Plot Chi Dihedral Angles

Overview and Methodology

What It Does

This script analyzes side-chain dihedral angles (χ1–χ5) for selected residues across a molecular dynamics trajectory. It produces heatmaps visualizing how these angles evolve over time.

How It Works

• Objective: Track torsional dynamics of side chains, which can reflect conformational shifts or interaction changes.
• Process:
  • Chi Selection: Automatically detects available χ1–χ5 angles per residue based on atom names.
  • Calculation: Computes dihedral angles frame by frame for each valid chi torsion.
  • Visualization: Plots a heatmap of dihedral angle evolution over time (−180° to 180°), with one row per residue–chi pair.

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Configuration and Inputs

Prerequisites

• Requires a loaded trajectory.
• Selection must include only protein residues.

Key Configuration Options

• Selections:

  • group_sel, group_name: Residue group to analyze (e.g., 'segid TOX', 'TOX').

• Chi Angles:

  • plot_angles: Choose 'All Available Chi Angles' or a specific one (e.g., 'Chi1 Only').
  • The script identifies which residues have the selected Chi angles and ignores incompatible ones.

• Plot Customization:

  • Figure size, label fonts, border width/color, and colormap can be customized.

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Output

• Chi Dihedral Heatmap:
  figures/*_Chi_Heatmap.png
  Each row represents a χ angle for a specific residue, colored by angle value (−180° to +180°). Horizontal axis is simulation time.

• Colorbar Figure:
  Inline figure displaying the angular color scale (used by the heatmap).

• Console Output:

  • Atom selections and angle availability diagnostics.
  • Notes about missing angles (e.g., ALA, GLY).
  • Save path for the final figure.

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Interpreting the Results

• Stable Horizontal Band:

  • Indicates a fixed rotamer or persistent side-chain orientation.

• Switching States:

  • Sharp transitions between two angle bands suggest conformational flips (e.g., rotamer transitions).

• Highly Dynamic Residues:

  • Broad or noisy angle patterns indicate flexible, surface-exposed, or disordered side chains.

• Missing Data:

  • Residues lacking a given χ angle (e.g., glycine) are skipped and noted in console output.

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Example Scenarios

Rotamer Transitions in Binding Sites

• Scenario: Monitor ligand-contacting residues for side-chain flipping.
• Observation: χ1 and χ2 of key residues switch between distinct angles during binding.
• Interpretation: Suggests dynamic adjustment or induced fit at the binding pocket.

Mutation Effects on Side-Chain Flexibility

• Scenario: Compare χ dynamics of wild-type vs. mutant protein.
• Observation: Certain χ angles show reduced variability in mutant.
• Interpretation: Mutation may restrict side-chain dynamics, altering local interactions.

Side Chain Rearrangement During Folding

• Scenario: Simulate folding of a small peptide.
• Observation: Gradual convergence of χ angles to distinct bands.
• Interpretation: Lock-in of native rotamer states as folding progresses.

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Usage Tips

• Chi Angle Coverage:

  • Not all residues have all χ angles. Use 'All Available Chi Angles' to auto-detect valid torsions.

• Selection Precision:

  • Use specific residue ranges (e.g., 'segid TOX and resid 10–20') to focus on functional regions.

• Color Interpretation:

  • Heatmap uses a circular colormap (twilight by default), ensuring continuous transitions around −180° ↔ +180°.

• Plot Clarity:

  • Increase fig_height_factor for more spacing per residue.
  • Use Chi1 Only mode for comparison across residues when only the first side-chain angle is of interest.

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