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Representing Structural Information with RasMol

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641
  • Abstract
  • Table of Contents
  • Figures
  • Literature Cited

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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PDF or HTML at Wiley Online Library

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
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

  •   Figure 5.4.1 RasMol running on the computer display. The viewer window is at upper left, behind the Command Line window at lower right.
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  •   Figure 5.4.2 Hemoglobin with the heme groups in thick bonds and the iron ions shown as small spheres.
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  •   Figure 5.4.3 Spacefilling (cpk) representation of hemoglobin with each chain colored differently.
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  •   Figure 5.4.4 Backbone representation of the hemoglobin protein chains, with the hemes still shown as spacefilling spheres.
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  •   Figure 5.4.5 Ribbon diagram (cartoon) of the hemoglobin protein chains, with the hemes as spacefilling spheres.
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  •   Figure 5.4.6 A quick overview representation of hemoglobin.
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  •   Figure 5.4.7 All histidines in hemoglobin are shown with spacefilling spheres.
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  •   Figure 5.4.8 Zooming in on one heme group, it is easy to locate histidines on either side of the iron ion. The one on the right is histidine 92, which coordinates with the iron ion.
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  •   Figure 5.4.9 Histidine 92 is displayed with a thick wireframe representation, colored by atom type.
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  •   Figure 5.4.10 Overview representation of the coordinate file for oxyhemoglobin in PDB entry 1hho.
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  •   Figure 5.4.11 The Download/Display File page for oxyhemoglobin at the PDB. The link at the bottom of the page allows access to coordinates of the biological unit.
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  •   Figure 5.4.12 Overview representation of sickle‐cell hemoglobin from PDB entry 1hbs.
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  •   Figure 5.4.13 ATP synthase in a spacefilling representation.
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  •   Figure 5.4.14 An alternate coloring scheme for hemoglobin.
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  •   Figure 5.4.15 A close‐up image of the histidine‐iron interaction in hemoglobin.
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  •   Figure 5.4.16 An alternate close‐up image of the histidine‐iron interaction in hemoglobin.
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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.
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library
 
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