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.
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
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.
load 1liu.pdb set perspectiveDepth off
Render as a cartoon with each chain collored differently: reset select protein spacefill off wireframe off cartoon on color chain
Render only Chain A as cartoon and color by secondary structure: reset restrict *:a center selected zoom 220 spacefill off wireframe off cartoon on color structure
Render only Chain A as rocket and color by secondary structure: reset restrict *:a center selected zoom 220 spacefill off wireframe off rocket on color structure
Render only Chain A as rocket and color by secondary structure: reset restrict *:a center selected zoom 220 spacefill off wireframe off strands on color group
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