Commits

History for

Commits on Jul 7, 2026

Upgraded "2D Diagram for Ig Domains" to allow integrated 2D and 3D views.
jiywang3
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2b5201a

Commits on Jun 8, 2026

users can choose to use both R2DT and RNAcanvas to show "2D Diagram for Nucleotides" integrated with 3D view. The base pairs are either from Fr3D or extended mmCIF with base pair information.
jiywang3
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970906e

Commits on Dec 15, 2025

Added an external link "AI Tutor" in the Help menu to use AI as a tutor to show users step-by-step instructions about how to build a custom view with five methods: Interactive, Sharable URL, Jupyte…
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f947788

Commits on Jul 18, 2025

Switched the transformation description in share links from trackball parameters to camera parameters used in BCF files. Fixed a bug in using node.js script.
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e1908cf

Commits on Jun 11, 2025

Upgraded three.js to version 177 and compiled three.js directly into iCn3D library. No need to include three.js as a separate library.
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c55ba37

Commits on May 12, 2025

Allowed to input MSA files (CLUSTALW or FASTA formats) to show both MSA and structure alignment via the menu "File > Open File > Multiple Seq. Alignment" in the "All Menus" mode; Added the "Stereo …
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1e3373b

Commits on Jul 31, 2023

Added the feature to show isoforms and exons as tracks with the button "Add Track" in the "Sequences & Annotations" window via the menu "Analysis > Sequences & Annotations". Also displayed pathogen…
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6c08f13

Commits on Apr 10, 2023

Improved the use of iCn3D in Jupyter Notebook by making the dialogs closable, and adding DelPhi potential and mutation analysis; added DelPhi potential as one option in the Virtual Reality (VR) vie…
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825e3fc

Commits on Aug 16, 2022

Enabled users to switch between "All Menus" and "Simple Menus", or customize the menus and save them in a file to be loaded by others. The customized menus are sticky and saved in cache.
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a07ce77

Commits on Jul 27, 2022

jQuery UI was upgraded from version 1.12.1 to 1.13.2.
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7434554

Commits on Jun 6, 2022

Users now can have Virtual Reality (VR) view on any iCn3D display; enabled to view multiple seqeunce alignment (MSA) instead of pairwise alignment; changed the tools in toolbar from buttons to icon…
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868bf5c

Commits on May 12, 2022

Fixed a bug in the dynamic VAST alignment in iCn3D with the menu "File > Realign Selection > by Structure Alignment".
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e4e9a65

Commits on Apr 15, 2022

Users can input multiple PDB, MMDB, or AlphaFold IDs with the menu "File > Retrieve by ID > MMDB or AlphaFold IDs". Users can also load multiple PDB files at the same time with the menu "File > Ope…
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af7a33f

Commits on Feb 7, 2022

Enabled to show mutations for AlphaFold structures in the menu "Analysis > Mutation". Fixed the 2D interaction network view of mutations.
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84b8e2f

Commits on Aug 27, 2021

AlphaFold predicted structures can be viewed at iCn3D with the menu "File > Retrieve by ID > AlphaFold UniProt ID".
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cd70be7

Commits on Aug 20, 2021

Dynamically generate "2D Cartoon" in the chain, domain, or secondary structure levels for selected residues in the menu "Analysis". The cartoons are draggable and clickable.
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71fe614

Commits on Jul 21, 2021

Changed the default view of glycan cartoons as hidden. Users can change the default at "Style > Prefereces > Show Glycan Cartoon" for your browser.
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258a23d

Commits on Jul 14, 2021

Now users can choose the color gradient and show the color legend for the "Custom Color" button in the Sequences & Annotations window.
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d679c17

Commits on Jun 25, 2021

Enabled to set the URL parameter "menumode" to "1" to show icons for those menus requiring internet access or license.
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6f70b87

Commits on May 3, 2021

iCn3D version 3.0.0 was converted to ES6 with classes and is available in npm with the package "icn3d". Users can use npm to install icn3d and generate Node.js scripts by calling icn3d functions. A…
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24b695e

Commits on Mar 16, 2021

Commits on Nov 24, 2020

Users now can alternate wild type and mutant, and their interaction networks in 3D for each SNP/ClinVar in the "Sequences & Annotation" window.
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committed
cdde2a0

Commits on Aug 3, 2020

Commits on Jul 20, 2020

Generated icn3dpy (the Jupyter Notebook widget of iCn3D) at https://pypi.org/project/icn3dpy; added "2D Interaction Map" in the menu "View > H-Bonds & Interactions"; added the shrink/expand icon in…
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58377f4

Commits on Jun 15, 2020

Users can now show "2D Interaction Graph" and also "Highlight Interactions in Table" in the menu "View > H-Bonds & Interactions". Users can also replay the share link step by step to learn how to g…
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c2cb9cf

Commits on Jun 6, 2020

Added halogen bonds, pi-cation, and pi-stacking interactions in the menu "View > H-Bonds & Interaction" and showed the interactions in sorted tables.
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20e0592

Commits on May 29, 2020

Added the following features: 1. save contents in any dialog/window using the save icon next to the closeicon, 2. set names for each tab/window using the menu "Windows > Your Note / Window Title", …
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b6bca77

Commits on May 21, 2020

Enabled to show interactions using force-directed graph in the menu 'View > H-Bonds & Interactions > Force-Directed Graph'. Enabled to calculate Solvent Accessible Surface Area (SASA) in the menu '…
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df5f8e6

Commits on Aug 21, 2019

Enabled the mobile style menu with the URL parameter "mobilemenu=1"
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317115c

Commits on Aug 2, 2019

Fixed the effect of Fog on sticks and spheres
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9ccfa2a
Fixed the effect of Fog on sticks and spheres
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7fa1112

Commits on Oct 18, 2018

Added set operations (union,intersection, exclusion) in 'Defined Sets'; added buttons 'Helix Sets' and 'Sheet Sets' in the 'Sequences and Annotations' window to define helix sets and sheet sets in …
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d3f4926

Commits on Jul 30, 2018

improved the 3D display of ribbons
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605f2ef