iCn3D Overview: web-based 3D structure viewer

 

  iCn3D ("I see in 3D") is a WebGL-based viewer for interactive viewing of three-dimensional macromolecular structures and chemicals on the web, without the need to install a separate application. It can be accessed from the "molecular graphic" that appears on the structure summary page for any record in the Molecular Modeling Database (MMDB).

As an example, open the MMDB summary page for 1TUP, then press the "3D view" button in the lower left hand corner of the molecular graphic to load a basic version of iCn3D into the page. Alternatively, press the "full-featured 3D viewer" button in the lower right hand corner of the molecular graphic to open the advanced (full feature) version of iCn3D in a separate window. You can also access the advanced version directly at /Structure/icn3d/full.html, where you can use the "File" menu to retrieve a structure by its ID or to open a structure file on your local computer.

iCn3D has the following features :

• Visualization of observed sequence variation for selected SARS-CoV-2 structures
• Availability of iCn3D in the Jupyter Notebook with the widget "icn3dpy"(pypi.org/project/icn3dpy)
• Visualization of a binding site or an interaction interface
• Ability to export models for 3D printing
• Displaying transmembrane proteins
• Showing the surface map, EM map, or electron density map
• Viewing 1D sequences and 2D interactions
• Aligning two structures, two chains, or a protein sequence to a structure and realigning these alignments .
• Addition of custom tracks in various formats (FASTA, bed file, etc.)
• Showing a force-directed graph for interactions
• Calculating and displaying solvent accessible surface area (SASA)
• Showing symmetry when available

More features are listed and described at /Structure/icn3d/icn3d.html

 

 

   

 

  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. If your browser doesn't support WebGL, you might need to modify the settings in the browser to enable WebGL, or update your web browser to a newer version that supports WebGL. (See the WebGL site for more information about compatibility with various web browsers.)  

 

  The source code for iCn3D is available from GitHub https://github.com/ncbi/icn3d.  

 

  Additional information about iCn3D is available on the following pages:

• iCn3D publications: Wang J, et al., 2020 (PubMed ID 31218344), Wang J, et al., 2022 (PubMed ID 35252351)
• iCn3D Help Document
• iCn3D Web API Help Document
• GitHub: https://github.com/ncbi/icn3d
• iCn3D Public Domain Notice