[17 August 2016] iCn3D 2.0 is now available on NCBI web servers (https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html) and on GitHub (https://github.com/ncbi/icn3d). New features in this release include:
- an interactions schematic (2D view) that is available when a structure is loaded as an MMDB file. It can be used to select/highlight molecular components (illustrated example) or interaction interfaces (illustrated example)
- calculation of secondary structures if the input PDB file does not define secondary structure information
- previous files src/icn3d.js, src/full_ui.js, and src/simple_ui.js have been separated into small files
The iCn3D help document provides additional details about the viewer, including examples of how iCn3D can be used.
[27 JULY 2016] New version of VAST+ featuring refined 3D alignments. A new version of VAST+ was released. It provides a refined structure-based alignment of similar macromolecular complexes, and displays the 3D superpositions in the recently released iCn3D, a WebGL-based structure viewer. The initial alignment of similar macromolecular complexes, which became available with the first release of VAST+, uses the complete set of individually aligned macromolecules and corresponding matching amino acids to calculate a superposition of the complex structures. In contrast, the new release of VAST+ identifies a subset set of amino acids that have highly similar 3D positions in the query and subject complex structure, and uses it to create a refined alignment that allows identification and visualization of the most similar portion of the structures (the structurally invariant core of the assembly), as well as the differences between the structures.
[28 APRIL 2016] iCn3D 1.0 is now available. It is a new WebGL-based viewer for interactive viewing of three-dimensional macromolecular structures on the web, without the need to install a separate application, and enables you to:
- interactively view 3D structures and corresponding sequence data
- interactively view superpositions of similar structures
- cutomize the display of a structure and generate a URL that allows you to share the link
- incorporate iCn3D into your own pages
An example of each is accessible from the "About iCn3D" page.
iCn3D 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, view the MMDB summary page for the Tumor Suppressor P53 Complexed with DNA (1TUP). Click on the spin icon in the molecular graphic to open the structure in the basic version of iCn3D, or click on the launch icon to open the structure in the advanced (full feature) version of iCn3D in a separate window.
You can also access the advanced version of iCn3D 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.
The source code is available from GitHub (https://github.com/ncbi/icn3d) for developers who would like to customize the program and/or contribute code, and for users who would like to run the program on their local computer.
[28 APRIL 2016] New structure summary pages featuring interactive molecular graphic. MMDB structure summary pages have been revised to feature interactive molecular graphics using iCn3D, a new WebGL-based viewer for three-dimensional macromolecular structures. A spin icon in the molecular graphic loads a basic version of iCn3D into the web page, enabling you to render the structure in the desired style and highlight molecules of interest by clicking on the corresponding interactions schematic. A launch icon opens the advanced (full feature) version of iCn3D in a separate window. As an example, view the MMDB summary page for Tumor Suppressor P53 Complexed With DNA (1TUP). Additional information is available in the MMDB help document and the About iCn3D page.