Structure and Function of Proteins 2010
Exercise 1: Introduction to DEEP-VIEW

Deep View (formerly Swiss-PDB Viewer) is a molecular graphics program. Apart from comprehensible visualization of structures, it has some powerful capabilities like viewing several proteins simultaneously and superimposing them for structural comparison, or building a preliminary three-dimensional model (based on multiple sequence alignment) for proteins of known sequence but unknown structure.

Deep View is under continuous development by Geneva Glaxo Welcome Experimental Research.

Lets begin with some conventions for the exercises that follow:

• The exercises screens are divided into two frames- the index frame at the left and the main exercise frame at the right. When you don't want to use the index, just minimize its frame.
• Indications like File→ Open PDB File mean choosing "file" at the main toolbar, and then selecting "Open PDB File" at the pull-down menu.
• When you download files at the beginning of an exercise, save them in the same (local) directory.

In this exercise, the basic features of Deep View are introduced based on a specific example structure: an antigenic peptide bound to a Major Histocompatibility Complex (MHC) molecule, HLA-A2.