Display Formats for Nucleic Acids
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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 for Nucleic Acid

This section of the Training Guide uses Zif68, 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

Isolate Nucleic

Here are a variety of ways to display nucleic acids:

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.

Cartoon Nucleic

Ball and Stick Format

select nucleic

spacefill 1.25

wireframe 1.0

color cpk


Ball and Stick Nucleic

Wireframe Format

select nucleic

wireframe 1.0

color cpk

Wireframe Nucleic

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

Adding Hbonds Between the Bases

Backbone Format

select nucleic

backbone 1.5

Backbone Nucleic


Ladder Format

A "ladder" effect with DNA in a backbone format:

select nucleic

backbone 1.5

calculate hbonds

hbonds 1.0

color hbonds white

set hbonds solid

set hbonds backbone

Ladder Nucleic

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:

select nucleic

spacefill 1.25

wireframe 1.0

select DA

color red

select DT

color yellow

select DC

color blue

select DG

color green

Color Code in Spacefill

Coloring Hydrogen Bonds By Base

You can add on to the previous script and color the hydrogen bonds by base (you may choose whatever colors you wish; these are simply our standard colors for nitrogenous bases):

Begin by removing the color hbonds white command from your previous script, then select all of the adenosine bases in the PDB file using select DA.

select DA

color red

select DT

color yellow

select DC

color blue

select DG

color green

Color Code Hbonds

Coloring the Backbone

You can continue with this script a little further, and color the backbone a solid color (whatever you wish):

select nucleic

color backbone purple

Coloring the Backbone
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