Altering the Jmol Display
Contributors

This Jmol Training Guide was created with funding from NIH Grant #1 R25 RR022749-01 and NSF-DUE #1323414 using the Jmol e-Poster Creator from the MSOE Center for BioMolecular Modeling

version 1.0
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 3-dimensional image of your molecule will change in the Display Window.

If you have typed a command incorrectly or the command is not recognized by Jmol, the text in the command line will be red. 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 so your display will match the buttons below, enter the following commands:

color cpk

cartoon off

spacefill off

At this point, you should have a blank display window.

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 this format off, type:

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, hydrogen 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. 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 0.9
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.

Note: The standard scale for designing models for 3D printing is backbone 1.5. The backbone 0.9 scale is a typical size used for e-posters in an online environment.

Pros and Cons of Various Display Formats

Each of these display options will render your molecule in a different format. Some of these options will look new to you and some of them will look very familiar. Different formats are used for different purposes. Which option you choose to display your molecule depends on the story you wish to tell. The advantage of using Jmol is that it enables you to represent the model in a variety of ways, thus illustrating different aspects of the molecule. A summary of the advantages and disadvantages of each format is provided below.

Advantages and Disadvantages Table

Note: Cartoon and strand formats are not used in designing models to be built using 3-D printing. Typically, backbone, wireframe and spacefill formats are used in combination to design a pleasing and sturdy model for 3-D printing.

Different Display Colors

Jmol has several common Display Color options to make your model look visually pleasing or to indicate specific features of the molecule. Below is a description of each of the Display Colors along with a Jmol button. Please click the button after each description to see how the Top 7 protein from 1qys.pdb will look with that color scheme.

To reset the Jmol so your display will match the buttons below, enter the following commands:

backbone 1.0

wireframe 1.0

CPK

This is the default color scheme used in Jmol and was developed by Corey and Pauling and later improved by Kultin. In the CPK color scheme, carbon is gray, hydrogen is white, oxygen is red, nitrogen is blue and sulfur is yellow. This is the standard color code utilized in many textbooks. (Many chemistry texts use CPK coloring, except that carbon is black instead of gray.)

To turn this color on, type:

color cpk

Color CPK

Chain

If a PDB file has multiple chains (also known as polypeptides), this color option will color each chain a different color.

To turn this color on, type:

color chain

Color Chain

Note: The Top 7 protein has only one polypeptide chain and therefore is colored one color when the "color chain" command is used. Many proteins have more than one polypeptide chain and will therefore have more than one color. For example, a molecule of human insulin from the file 3i3z.pdb has two chains and therefore would have two colors. Click the button below to see Color Chain on human insulin.

Color Chain – Human Insulin

Structure

This option will color the secondary structures different colors. Magenta is used to highlight helices, yellow to indicate beta sheets, and white for loop regions.

To turn this color on, type:

color structure

Color Structure

Temperature

Proteins are flexible, dynaimic structures. The arrangement of the atoms within the protein, as captured in the crystal structure, is much like a still photo. If a particular atom is in a different location in each protein in the crystal, the electron density is blurred. The B-value or temperature factor is a measure of the sharpness of the electron density around each atom, and hence, the certainty of the location of that atom in the protein, or the rigidity of the atom. Low B-values indicate stable atoms and are colored dark blue. High B-values indicate moving atoms and are colored red. Typically, lower B-values are found in the core of the protein, while higher B-values may be found on the surface of the protein.

To turn this color on, type:

color temperature

Color temperature

Custom Colors

This option allows you to color your molecule any solid color. Jmol recognizes a wide range of colors (for specific colors, visit: http://Jmol.sourceforge.net/jscolors/), or you can use RGB color codes entered between brackets and separated by commas [R,G,B] to specify a more specific color.

Click the next two buttons to see examples of color.

Color Red
Color [0, 255, 100]

Background Color of the Jmol Display Window

The default color for the background of the Display Window will be black. This can be modified by using the color background command followed by the color you wish to change the background to.

Click the next two buttons to see examples of different background colors.

Color Background White
Color Background Magenta

Note: We recommend that you avoid the red/green color combination in case you, or others, have problems with color blindness. Bright background colors from a computer monitor are also often hard on the eyes and therefore make it more difficult to focus on the protein. When creating an image for use on a poster, it is best to use a white background.



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