Digital Biology Friday: Seeing in 3D with Cn3D

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Sandra Porter

Why do I love Cn3D? Let me count the ways.

What does Cn3D do? (Hint: say "Cn3D" out loud).

Seriously, Cn3D is a program that draws lovely pictures of molecular structures by using experimental data from techniques like X-ray crystallography and nuclear magnetic resonance spectroscopy. Surprisingly (to some), and in contrast to many bioinformatics programs, Cn3D is really easy and fun to use.

Have you ever used programs like MS Office? Using Cn3D is at least 10 times easier.

An added benefit is that you don't have to try and find old copies of Netscape or other bits of obsolete software to make it run, like you do with other structure-viewing programs. This is because Cn3D is actively supported and even updated. It was developed and is maintained by the structure group at the National Center for Biotechnology Information (NCBI) and they are very conscientious and helpful.

I like Cn3D so much that I even wrote one lab manual that uses it for Exploring DNA Structure and am currently finishing up another (A Beginner's Guide to Molecular Structures).

More importantly, my student interns and my kids enjoy it.

Okay enough of the testimonial, let's have some fun.

The first thing that you need to do is get a copy of Cn3D.

i-b2466d99b192da09d3118cbd05660a04-cn3d_link.pngGo to

And click the Cn3D link on the left-hand side of the page.

This link will take you to a page with yet another link, your first challenge is to follow the link to get and install your own copy of Cn3D.

I won't even watch over your shoulder.

Once you've gotten Cn3D installed, it's time to get a structure to play with. DNA is rather fundamental, so we might as well start with a bit of DNA.

Here's a link to a DNA structure:


When you get there, click the large grey box that says View 3D Structure to download the structure onto your computer.


The structure file will be downloaded (probably onto your desktop) with the name: mmdb.cn3

Use one of these ways to open the file:

* Double click the file icon.
* Drag the file icon on top of the Cn3D icon.
* Open Cn3D first, click File, then browse to find the file and open it.

You are now looking at a drawing of a double-stranded DNA structure.


Open the Style menu and choose some of the Rendering and Coloring shortcuts to draw the structure in different ways and/or change the coloring.

Next week, we'll combine playing with a bit of learning.