Contents

• Introduction
  • The Multiple Alignment Extension to VMD
  • tRNA Synthetases: Precise translation machines
  
  
• Getting Started
  • Downloading Tutorial Files
  • The Aspartyl-tRNA Synthetase Aspartyl-adenylate Complex
  • Loading Molecules
  • Starting Multiple Alignment
  • Setting parameters for Multiple Structure Alignments
  • Aligning the molecules
  
  
• Comparing Protein Structure And Sequence
  • Protein Structure
  • Protein Sequence
  
  
• Residue Selection
  • Starting up Residue Selection
  • Exercise 1: Investigating Structure Conservation
  • Exercise 2: Sequence Conservation
  • Exercise 3: The physical meaning of Q
  • Summary of Results
  
  
• Phylogenetic Tree
  • Determining Structure-based Relationships
  
  
• Investigating Structural Alignment
  • RMSD per Residue
  • Pairwise RMSD
  
  
• Exporting File Formats
  • Exporting a PDB file from user-specified selections
  • Exporting a multiple alignment in FASTA format
  
  
• Appendices
  • Appendix A: $Q$
  • Appendix B: $Q_H$