Trajectory Analysis

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Tutorial files: ZIP TGZ

• Introduction
  • Required Programs
  • Recommended Programs
  • Getting Started
• Frames and Atom Groups
  • Trajectory Frames
  • Linking Atom Groups
• Trajectory Analysis
  • Input files
  • Setup environment
  • Parse structure
  • Parse all frames
  • Parse frames one-by-one
  • Handling multiple files
• Trajectory Analysis II
  • Input files
  • Setup environment
  • Parse structure
  • Handling multiple files
  • Link trajectory to atoms
  • Setup for calculations
  • Perform calculations
  • Plot results
• Essential Dynamics Analysis
  • Synopsis
  • Setup environment
  • Parse reference structure
  • EDA calculations
  • Multiple files
  • Analysis
  • Plotting
  • Visualization
• Trajectory Output
  • Input files
  • Setup environment
  • Load structure
  • Open trajectories
  • Output selected atoms
  • Output aligned frames

Acknowledgments

Continued development of Protein Dynamics Software ProDy and associated programs is partially supported by the NIH-funded R01 GM139297 entitled “Toward a deeper understanding of allostery and allotargeting by computational approaches”.