Cn3D

Cn3D is a small application whose purpose is to help you visualize 3-dimensional structures from NCBI’s Entrez structure database. It can be deployed on Windows, Macintosh and Unix-based systems.

It is able to display structure, sequence and alignment, as well as annotate and align data using various algorithms, such as block align single, BLAST single, thread single, extend single, and block align N.

The program welcomes you with a well-organized structure of features. You may import data from CN3 file format or via network by providing information about the PDB or MMDB ID, and export the image displayed in the main window to PNG file format.

You can make use of several view tools for analyzing data, namely zoom in or out of the structure, go to the next or previous frame, jump to the first or last frame, and turn on or off the stereo mode. You can control the animation by setting the preferred speed and playing, spinning or stopping the frames.

The tool lets you show aligned chains, domains or residues, reveal unaligned residues, as well as display selected domains or residues. You may annotate data, keep a list with your favorite items and show sequence viewer, message log, and log at startup.

Cn3D gives you the possibility to set up the rendering mode (e.g. bond sides, atom slices, atom stacks), pick the preferred projection type (perspective or orthographic), choose between several preset rendering profiles in case you do not have the time to manually configure the built-in parameters, and modify the font for structures and sequences.

All things considered, Cn3D integrates a powerful and easy-to-work-with set of features for viewing three-dimensional structures from the National Center for Biotechnology Information's Entrez retrieval service.