Cn3D installation
Installing the  Cn3D 4.3.1  3-D structure viewer

To install the free Cn3D macromolecular structure viewing program, select your operating system:

Once you have installed the program files for your platform, follow the instructions below to set up your browser to launch Cn3D from the NCBI web pages (if not already done by the installer).

Unfortunately, NCBI can no longer support a Unix version of Cn3D. However, an earlier release, Cn3D 4.1 for Unix, is still available. For Unix users who would like to take advantage of the program's newer features, Cn3D can be built as part of the NCBI Toolkit, which contains the Cn3D source code and make files (requires wxWidgets). A number of documents, including an electronic book, provide additional details about the Toolkit.

Configuring your browser


NCBI's web servers send data to Cn3D using the MIME type application/vnd.ncbi.cn3d. (Up to version 4.3, Cn3D used the MIME type chemical/ncbi-asn1-binary.) Many modern browsers will let you choose an application when downloading a file with a new MIME type for the first time. If your browser gives you an option to "open with," point it to the Cn3D application in the folder where you installed Cn3D 4.3.1. You will often also be given an option to automatically launch that application in the future.

To test whether your configuration is working after installing Cn3D, click on the image below, which should launch Cn3D 4.3.1 and should show a structure and viewpoint very like what's shown in this image:

Test Cn3D Click here to test Cn3D!

If Cn3D 4.3.1 does not launch via the test image, look below for hints on how to set up specific browsers. You may need to consult your system administrator for help.

Configuring Internet Explorer

On Windows, this should be done by the installer. If not, you'll need to set up a new file type in Explorer that associates the extension ".cn3" with the MIME type application/vnd.ncbi.cn3d and the Cn3D.exe application. (Up to version 4.3, Cn3D used the MIME type: chemical/ncbi-asn1-binary. As of version 4.3.1, Cn3D uses the MIME type: application/vnd.ncbi.cn3d. For users upgrading to version 4.3.1, it may be necessary re-associate the .cn3 file extension with this new MIME type.)

Configuring Firefox

Firefox allows you to configure a "download action" to automatically open the downloaded file in Cn3D by checking the "Do this automatically for files like this from now on" box in the download dialog window. (See for details.) To subsequently change this behavior in Firefox (or reconfigure it to open in Cn3D 4.3.1 instead of an earlier version), go to its File:Preferences panel, and select the Applications tab. In the Content Type column, click on the action corresponding to .cn3 files and select an alternative action from the pulldown menu.

Note to Macintosh Users:

Configuring helper applications on browsers under OSX seems to be difficult or impossible. In particular, Safari has no mechanism at all for configuring helper applications. This behavior is a considered a security feature on Mac computers, and not particular to Cn3D. However, you should be able to save data files to the desktop or a download folder and either a) drag & drop files onto the Cn3D icon, b) Ctrl-click on the .cn3 file and select from the "Open With" popup menu, or c) double-click on the .cn3 file (if the file-type association has already been established) to launch it manually.

Previous Versions of Cn3D

If for some reason you need an earlier release of Cn3D, some previous versions are still available here:

Revised 20 September 2016