Tutorial

• INTRO
• Flow of this tutorial
• PART 1: General principles.
• SOUP versus GRAPHICS
• The SOUP menu
• Residue numbering
• Script files
• Exercise
• General commands
• MENUS
• Graphics, displaying
• Graphics
  • Normal graphics options
  • Normal graphics options
  • Graphics, pull-down menus
  • Picking
  • The bottom menu
  • Fancy graphics
  • Colours
• COLOURS
• Exercise
• PART 2: Often used options.
• Other mens
• SOUP commands and MUTATIONS
• Accessibility
• Surface mapping
• Ab initio building
• Reminder: Script files
• Hydrogen bonds
• Structure regularisation
• Structure regularisation
• 2D graphics
• Ramachandran plot
• Structural superpositioning
• Structure verification
• Model building by homology
• The 3D database
• PART 3: Exercises
• PART 4: Options that require additional software
• GROMOS
• GRID
• RIBBONS and PLUTON
• PART 5: more complicate or less often used options
• The neural network