
  --output structure_with_water.pdb

This is particularly useful for studying solvation shells and water-mediated hydrogen bonds.

4. Contact Maps

You can also export contact maps as an alternative "2D visualization" of structural proximity:

python -m synth_pdb.main \
  --sequence "ALA-GLY-SER-THR-VAL" \
  --export-constraints contacts.csv \
  --constraint-format csv \
  --constraint-cutoff 8.0

The CSV file will contain pairs of residues that are within the 8.0 Angstrom cutoff, which can be plotted as a heatmap using libraries like matplotlib.