Please note the final release for Cn3D is 4.6, released 3/17/2023. This release covers minimal updates for Windows PC platforms only, and support for other platforms will no longer be available moving forward. Windows support will be available through 2024. We suggest leveraging the web based tool for visualizing 3D structures and the results of comparative structure analysis, iCn3D. Please use the feedback button on the iCn3D page for comments regarding this update and let us know about the new experience with iCn3D.

 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. While versions for Macintosh, and Unix have been available in the past, we can no longer support these platforms. The current version of Cn3D is expected to be the last publicly distributed version, and support may end by 2024. We recommend that our users switch to iCn3D for their structure visualization needs.Cn3D simultaneously displays structure, sequence, and alignment, and has powerful annotation and alignment editing features. To view 3D structures directly in a web browser, 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 4.6 Now!
  Web-based Structure Viewer
  • 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 4.6:
  • No new features have been added to this version of the Cn3D viewer. The application has been revised to comply with recent changes to the Protein Data Bank (PDB) macromolecular chain identifiers. The interface to the now defunct IBIS resource has been removed.
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 17 May 2023