Contents

• Introduction
  • Getting Started
  • Required Programs
  • Timeline in action: examine events in titin domain extension
  • Per-residue vs. per-selection calculations
  
  
• Interface and controls
• Trajectory analysis: titin domain extension
  • Secondary structure during titin domain extension
  • Thresholding and changing appearance: examining RMSF
  • Examine backbone hydrogen bonds during titin extension
  • Using Data Files and Data Collections
  
  
• Analysis Scripts
  • Simple user-defined all-residue scripts
  • Writing a .tcl script to generate a per-residue .tml data file
  • Writing a .tcl script to generate a per-selection .tml data file
  
  
• Acknowledgements