The Molecular Level

Hands-On Workshops

Introduction to Deep View (Swiss-PdbViewer)
For Students of Biochemistry

Outline and Resources

Introduction

This workshop outline is appropriate for students in the first semester of undergraduate biochemistry course. After about an hour of hands-on experience followed by individual work on the Deep View Tutorial, students should be capable of obtaining, displaying, and studying macromolecular models from the Protein Data Bank.

Assignment

Suggested materials to study before the workshop

1. Your biochemistry textbook, the chapters on amino-acid, peptide, and protein structure.
   
2. Deep View Tutorial: Molecular Modeling for Beginners

Outline

1) Brief Review of Protein Structure

(Click HERE for slide)

2) Where Protein Models Come From

(Click HERE for slides)

1. X-ray Crystallography
2. NMR
3. Homology Models

3) Introduction to Deep View

1. Learn Deep View: Self Guiding Tutorial
2. Deep View User Manual (pdf file): Click HERE.
3. Get a protein-structure file from the Protein Data Bank:
   Cytochrome b5, PDB file code 1CYO (fall 2006).
   We will use one of these files in the sections that follow.

4) Deep View Basic

1. Windows and Help
2. Manipulating the Model
3. Selecting and Displaying (from menus)
4. Coloring
5. Measuring and Labeling
6. Using the Control Panel
7. Making Pretty Pictures

5) Deep View Advanced

1. Surfaces
2. Comparing Models
3. Homology Modeling
4. Judging Model Quality

6) Next Steps

After completing this workshop, begin working on the Deep View Tutorial.

USM Biochemistry students (CHY 461) should complete sections 1-6 of the tutorial, carry out USM Assignment 1, and turn in the results by the date specified in the course calendar.

Resources

Get Deep View

Learn to View in Stereo

Get Protein Models

• Protein Data Bank: Experimental Models (Crystallographic and NMR)
• SWISS-MODEL: Homology Models

Additional Resources at The Molecular Level

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