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 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.

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 Now!
  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 12 July 2011 | | Help Desk | Disclaimer | Privacy statement | Accessibility |