Displaying Nucleic Acids
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

This section of the Training Guide uses Zif268, a zinc finger protein based on the PDB file 1zaa.pdb. This protein interacts with double-stranded DNA. Please see Getting Started with Jmol for information on how to download and open PDB files.

Display Formats for DNA and RNA

If your PDB file contains nucleic acid (DNA or RNA), there are several ways to display it. Here we show different examples of nucleic acid displays that you may choose. You can mix and match formats to display the nucleic acid backbone, nitrogenous bases and hydrogen bonds.

When referring to ALL of the nucleic acid in your PDB file, use the command select nucleic. However, you can also refer to the nucleic acid by chain (each strand of DNA will be its own chain). Click on each strand to find out its chain name, which will appear in the Jmol Console.

To isolate the DNA or RNA:

restrict nucleic
center nucleic

restrict nucleic; center nucleic - Zif268 PDB ID: 1zaa

Below are a variety of ways to display nucleic acids. We suggest you browse through the Jmol buttons to find a representation you like, then use the cassette of commands that accompany the button to display nucleic acids in your model.

Cartoon Format

select nucleic
cartoon on
color cpk

Note: We included color cpk here, though you may choose any color you wish. In cartoon format, the 'color cpk' command does produce standard cpk formats.

Note: Cartoon is a nice way to display nucleic acids in an electronic poster, but this format cannot be used to build a physical model using 3D printing.

select nucleic; cartoon on

Ball and Stick Format

select nucleic
spacefill 1.25
wireframe 1.0
color cpk

ball and stick format

Wireframe Format

select nucleic
wireframe 1.0
color cpk

wireframe 1.0

Hydrogen Bonds Between Bases

To add hydrogen bonds between the nitrogenous bases shown in ball and stick:

select nucleic
wireframe 1.0
spacefill 1.25
color cpk
calculate hbonds
hbonds 1.0 color hbonds white set hbonds solid set hbonds sidechain

or, using the single line commands, separated by semi-colons:

select nucleic; wireframe 1.0; spacefill 1.25; color cpk; calculate hbonds; hbonds 1.0; color hbonds white; set hbonds solid; set hbonds sidechain

hydrogen bonds between bases

Backbone Format

select nucleic
backbone 1.5

backbone format

Ladder Format

The 'ladder' format displays the nucleic acid backbone, with hbonds set to backbone.

select nucleic
backbone 1.5
calculate hbonds
hbonds 1.0
color hbonds white
set hbonds solid set hbonds backbone

twisted ladder format

Nucleic Acid Coloring Schemes

Coloring the Bases

Another way to show the nucleic acid is to display everything in spacefill and color-code each base. Here we use the same colors that are used in a standard DNA sequencing gel, except we color G yellow instead of black:

select nucleic
spacefill 1.25
wireframe 1.0
select DA
color green
select DT

color red
select DC
color blue
select DG
color yellow

or the single command line version:

select nucleic; spacefill 1.25; wireframe 1.0; select DA; color green; select DT; color red; select DC; color blue; select DG; color yellow

DNA Ladder Colored by Base

This format displays the DNA ladder, but color codes the rungs by type of base. Here we use standard colors in DNA sequencing gel, except we substitute yellow instead of black for G. Here we only provide the single command line script:

backbone only
backbone only; backbone 1.5; restrict nucleic; center nucleic; select nucleic; calculate hbonds; hbonds 1.0; set hbonds solid; set hbonds backbone; select DA; color red; select DT; color yellow; select DC; color blue; select DG; color green;

color coded ladder format

Ladder Format with Colored Bases and Solid Backbone

This series of commands is identical to the DNA Ladder Colored by Base cassette, except the color backbone command is added at the end to create a solid colored backbone. (You may choose any color you wish; here we used a soft color, lavender, so the base colors would 'pop'.)

backbone only
backbone only; backbone 1.5; restrict nucleic; center nucleic; select nucleic; calculate hbonds; hbonds 1.0; set hbonds solid; set hbonds backbone; select DA; color red; select DT; color yellow; select DC; color blue; select DG; color green; select nucleic; color backbone lavender

ladder format with single colored backbone

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