Altering the Jmol Display
Contributors
This Jmol Training Guide was created with funding from NIH Grant #1 R25 RR022749-01 and NSF-DUE #1323414 and #1725940. Revised 4/2021.

This Jmol Exploration was created using the Jmol Exploration Webpage Creator from the MSOE Center for BioMolecular Modeling.

version 2.0
Exploration Content

Display Formats in Jmol

Unless otherwise indicated, this section of the Training Guide uses the protein Top 7 based on PDB file 1qys.pdb. Please see Getting Started with Jmol for information on how to download and open PDB files.

The Command Line

Commands to alter the Jmol display are entered in the console. Click in the white area of the Jmol Console to enter commands. This area, highlighted by a magenta dollar sign ($), is where text commands are entered. After typing a command and hitting enter, the command will execute. You should see a change in the 3-dimensional image of your molecule will change in the Display Window.

If you type a command incorrectly or the command is not recognized by Jmol, the text in the command line will be red before you hit enter. When a correct command is entered, the text will turn black.

Common Display Formats

The first text commands we will explore are the Display Formats. These key terms, when typed into the command line, will change the way the molecule is displayed. Below is a description of each of the common Display Formats along with a Jmol button. Please click the button after each description to see how the Top 7 from 1qys.pdb looks when this command is entered.

To reset the Jmol display, load 1qys, then enter the following commands in the console:

background white
color cpk
backbone only
backbone off

These commands will be described in more detail below and in other Jmol Training Tutorials. At this point, you should have a blank display window. Click on the Jmol buttons to compare what you expect to see with what is in your Jmol window.

clearing display (you'll see a white screen)

Wireframe

The thin wire represents the bonds between atoms and the ends and bends of the wires represent the locations of the atoms. The advantage of the wireframe is that all of the atoms are displayed. However, it is difficult to distinguish secondary structures in this format.

To turn this format on, type:

wireframe on

wireframe on

To turn off wireframe, use the command:

wireframe off

Backbone

The alpha carbon backbone format only displays the position of the alpha carbon in each amino acid by a bend in the backbone. All of the other atoms within the amino acid are not displayed. The advantage of this display format is that it clearly illustrates the secondary structures within a molecule.

To turn this format on, type:

backbone on

backbone on

To turn this format off, type:

backbone off

Spacefill

In this format, each atom is displayed as a sphere representing the volume that atom occupies in space. For example, nitrogen atoms are smaller than carbon atoms, which are smaller than sulfur atoms. This format best represents the volume and three-dimensional shape of a molecule. However, identifying the secondary structures or any internal atoms in this display format is challenging.

To turn this format on, type:

spacefill on

spacefill on

To turn this format off, type:

spacefill off

Cartoon

This format shows the molecule as if it were traced with a ribbon. This version may be familiar as it is often seen in textbooks. Secondary structures are easily identified within this format with the alpha helix represented as a coiled structure and the beta strand represented as a gently pleated structure. Turns and loops are indicated by thin lines. The direction of the protein chain can also be identified by arrows at the ends of beta strands.

To turn this format on, type:

cartoon on

cartoon on

To turn this format off, type:

cartoon off

Strands

This format is similar to Cartoon, except that rather than displaying a solid ribbon, there are several 'strands' or thin lines that make up the model.

To turn this format on, type:

strands on

strands on

To turn this format off, type:

strands off

Altering the Thickness of a Display Format

Many of the display formats can be further altered by changing the thickness. To do this, simply add a number after any display format typed into the Command Line and then hit ENTER.

Click the buttons below to see varying sizes of the backbone format.

backbone on
backbone 0.5
backbone 1.0
backbone 1.5

Note: The number added after the Display Format must include a decimal. For example, you will need to enter backbone 1.5 and not simply backbone 1. This number represents the thickness you want in Ångströms (1 x 10-10 meters). So if you enter backbone 1.0, you will be showing a Display Format with a one Ångström diameter backbone. Omitting the decimal reverts to a Rasmol scale, in which 1 Ångström = 250 Rasmol units. Compare the button below with those above to see the difference between backbone 1 and backbone 1.0.

backbone 1
Jmol