Representing Structural Information with RasMol
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- 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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- 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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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. View Image -
Figure 5.4.2 Hemoglobin with the heme groups in thick bonds and the iron ions shown as small spheres. View Image -
Figure 5.4.3 Spacefilling (cpk) representation of hemoglobin with each chain colored differently. View Image -
Figure 5.4.4 Backbone representation of the hemoglobin protein chains, with the hemes still shown as spacefilling spheres. View Image -
Figure 5.4.5 Ribbon diagram (cartoon) of the hemoglobin protein chains, with the hemes as spacefilling spheres. View Image -
Figure 5.4.6 A quick overview representation of hemoglobin. View Image -
Figure 5.4.7 All histidines in hemoglobin are shown with spacefilling spheres. View Image -
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. View Image -
Figure 5.4.9 Histidine 92 is displayed with a thick wireframe representation, colored by atom type. View Image -
Figure 5.4.10 Overview representation of the coordinate file for oxyhemoglobin in PDB entry 1hho. View Image -
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. View Image -
Figure 5.4.12 Overview representation of sickle‐cell hemoglobin from PDB entry 1hbs. View Image -
Figure 5.4.13 ATP synthase in a spacefilling representation. View Image -
Figure 5.4.14 An alternate coloring scheme for hemoglobin. View Image -
Figure 5.4.15 A close‐up image of the histidine‐iron interaction in hemoglobin. View Image -
Figure 5.4.16 An alternate close‐up image of the histidine‐iron interaction in hemoglobin. View Image
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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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