Protein Modeling Exercise

Instructions for accessing material for the Chem 355 Modeling Project

1. Go to http://dcchem.wikispaces.com/Protein+possibilities and choose a protein from the available list. Edit the page by adding your name; save the page.

2. On the PDB website for your protein, click the "Structure" tab and choose "Download Files." Click "PDB file" to download the file to your computer. Also search for "1HEW" and download the pdb file, as that is the file that will be used in the tutorial.

3. Download the Swiss Viewer (http://www.expasy.ch/spdbv/text/download.htm). The instructions are written for version 3.7 using Mac OS 9 (Classic). There are PC versions and also a beta version of a Mac OS X program. Last year, students used the PC version and the Mac OS 9 version successfully. The tutorial author recommends against using the Mac OS X version. Do not use a beta version!

4. Go to the tutorial/assignment site (http://www.usm.maine.edu/~rhodes/SPVTut/index.html) There is a menu to the left; you will do the first six lessons and then do assignment 1 for your protein.

Opening the file can present a problem -- the default application is generally Graphic Converter on a Mac. I do it this way: hold down the control key, click and hold on the icon for your pdb file. A menu appears. Navigate to "Open With..." and choose "other." Find the Swiss Viewer on the computer and choose it.