# ADVANCED MOLECULAR MODELING

Tutorial and Protein Structure Analysis Project Using SwissPdb Viewer(Revised May 29, 1997)

Gale Rhodes Department of Chemistry University of Southern Maine Portland, Maine, USA 04103

Please send comments, corrections, and suggestions to rhodes@usm.maine.edu.

#### Contents
Instructions for All Biochemistry Students at USM
Special Instructions for Users of the USM Computer Lab

## Instructions for All Biochemistry Students at USM

This tutorial and the assignments at the end are required of all students in Biochemistry lab (CHY 362). A prerequisite for this tutorial is the INTRODUCTION TO MOLECULAR MODELING: A Tutorial for RasMol. In that tutorial, you will learn about atomic coordinate files in PDB format, obtaining files from the Protein Data Bank, and basic features of molecular graphics programs.

All necesssary programs and files needed for this tutorial are available on USM Power Macintosh computers. These instructions provide the information you need to find the items you need and to prepare for the tutorial.

If you try to carry out this tutorial on your own computer, or on a USM PC, you will need to obtain SwissPdbViewer and associated files from the World Wide Web, following instructions in the tutorial. You are ultimately responsible for installing the programs and getting them to work on your computer. I provide you all the means to carry out this work on Power Macintosh computers at USM, and I cannot grant you extra time if you have problems with your own computer or with a non-Macintosh USM computer.

If you are carrying out this tutorial using you own computer at home, or using a USM PC, you can now close this window and begin the tutorial.

## Special Instructions for Users of the USM Computer Lab

1) In order to use USM Macintosh computers for this exercise, you must have a student computer account. If you do not have an account, go to Academic Computing Services (ACS) in Luther Bonney Hall and ask to set up an account.

2) If you do not know the meaning of such terms as select, drag, double click, dialog box, and save as, then you need to complete all the exercises in the program MACINTOSH BASICS. Ask me or someone at ACS to help you find this program (location 10/06/97: MACAPPS/Course Materials/Chy 105/Macintosh Basics/Macintosh Basics v.4.7.1). Then simply place the mouse pointer on the MACINTOSH BASICS symbol and click the mouse button twice in quick succession. Follow the instructions that appear on the screen. In preparing the tutorial, I have assumed that you are familiar with all the operations discussed in MACINTOSH BASICS.

3) All necessary materials for this tutorial are provided on the USM Macintosh computer network (location 10/06/97: MACAPPS/Course Materials/BIOCHEM/SwissPdbViewer 2.5/SwissPdbViewer).

4) Use a USM Power Macintosh computer that has at least 32 megabytes of random-access memory (RAM). The Power Macintosh 7200 or a newer model is best. Look "under the hood" of your Mac by choosing About This Computer under the Apple menu. Total Memory should be at least 32,000K -- if not, use a different computer or ask someone to help you turn on virtual memory to achieve at least 32 Mbytes.

5) Find the folder MACAPPS/Course Materials/BIOCHEM/SwissPdbViewer. Drag the folder to the desktop. Your Macintosh will make a local copy of the folder and its contents. For the fastest file loading and computing, use the local copy of all of the program and all files during the tutorial.

Close this window to begin the tutorial.