Representing Structural Information with RasMol

David S. Goodsell1

1 The Scripps Research Institute, La Jolla
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 5.4
DOI:  10.1002/0471250953.bi0504s11
Online Posting Date:  October, 2005
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Abstract

This unit describes the use of RasMol, a popular interactive molecular graphics program, for the display of biomolecular structures. The unit begins with a general guide to obtaining molecular coordinates from the Protein Data Bank and displaying them with RasMol, and then describes several molecular representations that are useful for different applications, along with methods for ensuring that one is viewing the appropriate biological unit and some ideas for customizing one's molecular graphics session.

Keywords: Molecular graphics; RasMol; visualization; protein structure

     
 
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Table of Contents

  • Basic Protocol 1: Using RasMol to Display a Protein Structure
  • Support Protocol 1: Downloading and Installing RasMol on a Local Computer
  • Support Protocol 2: Downloading Coordinates from the Protein Data Bank
  • Alternate Protocol 1: Two Useful Views in RasMol
  • Basic Protocol 2: Viewing the Appropriate Biological Unit
  • Basic Protocol 3: Customizing a RasMol Session
  • Guidelines for Understanding the Results
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

   Goodsell, D.S. 2003. Looking at molecules: An essay on art and science. ChemBioChem 4:1293‐1298.
   Goodsell, D.S. 2005. Visual methods from atoms to cells. Structure 13:347‐354.
   Olson, A.J. and Goodsell, D.S. 1992a. Macromolecular graphics. Curr. Opin. Struct. Biol. 2:193‐201.
   Olson, A.J. and Goodsell, D.S. 1992b. Visualizing biological molecules. Sci. Am. 267:76‐81.
   Richardson, J.S. 1992. Looking at proteins: Representations, folding, packing, and design. Biophys. J. 63:1186‐1209.
Internet Resources
   http://www.rcsb.org/pdb
  Web site for the Protein Data Bank (PDB).
   http://www.rcsb.org/pdb/software‐list.html
  Contains links to many molecular graphics programs and provides access to macromolecular coordinates.
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