Commits

History for

Commits on Jun 23, 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.
jiywang3
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f104d38

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.
jiywang3
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c55ba37

Commits on May 14, 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 …
jiywang3
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a2613d0

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 …
jiywang3
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1e3373b

Commits on Dec 11, 2024

Added the feature to show 2D Depiction/Diagram for chemical view with cid or smiles as input via the menu "Analysis > 2D Depiction"; fixed the positions of point lights relative to the camera.
jiywang3
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2231030

Commits on Nov 12, 2024

Enabled to convert chemical SMILES to 3D structure via the menu "File > Retrieve by ID > Chemical SMILES".
jiywang3
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37d5d6f

Commits on Jul 29, 2024

Show atom details for the interaction of one ligand/residue with protein via the menu "Analysis > Interaction" and then the button "2D Interaction for One Ligand/Residue".
jiywang3
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5e0f656

Commits on Jul 15, 2024

Switch electron density data from RCSB DSN6 to PDBe Density Server.
jiywang3
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fbd88da

Commits on Mar 25, 2024

Replaced MMTF data with Binary CIF data. Both "mmtfid" and "bcifid" inputs get the Binary CIF data.
jiywang3
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eb0a33f

Commits on Feb 5, 2024

Added an option to load MTZ files from RCSB to show electrondensity maps; fixed a bug in saving sets; fixed a bug in the replay of rotating structures with a matrix. JIRA DD-3999,DD-4006
jiywang3
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88f7fe7

Commits on Sep 14, 2023

Upgraded three.js to version 151, and improved the image quality.
jiywang3
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81cdd7b

Commits on Aug 23, 2023

Added logs for menu usages, and updated iCn3D tutorials at https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#videos.
jiywang3
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d7fde7c

Commits on May 3, 2023

Fixed a bug in relaigning structures.
jiywang3
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791ad47

Commits on Apr 26, 2023

To improve the performance of embedding several structures in a single page, added the URL parameter "imageonly=1" to render the structure into a static image instead of interactive 3D view. The im…
jiywang3
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1262faf

Commits on Apr 24, 2023

Fixed the secondary structures of mutant in the mutation analysis; fixed the lower case in the sequences of VAST+ alignment.
jiywang3
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1bc69de

Commits on Apr 14, 2023

Added more menus to the VR view of iCn3D to measure distance, toggle highlight, etc.
jiywang3
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99c385c

Commits on Apr 11, 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…
jiywang3
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1905e17

Commits on Apr 3, 2023

Commits on Jan 12, 2023

Mapped PDB residue numbers with NCBI residue numbers; replaced jQuery promise with JavaScript Promise, await, and async.
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746e1a5

Commits on Jul 27, 2022

jQuery UI was upgraded from version 1.12.1 to 1.13.2.
jiywang3
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3215c06

Commits on Apr 18, 2022

Added "[comment]" in front of logs to diferentiate from commands in the command window. If "mmdbid" is the input and the parameter "bu" is not defined, set "bu" as 1 (biological unit).
jiywang3
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315ab49

Commits on Apr 14, 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…
jiywang3
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ec4cfc2

Commits on Feb 17, 2022

Another paper about iCn3D was published in Frontiers (https://www.frontiersin.org/articles/10.3389/fmolb.2022.831740/full). Fixed some bugs as well.
jiywang3
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9d43d0d

Commits on Jan 28, 2022

Upgrade three.js from version 128 to 137 to avoid the security issues related to iframe.
jiywang3
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6b2b976

Commits on Jan 27, 2022

Enabled to show the map of AlphaFold predicted aligned error on the fly in the menu "File > Retrieve by ID > AlphaFold UniProt ID", and load custom aligned error files in the menu "File > Open File…
jiywang3
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4f0fadf

Commits on Jan 18, 2022

Now users can see the common interactions in several structures when they are aligned and their interactions are shown. iCn3D now shows asymmetric unit instead of biological unit since asymmetri un…
jiywang3
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b860005

Commits on Sep 28, 2021

Showed Conserved Domains for all structures in the Sequences & Annotations window.
jiywang3
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e586620

Commits on Sep 17, 2021

Users can load multiple structures by appending PDB files with the menu "File > Open File > PDB File (appendable)" to othe PDB files or other structures, which are retrieved by IDs such as "mmdbid"…
jiywang3
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3da67b6

Commits on Aug 27, 2021

AlphaFold predicted structures can be viewed at iCn3D with the menu "File > Retrieve by ID > AlphaFold UniProt ID".
jiywang3
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cd70be7

Commits on Jun 2, 2021

Added an option to load predefined alignments in the menu "File > Align > Multiple Chains". Enabled to change the shininess, lights, and thickness in the menu "Style > Preferences".
jiywang3
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9ebe865

Commits on May 10, 2021

Fixed the URL parameters in full.html.
jiywang3
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b87b88b

Commits on May 7, 2021

Added icn3d.module.js in the build directory. Upgraded three.js from version 103 to version 128. THREE.Geometry was replaced with THREE.BufferGeometry.
jiywang3
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f46f7c4

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…
jiywang3
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24b695e

Commits on Jan 27, 2021

Converted the interaction part of iCn3D to Node.js (in the directory icn3dnode) to allow batch-mode analysis. Expanded the chain-chain alignment to multiple chain alignment in the menu "File > Alig…
jiywang3
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43593b2