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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 https://www.ncbi.nlm.nih.gov/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 2.20.0 is now available on NCBI web servers and from GitHub (https://github.com/ncbi/icn3d). Users can now view the electrostatic potential map for any subset of 3D structures within 30,000 atoms. The potential is calculated using the DelPhi program by solving linear Poisson-Boltzmann equation. Users can show the potential on surface or show equipotential map. The potential map shows the effect of charges on molecular interactions qualitatively. This example shows the electrostatic potential for the binding of Gleevec to Abl2. The ligand shows the -25 mV (red) and +25 mV (blue) equipotential map with a grid size 65, salt concentration 0.15 M, and pH 7. The protein shows the surface potential with a gradient from -75 mV (red) to +75 mV (blue). This new feature can be accessed from the menu "Analysis > DelPhi Potential". Users can also download the PQR file format with assigned partial charges.
Other recently introduced features include:
More features are listed and described at www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html
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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.)
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The source code for iCn3D is available from GitHub https://github.com/ncbi/icn3d for those who would like to run the program locally, and for those who would like to customize iCn3D and/or contribute code:
- The complete distribution copy of iCn3D can be obtained for use on your local computer from:
https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.24.5.zip.
That file includes the code written by NCBI as well as the corresponding third party JavaScript libraries such as jQuery and Three.js.
- The development version of iCn3D is available for developers who want to customize and/or contribute code to the iCn3D program. Click on the "Download ZIP" button in the upper right corner of the GitHub page to download that version, which includes only the code written at NCBI but not the corresponding third party javascript libraries like jQuery or Three.js.
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Additional information about iCn3D is available on the following pages:
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