Plot Secondary Structure Evolution - k-ngo/CATMD GitHub Wiki

Plot Secondary Structure Evolution

Overview and Methodology

What It Does

This script visualizes how secondary structures change over the course of a molecular dynamics simulation. It tracks secondary structure assignments per residue over time and plots them as a heatmap.

How It Works

  • Objective: Reveal transient or stable secondary structures (e.g., helix formation, unfolding events).
  • Process:
    • DSSP Assignment: Computes secondary structure for each residue using the DSSP algorithm.
    • Frame Sampling: Applies DSSP at each specified frame.
    • Heatmap Plotting: Converts structural codes (e.g., H, E, C) into a visual map showing structural evolution per residue.

Configuration and Inputs

Prerequisites

  • Requires a loaded trajectory.
  • Requires the dssp executable to be installed and accessible.

Key Configuration Options

  • Selections:
    • group_sel, group_name: Single group of residues to track (e.g., (segid TOX and resid 15-25)).

Outputs

  • Heatmap:

    • *_SecondaryStructure.png: Shows structural transitions for each residue across the trajectory.

  • Colorbar:

    • Shows secondary structure types (Coil, α-helix, β-sheet, etc.) using distinct colors.

  • Terminal Logs:

    • Selection details and number of frames processed.

Interpreting the Results

Heatmap

  • Rows: Individual residues in the selection.
  • Columns: Time points across the simulation.
  • Colors: Type of secondary structure:
    • α-helix (blue): Stable helices.
    • β-sheet (green): Extended strand formation.
    • Coil (gray): Disordered or flexible regions.
    • Turns, Bends, 3-10 and π-helices: Additional structural motifs.

Changes in color patterns over time indicate structural rearrangements.

Example Scenarios

Helix Stability Check

  • Scenario: A helical region is expected to remain stable.
  • Observation: Continuous blue bar throughout simulation.
  • Interpretation: The helix persists, indicating structural integrity under the simulated conditions.

Folding Events

  • Scenario: An unstructured peptide begins folding midway.
  • Observation: Transition from coil to α-helix.
  • Interpretation: Indicates emergence of ordered structure, possibly due to environmental stabilization or interactions.

Ligand-Induced Structural Change

  • Scenario: A loop near the binding site gains structure upon ligand binding.
  • Observation: Coil turns into short helix or sheet after a specific time point.
  • Interpretation: The ligand induces local ordering, potentially affecting function or binding affinity.

Usage Tips

  • Selection Requirement: Only one selection group is supported per run.
  • Protein-Only: Make sure the selection contains protein atoms (DSSP only analyzes proteins).
  • Frame Sampling: Use a smaller step to capture fast structural transitions.
  • Axis Labeling: Adjust time_total to match your simulation units (e.g., 300 ns).