Tip of the Week: Update to NCBI’s Cn3D Viewer

As I say in the tip movie, I like to visit NCBI’s homepage & just roam around over there to get an idea of what’s new. They develop so many bioscience tools, algorithms & other resources that there’s always SOMETHING new. Today I found out that they have updated their Cn3D interactive 3D viewer software from version 4.1 to 4.3 – version 4.2 was a preview version released only in a bundle with CDTree software. The 4.3 version is a stand alone version that can communicate with CDTree, and that allows users some advanced features compared to the 4.1 version of the Cn3D software. It may be important to note for some of you that 4.3 is only offered for Windows & Mac. Users wanting to use a Unix version will have to continue using version 4.1, as explained here.

Before using the Cn3D software you must download it to your computer. Previously downloading the 4.1 version of Cn3D does not affect your ability download and use the 4.3 version. In fact you can use them side-by-side, if you wish. As I said, the Cn3D software is a 3D interactive viewer so once you download the software you will probably visit another database that provides protein structure views in a Cn3D format. In the tip I use the myosin VI structure summary page from NCBI’s Molecular Modeling Database (MMDB) as my example. I didn’t have time to show you how to access the page in the tip movie, but it is the exact page we use in our full MMDB tutorial so you can find all the details there. (NOTE: I’ll be updating the MMDB tutorial soon, so watch for that announcement later.)

Opening the myosin vi file in the Cn3D viewer allows you rotate the molecule, label it as you desire, or view it in stereo. The controls are pretty intuitive & you can click around & see how it affects your image. For example, under the “Style>Rendering Shortcuts” menu you can render the molecule as worms, tubes, wire, ball & stick or space filled using the . You can also go under the “Style>Coloring Shortcuts” and select to color the image by domains, residues, charge, and many other options. If you want more details, check out the Cn3D “Help” menu or the Cn3D citation (below), or work through their tutorial.

I know MMDB and GoMiner use the Cn3D viewer – are there other resources where you use the Cn3D software?


Baxevanis AD. (2008) Searching NCBI databases using Entrez. Curr Protoc Bioinformatics. 2008 Dec;Chapter 1:Unit 1.3. DOI: 10.1002/0471250953.bi0103s24

Wang Y, Geer LY, Chappey C, Kans JA, Bryant SH. (2000) Cn3D: sequence and structure views for Entrez. Trends Biochem Sci. 2000 Jun;25(6):300-2. DOI: 10.1016/S0968-0004(00)01561-9 (subscription required)