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Wang J, Youkharibache P, Marchler-Bauer A, Lanczycki C, Zhang D, Lu S, Madej T, Marchler GH, Cheng T, Chong LC, Zhao S, Yang K, Lin J, Cheng Z, Dunn R, Malkaram SA, Tai C-H, Enoma D, Busby B, etc. (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA)
iCn3D was initially developed as a web-based 3D molecular viewer. It then evolved from visualization into a full-featured interactive structural analysis software. More recently, with the growth of structural databases, the need to analyze large structural datasets systematically led us to use Python scripts and convert the code to be used in Node.js scripts. We showed a few examples of Python scripts at https://github.com/ncbi/icn3d/tree/master/icn3dpython to export secondary structures or PNG images from iCn3D. Users just need to replace the URL in the Python scripts to export other annotations from iCn3D. Furthermore, any interactive iCn3D feature can be converted into a Node.js script to be run in batch mode. Currently available Node.js analysis scripts examples are available at https://github.com/ncbi/icn3d/tree/master/icn3dnode. We also review new features such as DelPhi electrostatic potential, 3D view of mutations, alignment of multiple chains, assembly of multiple structures by realignment, dynamic symmetry calculation, 2D cartoons at different levels, and use of iCn3D in Jupyter Notebook as described at https://github.com/ncbi/icn3d/tree/master/jupyternotebook.