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arXiv · 2308.00563

PDBImages: A Command Line Tool for Automated Macromolecular Structure Visualization

Adam Midlik·Sreenath Nair·Stephen Anyango·Mandar Deshpande·David Sehnal·Mihaly Varadi·Sameer Velankar
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Abstract

Summary: PDBImages is an innovative, open-source Node.js package that harnesses the power of the popular macromolecule structure visualization software Mol*. Designed for use by the scientific community, PDBImages provides a means to generate high-quality images for PDB and AlphaFold DB models. Its unique ability to render and save images directly to files in a browserless mode sets it apart, offering users a streamlined, automated process for macromolecular structure visualization. Here, we detail the implementation of PDBImages, enumerating its diverse image types and elaborating on its user-friendly setup. This powerful tool opens a new gateway for researchers to visualize, analyse, and share their work, fostering a deeper understanding of bioinformatics. Availability and Implementation: PDBImages is available as an npm package from https://www.npmjs.com/package/pdb-images. The source code is available from https://github.com/PDBeurope/pdb-images. Contact: mvaradi@ebi.ac.uk, sameer@ebi.ac.uk

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Adam Midlik, Sreenath Nair, Stephen Anyango, Mandar Deshpande, David Sehnal, Mihaly Varadi, Sameer Velankar. 2023-08-01. PDBImages: A Command Line Tool for Automated Macromolecular Structure Visualization. https://doi.org/10.1093/bioinformatics%2Fbtad744

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