Cn3D macromolecular structure viewer
About Cn3D
  Cn3D ("see in 3D") is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez Structure database. Cn3D is provided for Windows and Macintosh, and can be compiled on Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features. (For those who prefer to view 3D structures on the web, without the need to install a separate application, iCn3D ("I see in 3D") is available as of April 2016.)

Below is a relatively simple sample of what Cn3D can do. There are many more examples in the Tutorial, along with instructions to help new users get started!


  This example is a curated CD of the WD40 domain, which is a multi-functional 7-fold beta propeller. Cn3D is showing a representative protein structure, the family alignment, and annotation panels with information about annotated features of this protein family. Highlighted in both structure and sequence windows are the conserved residues in a pattern characteristic to this domain.

Download Cn3D 4.3.1 Now!
  Web-based Structure Viewer new resource
  • iCn3D ("I see in 3D"), released in April 2016, provides interactive views of three-dimensional macromolecular structures on the web.
  • There is no need to install a separate application in order to use iCn3D; you just need to use a web browser that supports WebGL.
  • iCn3D also allows you to cutomize the display of a structure and generate a URL that allows you to share the link, and to incorporate iCn3D into your own web pages.
New Features in Cn3D 4.3.1:
  • View superpositions of structures that have similar molecular complexes, as identified by the newly released VAST+ (an enhanced version of the existing Vector Alignment Search Tool). The VAST+ help document provides additional details about the tool and examples of how it can be used to learn more about proteins.
  • Cn3D 4.3.1 uses the MIME type: application/vnd.ncbi.cn3d.
    (Up to version 4.3, Cn3D used the MIME type chemical/ncbi-asn1-binary.)
New Features in Cn3D 4.3:
  • View biological units and crystallographic symmetry from MMDB
  • Stereo views
  • New alignment algorithms
  • New highlighting features
  • More robust handling of sequence identifiers
  • Communication with CDTree
    (These features are also available in Cn3D 4.2, a preview release packaged with the CDTree software package. Cn3D 4.3 is the subsequent, standalone version of that release.)

New Features in Cn3D 4.1:

  • Improved sequence alignment algorithms
  • Automatic VAST alignment import
  • Taxonomy viewer

New Features in Cn3D 4.0:

  • Re-written in C++ to improve performance and extendibility
  • Improved OpenGL rendering speed
  • New user interface using wxWidgets
  • Complete alignment editing system, along with algorithms for constructing new alignments
  • Extensive structure and alignment annotation features
  • Detailed style control
  • High-resolution image export
  • Built-in help system

Revised 20 September 2016