PDBImages: A Command Line Tool for Automated Macromolecular Structure Visualization

TL;DR

PDBImages is an open-source Node.js tool that automates high-quality visualization of macromolecular structures from PDB and AlphaFold models, enabling streamlined image generation without a browser.

Contribution

It introduces a command line package that simplifies automated visualization of macromolecular structures directly from structure files.

Findings

Supports various image types for structures

Enables browserless, automated image rendering

Facilitates easy sharing and analysis of structural data

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