## DeepView Tutorial

## What DeepView Can Do

Gale Rhodes
Contact Information

Do you know about the
Grameen Foundation?

Quick Links
• Keyboard Command Modifiers
• Direct Import of Files
• User Guide
• User Manual (pdf)

## Contents

### Overview

1. Getting Started

2. Windows and Help

3. Manipulating the Model

4. Selecting and Displaying

5. Coloring

6. Measuring and Labeling

Assessing Your Command
of DeepView: Assignment 1

7. Mutating and Changing
Side-Chain Conformations

8. Using a Ramachandran Plot

9. Judging the Quality of Models

- General
- Crystallographic Models
- NMR Models
- Homology Models

10. Working with
Oligomeric Proteins

11. Comparing Proteins

12. Making Images for Publication

Assessing Your Command of
DeepView: Assignment 2

ADVANCED TUTORIALS
by DeepView Developers
1. Introduction
2. (This Tutorial)
3. Analyzing Active Sites
4. Building a Functional Unit from a Monomer
5. Crystal Symmetries
6. Electron-Density Maps
7. Energy Minimization
8. Identifying Distorted Residues
9. Superimposing Proteins
10. Searching 3D Motifs
11. Fitting Residues Into Electron Density
12. Making Phi-Psi Statistics
13. Homology Modeling
14. Building Loops
15. SwissModel Workspace
Open in a separate window:

Protein Data Bank

#### Viewing in Stereo

#### Actions of Key Modifiers

#### DeepView Home

#### DeepView USM Mirror
(faster service in USA)

#### DeepView User Guide

#### DeepView User Manual (pdf)

To Use Tutorial Off-line

Click here to download the tutorial pages for off-line use. This is a zip archive. After unzipping, open the file index.html with your browser and proceed as usual.

Some links to pages outside the main tutorial directory will not work.

The Molecular Level