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)

Click here to download the tutorial pages for off-line use (for version 3.9—version 4.0 revision will replace the old archive when complete). This is a zip archive. Use Zipit or Stuffit Expander with Dropstuff/Expander Enhancer (Mac), or Winzip (Windows) to open the archive. Then open the file index.html with your browser and proceed as usual.

The Molecular Level