Tutorial
INTRO
Flow of this tutorial
PART 1: General principles.
SOUP versus GRAPHICS
The SOUP menu
Residue numbering
General commands
MENUS
Graphics, displaying
Graphics
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
Hydrogen bonds
Script files
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