{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/pdbimages-a-command-line-tool-for-automated","title":"PDBImages: A Command Line Tool for Automated Macromolecular Structure Visualization","arxiv_id":"2308.00563","date":"2023-08-01","proceeding":null,"authors":["Adam Midlik","Sreenath Nair","Stephen Anyango","Mandar Deshpande","David Sehnal","Mihaly Varadi","Sameer Velankar"],"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","url_abs":"https://arxiv.org/abs/2308.00563v1","url_pdf":"https://arxiv.org/pdf/2308.00563v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"pdbimages-a-command-line-tool-for-automated","repo_url":"https://github.com/pdbeurope/pdb-images","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[{"method_slug":"alphafold","method_name":"AlphaFold"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}