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Atoms and Bonds

Jmol contains a number of commands that can be used to display and highlight molecular models. For example, there are commands to produce various geometric shapes that represent atoms and bonds. Typically, atoms are rendered as, or represented by, spheres while bonds are rendered as sticks. Atoms and bonds can also be colored in different ways to illustrate various properties. When Jmol first opens a structure file it uses a "Ball & Stick" rendering of a molecule. Below is a "Ball & Stick" model for and aspartic acid residue in the protein pyruvate kinase.

The commands that are used to produce this model are "spacefill" for atoms and "wireframe" for bonds. Commands often have arguments which determine how the rendering is done. If not argument is provided a default value is used. The default for the "spacefill" command is to use the vander Waals radius:

The default for the "wireframe" command is to use sticks that are 1 pixel wide:

In all to the models used so far, the atoms and bonds were colored by atom type; carbons=grey, oxygen=red, and nitrogen=blue. The "color" command has no default argument. To color a model by atom type you use the command "color cpk". The "cpk" has historical meaning and stands for Corey-Pauling-Kulton (Robert Corey, Linus Pauling and W.L. Koltun), who in the 1960's first developed models that used colors to identify atoms.To recreate the Ball & Stick model that is shown above, using the 1liu.pdb structure for pyruvate kinase, requires the following steps. This is the same structure that you opened with Jmol back on the "Before you get started" page.

1. Restrict the selection to residue number 67 in chain A of pyruvate kinase, which is an aspartyl residue.
2. Center the selection in the image screen.
3. Zoom in on the selection.
4. Render the atoms in this selection as spheres that have radii that are 20% of their vander Waals radii.
5. Render the bonds that connect the atoms in the selection by sticks that are 0.15 Angstroms wide
6. Color the atoms in this selection according to their atom type.

Below are the corresponding commands you should type at the command line in the Jmol Rasmol Script console of the standalone version of Jmol. Clicking on each of the commands in the image below will take you to the corresponding entry for that command in the Jmol help file.

Try the following

• Relaunch Jmol and load the structure for pyruvate kinase (1liu.pdb). If you need help with this go back to "Creating Models".
• Open the Rasmol Scripts console window and execute the following commands:
  • Command Line: select all <return>
  • Command Line: spacefill on <return>
  • Command Line: wireframe off <return>
  • Command Line: color green <return>
• This will allow you to see the effects of the commands described in the figure above. Now execute tha commands descrbed in the figure above.

Below is an embedded Jmol image of pyruvate kinase (1liu.pdb) which you can use to interactively execute each of these commands. When inititially loaded, the pyruvate kinase is rendered as green, vander Waals spheres, so that you can observe the effect of each command. Click on each command in succession.

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