MOLECULAR MODELING
FOR BEGINNERS

Tutorial For SwissPdbViewer

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

Thanks to students in my fall 1997 biochemistry course, and also to Nicolas Guex, for testing this tutorial and making many helpful suggestions. I will appreciate all comments, corrections, and suggestions.

Revised for Version 3.5b1 May 10, 1999.

If you are still using version 3.1 or earlier, I recommend that you obtain the latest version. As of 4/23/99, version 3.15b1 is only available from the Switzerland server, and not from PDB mirror sites.

SGI and Linux versions are now available. I am not yet aware if there are significant differences between these and the Mac and PC versions.

NOTE: Within the tutorial, links to supplementary information usually appear in a second browser window. The tutorial window is still open, behind the new window. After reading the accessory page, simply close the extra window to return to the tutorial, or move it behind the tutorial window for continued reference.

TEACHERS: Please request permission to use this tutorial in your courses.
Here's why.

USM Students: See Special Instructions.

Overview

This tutorial provides an introduction to macromolecular modeling with SwissPdbViewer, including review of many basic concepts in protein structure. You will first learn how to obtain structure files for viewing, and then carry out exercises in manipulating, analyzing, and comparing protein structures. Sections 1 through 6 give the essentials that everyone will need for using SPdbV as a basic molecular viewer. Sections 7 through 11 add operations of intermediate complexity, such as working with multiple chains and models. Section 12, Advanced Tutorials and Projects, provides experience in the detailed analysis of protein structure, including homology modeling, which entails using known structures to build models of proteins for which only the amino-acid sequence is known.

SwissPdbViewer (hereafter called SPdbV) is a friendly but powerful molecular graphics program. It is designed especially for use with computing tools available from the ExPASy Molecular Biology Server in Geneva, Switzerland. While SPdbV is simple to use for viewing structures and creating vivid illustrations, it also shines as an analytical tool. SPdbV allows you to build models from scratch, simply by giving an amino-acid sequence. SPdbV can find hydrogen bonds within proteins and between proteins and ligands. It allows you to examine electron-density maps from crystallographic structure determination, and to judge the quality of maps and models. It allows you to view several proteins simultaneously and superimpose them to compare their structures. For proteins of known sequence but unknown structure, SPdbV submits amino acid sequences to ExPASy to find homologous proteins, onto which you can subsequently align your sequence to build a preliminary three-dimensional model. Then SPdbV submits your alignment to ExPASy, where a server called SWISS-MODEL builds a final model, called a homology model, and returns it to you by e-mail.

SwissPdbViewer is under continuing development by Nicolas Guex & Manuel C. Peitsch of Geneva Glaxo Welcome Experimental Research. Thanks to Glaxo, Nicolas, Manuel, and their colleagues for making this marvelous tool available to everyone. The program has been described in these articles:

  • Swiss-PdbViewer: A new fast and easy to use PDB viewer for the Macintosh, N. Guex, Experientia 52, A26 (1996).
  • Swiss-PdbViewer: A Fast and Easy-to-use PDB Viewer for Macintosh and PC, N. Guex and M.C. Peitsch,, Protein Data Bank Quarterly Newsletter 77, 7 (1996).
  • SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling, N. Guex and M.C. Peitsch, Electrophoresis 1997, 18, in press.
The ExPASy Molecular Biology Server is described in Appel R.D., Bairoch A., Hochstrasser D.F. in "A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server", Trends Biochem. Sci. 19:258- 260(1994). Since August 1993, the server has handled tens of millions of connections from users around the world.

Conventions Used In This Tutorial

If you do not have the latest version of SwissPdbViewer, you should obtain it before proceeding (see instructions in Section 1). Recent releases of SPdbV have eliminated almost all differences between the Power Macintosh and PC versions. The main difference is that option-key functions on the Mac require the right mouse button on the PC.

In this tutorial, instructions for giving a command or using a menu will always appear in consistent formats. Usually, such commands will appear at the beginning of a new line. Here are some sample instructions and their meanings:

<return>
means press the key labeled return on the computer keyboard. All key-press instructions are enclosed in <these things>, and names of keys in written text are underlined.

heading: show
means click on the word show, which is the heading of the show column in the Control Panel.

Display: Backbone
means pull down the Display menu and select Backbone. All menu instructions are in bold type with a colon separating the names of menus, submenus, and commands.

PDB File Names -- A Slight Departure from Convention

PDB file names consist of a number followed by three characters -- for example, 1HEW. Although it does not follow common convention, at this web site I use capitals for the letters of PDB file codes, primarily because many file names contain the number 1 or the letter L, which are identical in most fonts if not capitalized. The number zero practically never occurs in PDB file names, so there is little chance of confusion with the capital letter O.

Next Section: 1. Getting Started

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